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Sample records for active site model

  1. Active site modeling in copper azurin molecular dynamics simulations

    NARCIS (Netherlands)

    Rizzuti, B; Swart, M; Sportelli, L; Guzzi, R

    2004-01-01

    Active site modeling in molecular dynamics simulations is investigated for the reduced state of copper azurin. Five simulation runs (5 ns each) were performed at room temperature to study the consequences of a mixed electrostatic/constrained modeling for the coordination between the metal and the po

  2. Inhibition and active-site modelling of prolidase.

    Science.gov (United States)

    King, G F; Crossley, M J; Kuchel, P W

    1989-03-15

    Consideration of the active-site model of prolidase led us to examine azetidine, pyrrolidine and piperidine substrate analogs as potential in vivo inhibitors of the enzyme. One of these, N-benzyloxycarbonyl-L-proline, was shown to be a potent competitive inhibitor of porcine kidney prolidase (Ki = 90 microM); its rapid protein-mediated permeation of human and sheep erythrocytes suggests that it may be effective in vivo. The higher homolog, N-benzyloxycarbonyl-L-pipecolic acid, was also a potent inhibitor of the enzyme while the antihypertensive drugs, captopril and enalaprilat, were shown to have mild and no inhibitory effects, respectively. Analysis of inhibitor action and consideration of X-ray crystallographic data of relevant Mn2+ complexes allowed the active-site model of prolidase to be further refined; a new model is presented in which the substrate acts as a bidentate ligand towards the active-site manganous ion. Various aspects of the new model help to explain why Mn2+ has been 'chosen' by the enzyme in preference to other biologically available metal ions. PMID:2924773

  3. Modeling Steroid 5alpha-reductase and Characterizing Its Potential Active Sites

    Institute of Scientific and Technical Information of China (English)

    OU Min-Rui; LI Jun-Qian

    2012-01-01

    Steroid 5alpha-reductase of human is an enzyme in the biosynthetic pathway from testosterone (T) to dihydrotestosterone (DHT). Up to now, no crystal structure of this enzyme has been reported. However, knowledge of the tertiary structure and possible active sites is essential for understanding the catalysis mechanism and for the design of inhibitors. A model with putative active sites has been created and evaluated by using homology modeling and molecular docking techniques based on the bioinformatics knowledge. The homology model is optimized in Swiss PDB Viewer with MM method and substrate structures before docking are also optimized on HF/6-31G. The active site for the docking of NADP, T, DHT and Finasteride is located near the N-terminus of enzyme. Four active amino acids in the active site are identified as Ala26, Arg53, Arg176 and Lys177. Reaction procedure, binding pattern of active sites, the types of weak interaction and so on are also discussed.

  4. A three-dimensional model of mammalian tyrosinase active site accounting for loss of function mutations.

    Science.gov (United States)

    Schweikardt, Thorsten; Olivares, Concepción; Solano, Francisco; Jaenicke, Elmar; García-Borrón, José Carlos; Decker, Heinz

    2007-10-01

    Tyrosinases are the first and rate-limiting enzymes in the synthesis of melanin pigments responsible for colouring hair, skin and eyes. Mutation of tyrosinases often decreases melanin production resulting in albinism, but the effects are not always understood at the molecular level. Homology modelling of mouse tyrosinase based on recently published crystal structures of non-mammalian tyrosinases provides an active site model accounting for loss-of-function mutations. According to the model, the copper-binding histidines are located in a helix bundle comprising four densely packed helices. A loop containing residues M374, S375 and V377 connects the CuA and CuB centres, with the peptide oxygens of M374 and V377 serving as hydrogen acceptors for the NH-groups of the imidazole rings of the copper-binding His367 and His180. Therefore, this loop is essential for the stability of the active site architecture. A double substitution (374)MS(375) --> (374)GG(375) or a single M374G mutation lead to a local perturbation of the protein matrix at the active site affecting the orientation of the H367 side chain, that may be unable to bind CuB reliably, resulting in loss of activity. The model also accounts for loss of function in two naturally occurring albino mutations, S380P and V393F. The hydroxyl group in S380 contributes to the correct orientation of M374, and the substitution of V393 for a bulkier phenylalanine sterically impedes correct side chain packing at the active site. Therefore, our model explains the mechanistic necessity for conservation of not only active site histidines but also adjacent amino acids in tyrosinase. PMID:17850513

  5. Metal ion site engineering indicates a global toggle switch model for seven-transmembrane receptor activation

    DEFF Research Database (Denmark)

    Elling, Christian E; Frimurer, Thomas M; Gerlach, Lars-Ole;

    2006-01-01

    for monoamine binding in TM-III, was used as the starting point to engineer activating metal ion sites between the extracellular segments of the beta2-adrenergic receptor. Cu(II) and Zn(II) alone and in complex with aromatic chelators acted as potent (EC50 decreased to 0.5 microm) and efficacious agonists...... in sites constructed between positions III:08 (Asp or His), VI:16 (preferentially Cys), and/or VII:06 (preferentially Cys). In molecular models built over the backbone conformation of the inactive rhodopsin structure, the heavy atoms that coordinate the metal ion were located too far away from each other...... to form high affinity metal ion sites in both the bidentate and potential tridentate settings. This indicates that the residues involved in the main ligand-binding pocket will have to move closer to each other during receptor activation. On the basis of the distance constraints from these activating metal...

  6. Kinetic model of ethopropazine interaction with horse serum butyrylcholinesterase and its docking into the active site.

    Science.gov (United States)

    Golicnik, Marko; Sinko, Goran; Simeon-Rudolf, Vera; Grubic, Zoran; Stojan, Jure

    2002-02-01

    The action of a potent tricyclic cholinesterase inhibitor ethopropazine on the hydrolysis of acetylthiocholine and butyrylthiocholine by purified horse serum butyrylcholinesterase (EC 3.1.1.8) was investigated at 25 and 37 degrees C. The enzyme activities were measured on a stopped-flow apparatus and the analysis of experimental data was done by applying a six-parameter model for substrate hydrolysis. The model, which was introduced to explain the kinetics of Drosophila melanogaster acetylcholinesterase [Stojan et al. (1998) FEBS Lett. 440, 85-88], is defined with two dissociation constants and four rate constants and can describe both cooperative phenomena, apparent activation at low substrate concentrations and substrate inhibition by excess of substrate. For the analysis of the data in the presence of ethopropazine at two temperatures, we have enlarged the reaction scheme to allow primarily its competition with the substrate at the peripheral site, but the competition at the acylation site was not excluded. The proposed reaction scheme revealed, upon analysis, competitive effects of ethopropazine at both sites; at 25 degrees C, three enzyme-inhibitor dissociation constants could be evaluated; at 37 degrees C, only two constants could be evaluated. Although the model considers both cooperative phenomena, it appears that decreased enzyme sensitivity at higher temperature, predominantly for the ligands at the peripheral binding site, makes the determination of some expected enzyme substrate and/or inhibitor complexes technically impossible. The same reason might also account for one of the paradoxes in cholinesterases: activities at 25 degrees C at low substrate concentrations are higher than at 37 degrees C. Positioning of ethopropazine in the active-site gorge by molecular dynamics simulations shows that A328, W82, D70, and Y332 amino acid residues stabilize binding of the inhibitor. PMID:11811945

  7. A kinetic description for sodium and potassium effects on (Na+ plus K+)-adenosine triphosphatase: a model for a two-nonequivalent site potassium activation and an analysis of multiequivalent site models for sodium activation.

    Science.gov (United States)

    Lindenmayer, G E; Schwartz, A; Thompson, H K

    1974-01-01

    1. Dissociation constants for sodium and potassium of a site that modulates the rate of ouabain-(Na(+)+K(+))-ATPase interaction were applied to models for potassium activation of (Na(+)+K(+))-ATPase. The constants for potassium (0.213 mM) and for sodium (13.7 mM) were defined, respectively, as activation constant, K(a) and inhibitory constant, K(i).2. Tests of the one- and the two-equivalent site models, that describe sodium and potassium competition, revealed that neither model adequately predicts the activation effects of potassium in the presence of 100 or 200 mM sodium.3. The potassium-activation data, obtained at low potassium and high sodium, were explained by a two-nonequivalent site model where the dissociation constants of the first site are 0.213 mM for potassium and 13.7 mM for sodium. The second site was characterized by dissociation constants of 0.091 mM for potassium and 74.1 mM for sodium.4. The two-nonequivalent site model adequately predicted the responses to concentrations of potassium between 0.25 and 5 mM in the presence of 100-500 mM sodium. At lower sodium concentrations the predicted responses formed an upper limit for the function of observed activities. This limit was reached at lower concentrations of potassium and higher concentrations of sodium, which inferred saturation of the sodium-activation sites with sodium.5. Sodium-activation data were corrected for sodium interaction with potassium-activation sites by use of the two-nonequivalent site model for potassium activation. Tests of equivalent site models suggested that the corrected data for sodium activation may be most consistent with a model that has three-equivalent sites. Other multiequivalent site models (n = 2, 4, 5 or 6), however, cannot be statistically eliminated as possibilities. The three-equivalent site activation model was characterized by dissociation constants of 1.39 mM for sodium and 11.7 mM for potassium. The system theoretically would be half-maximally activated by

  8. Use of an Improved Matching Algorithm to Select Scaffolds for Enzyme Design Based on a Complex Active Site Model.

    Directory of Open Access Journals (Sweden)

    Xiaoqiang Huang

    Full Text Available Active site preorganization helps native enzymes electrostatically stabilize the transition state better than the ground state for their primary substrates and achieve significant rate enhancement. In this report, we hypothesize that a complex active site model for active site preorganization modeling should help to create preorganized active site design and afford higher starting activities towards target reactions. Our matching algorithm ProdaMatch was improved by invoking effective pruning strategies and the native active sites for ten scaffolds in a benchmark test set were reproduced. The root-mean squared deviations between the matched transition states and those in the crystal structures were < 1.0 Å for the ten scaffolds, and the repacking calculation results showed that 91% of the hydrogen bonds within the active sites are recovered, indicating that the active sites can be preorganized based on the predicted positions of transition states. The application of the complex active site model for de novo enzyme design was evaluated by scaffold selection using a classic catalytic triad motif for the hydrolysis of p-nitrophenyl acetate. Eighty scaffolds were identified from a scaffold library with 1,491 proteins and four scaffolds were native esterase. Furthermore, enzyme design for complicated substrates was investigated for the hydrolysis of cephalexin using scaffold selection based on two different catalytic motifs. Only three scaffolds were identified from the scaffold library by virtue of the classic catalytic triad-based motif. In contrast, 40 scaffolds were identified using a more flexible, but still preorganized catalytic motif, where one scaffold corresponded to the α-amino acid ester hydrolase that catalyzes the hydrolysis and synthesis of cephalexin. Thus, the complex active site modeling approach for de novo enzyme design with the aid of the improved ProdaMatch program is a promising approach for the creation of active sites with

  9. Use of an Improved Matching Algorithm to Select Scaffolds for Enzyme Design Based on a Complex Active Site Model.

    Science.gov (United States)

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

    2016-01-01

    Active site preorganization helps native enzymes electrostatically stabilize the transition state better than the ground state for their primary substrates and achieve significant rate enhancement. In this report, we hypothesize that a complex active site model for active site preorganization modeling should help to create preorganized active site design and afford higher starting activities towards target reactions. Our matching algorithm ProdaMatch was improved by invoking effective pruning strategies and the native active sites for ten scaffolds in a benchmark test set were reproduced. The root-mean squared deviations between the matched transition states and those in the crystal structures were cephalexin using scaffold selection based on two different catalytic motifs. Only three scaffolds were identified from the scaffold library by virtue of the classic catalytic triad-based motif. In contrast, 40 scaffolds were identified using a more flexible, but still preorganized catalytic motif, where one scaffold corresponded to the α-amino acid ester hydrolase that catalyzes the hydrolysis and synthesis of cephalexin. Thus, the complex active site modeling approach for de novo enzyme design with the aid of the improved ProdaMatch program is a promising approach for the creation of active sites with high catalytic efficiencies towards target reactions. PMID:27243223

  10. Synthesis and Characterization of Porphyrin.Trisbenzimidazole Dinucleating Ligand and Its Heterodinuclear Complex as CcO Active Site Model

    Institute of Scientific and Technical Information of China (English)

    LuWei-bing; WangCun-xin; DengLi-zhi; ZhouXiao-hai; RenJian-guo

    2003-01-01

    A new dinucleating ligand having two metalbinding sites has been designed and synthesized as model ligand for Cytochrome c Oxidase. The corresponding heterodinuclear complex, as an active site model of Cytochrome c Oxidase, consisting of a porphyrinatocobalt compound covalently linked with a copper derivative of tris(2-benzimidazylmethyl)amine bearing three benzimidazole ligands for copper was synthesized and spectroscopically characterized. The spectra data suggest that there are interactions between the cobalt and copper coordination units. The cobalt is coordinated to four central nitrogens of the porphyrin and the copper has pentacoordinate geometry with the four tertiary amine nitrogens and a chloride.

  11. Synthesis and Characterization of Porphyrin- Trisbenzimidazole Dinucleating Ligand and Its Heterodinuclear Complex as CcO Active Site Model

    Institute of Scientific and Technical Information of China (English)

    Lu Wei-bing; Wang Cun-xin; Deng Li-zhi; Zhou Xiao-hai; Ren Jian-guo

    2003-01-01

    A new dinucleating ligand having two metal-binding sites has been designed and synthesized as model lig-and for Cytochrome c Oxidase. The corresponding heterodi-nuclear complex, as an active site model of Cytochrome c Oxi-dase, consisting of a porphyrinatocobalt compound covalently linked with a copper derivative of tris(2-benzimidazylmethyl)amine bearing three benzimidazole ligands for copper was syn-thesized and spectroscopically characterized. The spectra data suggest that there are interactions between the cobalt and copper coordination units. The cobalt is coordinated to four central nitrogens of the porphyrin and the copper has pentaeo-ordinate geometry with the four tertiary amine nitrogens and a chloride.

  12. Modelling active sites for the Beckmann rearrangement reaction in boron-containing zeolites and their interaction with probe molecules.

    Science.gov (United States)

    Lezcano-González, Inés; Vidal-Moya, Alejandro; Boronat, Mercedes; Blasco, Teresa; Corma, Avelino

    2010-06-28

    Theoretical calculations and in situ solid state NMR spectroscopy have been combined to get insight on the nature of the active sites for the Beckmann rearrangement reaction in borosilicate zeolites. The interaction of a B site in zeolite Beta with a series of probe molecules (ammonia, pyridine, acetone and water) has been modelled and the (15)N and (11)B NMR isotropic chemical shift of the resulting complexes calculated and compared with experimental in situ NMR results. This approach has allowed validation of the methodology to model the adsorption on a zeolite boron site of molecules of varying basicity which are either protonated or non-protonated. The limitation is that theoretical calculations overestimate the effect of molecular adsorption through hydrogen bonds on the calculated isotropic (11)B NMR chemical shift.Theoretical and experimental results on the adsorption of acetophenone and cyclohexanone oximes on zeolite B-Beta indicate that Brønsted acid sites protonate the oximes, changing the boron coordination from trigonal to tetrahedral. Comparison of theoretical and experimental (15)N NMR chemical shifts of the adsorbed amides (acetanilide and epsilon-caprolactam) indicates that they are non-protonated, and the (11)B NMR spectra show that, as expected, boron remains in trigonal coordination with an isotropic delta(11)B(exp) which differs from the calculated value delta(11)B(calc).

  13. Active-site models for complexes of quinolinate synthase with substrates and intermediates

    Energy Technology Data Exchange (ETDEWEB)

    Soriano, Erika V.; Zhang, Yang; Colabroy, Keri L.; Sanders, Jennie M.; Settembre, Ethan C.; Dorrestein, Pieter C.; Begley, Tadhg P.; Ealick, Steven E., E-mail: see3@cornell.edu [Cornell University, Ithaca, NY 14853-1301 (United States)

    2013-09-01

    Structural studies of quinolinate synthase suggest a model for the enzyme–substrate complex and an enzyme–intermediate complex with a [4Fe–4S] cluster. Quinolinate synthase (QS) catalyzes the condensation of iminoaspartate and dihydroxyacetone phosphate to form quinolinate, the universal precursor for the de novo biosynthesis of nicotinamide adenine dinucleotide. QS has been difficult to characterize owing either to instability or lack of activity when it is overexpressed and purified. Here, the structure of QS from Pyrococcus furiosus has been determined at 2.8 Å resolution. The structure is a homodimer consisting of three domains per protomer. Each domain shows the same topology with a four-stranded parallel β-sheet flanked by four α-helices, suggesting that the domains are the result of gene triplication. Biochemical studies of QS indicate that the enzyme requires a [4Fe–4S] cluster, which is lacking in this crystal structure, for full activity. The organization of domains in the protomer is distinctly different from that of a monomeric structure of QS from P. horikoshii [Sakuraba et al. (2005 ▶), J. Biol. Chem.280, 26645–26648]. The domain arrangement in P. furiosus QS may be related to protection of cysteine side chains, which are required to chelate the [4Fe–4S] cluster, prior to cluster assembly.

  14. In Silico Structure Prediction of Human Fatty Acid Synthase-Dehydratase: A Plausible Model for Understanding Active Site Interactions.

    Science.gov (United States)

    John, Arun; Umashankar, Vetrivel; Samdani, A; Sangeetha, Manoharan; Krishnakumar, Subramanian; Deepa, Perinkulam Ravi

    2016-01-01

    Fatty acid synthase (FASN, UniProt ID: P49327) is a multienzyme dimer complex that plays a critical role in lipogenesis. Consequently, this lipogenic enzyme has gained tremendous biomedical importance. The role of FASN and its inhibition is being extensively researched in several clinical conditions, such as cancers, obesity, and diabetes. X-ray crystallographic structures of some of its domains, such as β-ketoacyl synthase, acetyl transacylase, malonyl transacylase, enoyl reductase, β-ketoacyl reductase, and thioesterase, (TE) are already reported. Here, we have attempted an in silico elucidation of the uncrystallized dehydratase (DH) catalytic domain of human FASN. This theoretical model for DH domain was predicted using comparative modeling methods. Different stand-alone tools and servers were used to validate and check the reliability of the predicted models, which suggested it to be a highly plausible model. The stereochemical analysis showed 92.0% residues in favorable region of Ramachandran plot. The initial physiological substrate β-hydroxybutyryl group was docked into active site of DH domain using Glide. The molecular dynamics simulations carried out for 20 ns in apo and holo states indicated the stability and accuracy of the predicted structure in solvated condition. The predicted model provided useful biochemical insights into the substrate-active site binding mechanisms. This model was then used for identifying potential FASN inhibitors using high-throughput virtual screening of the National Cancer Institute database of chemical ligands. The inhibitory efficacy of the top hit ligands was validated by performing molecular dynamics simulation for 20 ns, where in the ligand NSC71039 exhibited good enzyme inhibition characteristics and exhibited dose-dependent anticancer cytotoxicity in retinoblastoma cancer cells in vitro.

  15. In Silico Structure Prediction of Human Fatty Acid Synthase-Dehydratase: A Plausible Model for Understanding Active Site Interactions.

    Science.gov (United States)

    John, Arun; Umashankar, Vetrivel; Samdani, A; Sangeetha, Manoharan; Krishnakumar, Subramanian; Deepa, Perinkulam Ravi

    2016-01-01

    Fatty acid synthase (FASN, UniProt ID: P49327) is a multienzyme dimer complex that plays a critical role in lipogenesis. Consequently, this lipogenic enzyme has gained tremendous biomedical importance. The role of FASN and its inhibition is being extensively researched in several clinical conditions, such as cancers, obesity, and diabetes. X-ray crystallographic structures of some of its domains, such as β-ketoacyl synthase, acetyl transacylase, malonyl transacylase, enoyl reductase, β-ketoacyl reductase, and thioesterase, (TE) are already reported. Here, we have attempted an in silico elucidation of the uncrystallized dehydratase (DH) catalytic domain of human FASN. This theoretical model for DH domain was predicted using comparative modeling methods. Different stand-alone tools and servers were used to validate and check the reliability of the predicted models, which suggested it to be a highly plausible model. The stereochemical analysis showed 92.0% residues in favorable region of Ramachandran plot. The initial physiological substrate β-hydroxybutyryl group was docked into active site of DH domain using Glide. The molecular dynamics simulations carried out for 20 ns in apo and holo states indicated the stability and accuracy of the predicted structure in solvated condition. The predicted model provided useful biochemical insights into the substrate-active site binding mechanisms. This model was then used for identifying potential FASN inhibitors using high-throughput virtual screening of the National Cancer Institute database of chemical ligands. The inhibitory efficacy of the top hit ligands was validated by performing molecular dynamics simulation for 20 ns, where in the ligand NSC71039 exhibited good enzyme inhibition characteristics and exhibited dose-dependent anticancer cytotoxicity in retinoblastoma cancer cells in vitro. PMID:27559295

  16. Homology models of dipeptidyl peptidases 8 and 9 with a focus on loop predictions near the active site.

    Science.gov (United States)

    Rummey, Christian; Metz, Günther

    2007-01-01

    Dipeptidyl peptidase 4 (DP4) inhibitors are currently under intensive investigation in late-stage clinical trials as a treatment for type II diabetes. Lack of selectivity toward the related enzymes DP8 and DP9 has recently emerged as a possible source of drug-induced toxicity. Unlike DP4, X-ray structures of DP8 and DP9 are not yet available. As an aid to understanding the structural basis for selectivity, the authors have constructed homology models of DP8 and DP9 based on the X-ray coordinates of DP4. Accurate sequence alignment reveals common structural features indicative for a well-preserved overall fold comprising two domains, namely, a hydrolase domain and a so-called beta-propeller, which together form the active site deeply buried within the protein. The conformation of two loops inside this deep cavity is particularly relevant for the active sites. The authors used a published protocol for loop prediction based on conformational sampling and energy analysis to generate plausible solutions for these two loops. The predictive power of the approach was successfully evaluated for the template protein DP4 and two additional known structures from the same protein family, namely, FAP and DPX. The authors also show that inclusion of the covalent ligand NVP-728 greatly enhances the refinement. Based on the established evaluation protocol, the corresponding loops of DP8 and DP9 were predicted and the resulting active sites were compared with DP4. In particular, the authors conclude that differences in the P2-pocket are relevant for the design of selective DP4 inhibitors. The loss of key interactions in DP8 and DP9 as predicted from their models is consistent with the selectivity profile of the DP4 clinical candidate MK-431.

  17. Synthesis, Characterization of Heterodinuclear Co-Cu Complex and Its Electrocatalytic Activity towards 02 Reduction: Implications for Cytochrome c Oxidase Active Site Modeling

    Institute of Scientific and Technical Information of China (English)

    卢卫兵; 汪存信; 周晓海; 任建国

    2003-01-01

    A new dinudeating ligand consisting of a tetraphanylporphyrin derivative covalently linked with tris(2-benzimidazylmethyl)-amine and its homodinudear Co-Co and heterodinnelear Co-Cu complexes were synthesized and spectroscopically character-ized. The heterobimetallie cobalt-copper complex bearing three benzimidazole ligands for copper, as cytochrome c oxidase ac-tive site model, was applied to the surface of glassy carbon elec-trode to show electrocatalytie activity for O2 reduction in aque-ous solution at an addity level dose to physiological pH value.The kinetic parameters of this electrocatalytic process were ob-tained.

  18. Molecular Modeling of Peroxidase and Polyphenol Oxidase: Substrate Specificity and Active Site Comparison

    Directory of Open Access Journals (Sweden)

    Lalida Shank

    2010-09-01

    Full Text Available Peroxidases (POD and polyphenol oxidase (PPO are enzymes that are well known to be involved in the enzymatic browning reaction of fruits and vegetables with different catalytic mechanisms. Both enzymes have some common substrates, but each also has its specific substrates. In our computational study, the amino acid sequence of grape peroxidase (ABX was used for the construction of models employing homology modeling method based on the X-ray structure of cytosolic ascorbate peroxidase from pea (PDB ID:1APX, whereas the model of grape polyphenol oxidase was obtained directly from the available X-ray structure (PDB ID:2P3X. Molecular docking of common substrates of these two enzymes was subsequently studied. It was found that epicatechin and catechin exhibited high affinity with both enzymes, even though POD and PPO have different binding pockets regarding the size and the key amino acids involved in binding. Predicted binding modes of substrates with both enzymes were also compared. The calculated docking interaction energy of trihydroxybenzoic acid related compounds shows high affinity, suggesting specificity and potential use as common inhibitor to grape ascorbate peroxidase and polyphenol oxidase.

  19. Novel dimeric β-helical model of an ice nucleation protein with bridged active sites

    Directory of Open Access Journals (Sweden)

    Walker Virginia K

    2011-09-01

    Full Text Available Abstract Background Ice nucleation proteins (INPs allow water to freeze at high subzero temperatures. Due to their large size (>120 kDa, membrane association, and tendency to aggregate, an experimentally-determined tertiary structure of an INP has yet to be reported. How they function at the molecular level therefore remains unknown. Results Here we have predicted a novel β-helical fold for the INP produced by the bacterium Pseudomonas borealis. The protein uses internal serine and glutamine ladders for stabilization and is predicted to dimerize via the burying of a solvent-exposed tyrosine ladder to make an intimate hydrophobic contact along the dimerization interface. The manner in which PbINP dimerizes also allows for its multimerization, which could explain the aggregation-dependence of INP activity. Both sides of the PbINP structure have tandem arrays of amino acids that can organize waters into the ice-like clathrate structures seen on antifreeze proteins. Conclusions Dimerization dramatically increases the 'ice-active' surface area of the protein by doubling its width, increasing its length, and presenting identical ice-forming surfaces on both sides of the protein. We suggest that this allows sufficient anchored clathrate waters to align on the INP surface to nucleate freezing. As PbINP is highly similar to all known bacterial INPs, we predict its fold and mechanism of action will apply to these other INPs.

  20. Determination of structure-activity relationships between fentanyl analogs and human μ-opioid receptors based on active binding site models

    Institute of Scientific and Technical Information of China (English)

    Ming Liu; Xiaoli Liu; Ping Wan; Qiangsan Wu; Wenxiang Hu

    2011-01-01

    Fentanyl is a potent and widely used clinical narcotic analgesic, as well as a highly selective μ-opioid agonist. The present study established a homologous model of the human μ-opioid receptor; an intercomparison of three types of μ-opioid receptor protein sequence homologous rates was made. The secondary receptor structure was predicted, the model reliability was assessed and verified using the Ramachandran plot and ProTab analysis. The predictive ability of the CoMFA model was further validated using an external test set. Using the Surflex-Dock program, a series of fentanyl analog molecules were docked to the receptor, the calculation results from Biopolymer/SiteID showed that the receptor had a deep binding area situated in the extracellular side of the transmembrane domains (TM) among TM3, TM5, TM6, and TM7. Results suggested that there might be 5 active areas in the receptor. The important residues were Asp147, Tyr148, and Tyr149 in TM3, Trp293, and His297 in TM6, and Trp318, His319, Ile322, and Tyr326 in TM7, which were located at the 5 active areas. The best fentanyl docking orientation position was the piperidine ring, which was nearly perpendicular to the membrane surface in the 7 TM domains. Molecular dynamic simulations were applied to evaluate potential relationships between ligand conformation and fentanyl substitution.

  1. Models of the Ni-L and Ni-SIa States of the [NiFe]-Hydrogenase Active Site.

    Science.gov (United States)

    Chambers, Geoffrey M; Huynh, Mioy T; Li, Yulong; Hammes-Schiffer, Sharon; Rauchfuss, Thomas B; Reijerse, Edward; Lubitz, Wolfgang

    2016-01-19

    A new class of synthetic models for the active site of [NiFe]-hydrogenases are described. The Ni(I/II)(SCys)2 and Fe(II)(CN)2CO sites are represented with (RC5H4)Ni(I/II) and Fe(II)(diphos)(CO) modules, where diphos = 1,2-C2H4(PPh2)2(dppe) or cis-1,2-C2H2(PPh2)2(dppv). The two bridging thiolate ligands are represented by CH2(CH2S)2(2-) (pdt(2-)), Me2C(CH2S)2(2-) (Me2pdt(2-)), and (C6H5S)2(2-). The reaction of Fe(pdt)(CO)2(dppe) and [(C5H5)3Ni2]BF4 affords [(C5H5)Ni(pdt)Fe(dppe)(CO)]BF4 ([1a]BF4). Monocarbonyl [1a]BF4 features an S = 0 Ni(II)Fe(II) center with five-coordinated iron, as proposed for the Ni-SIa state of the enzyme. One-electron reduction of [1a](+) affords the S = 1/2 derivative [1a](0), which, according to density functional theory (DFT) calculations and electron paramagnetic resonance and Mössbauer spectroscopies, is best described as a Ni(I)Fe(II) compound. The Ni(I)Fe(II) assignment matches that for the Ni-L state in [NiFe]-hydrogenase, unlike recently reported Ni(II)Fe(I)-based models. Compound [1a](0) reacts with strong acids to liberate 0.5 equiv of H2 and regenerate [1a](+), indicating that H2 evolution is catalyzed by [1a](0). DFT calculations were used to investigate the pathway for H2 evolution and revealed that the mechanism can proceed through two isomers of [1a](0) that differ in the stereochemistry of the Fe(dppe)CO center. Calculations suggest that protonation of [1a](0) (both isomers) affords Ni(III)-H-Fe(II) intermediates, which represent mimics of the Ni-C state of the enzyme.

  2. Femtomolar Zn(II) affinity in a peptide-based ligand designed to model thiolate-rich metalloprotein active sites.

    Science.gov (United States)

    Petros, Amy K; Reddi, Amit R; Kennedy, Michelle L; Hyslop, Alison G; Gibney, Brian R

    2006-12-11

    Metal-ligand interactions are critical components of metalloprotein assembly, folding, stability, electrochemistry, and catalytic function. Research over the past 3 decades on the interaction of metals with peptide and protein ligands has progressed from the characterization of amino acid-metal and polypeptide-metal complexes to the design of folded protein scaffolds containing multiple metal cofactors. De novo metalloprotein design has emerged as a valuable tool both for the modular synthesis of these complex metalloproteins and for revealing the fundamental tenets of metalloprotein structure-function relationships. Our research has focused on using the coordination chemistry of de novo designed metalloproteins to probe the interactions of metal cofactors with protein ligands relevant to biological phenomena. Herein, we present a detailed thermodynamic analysis of Fe(II), Co(II), Zn(II), and[4Fe-4S]2(+/+) binding to IGA, a 16 amino acid peptide ligand containing four cysteine residues, H2N-KLCEGG-CIGCGAC-GGW-CONH2. These studies were conducted to delineate the inherent metal-ion preferences of this unfolded tetrathiolate peptide ligand as well as to evaluate the role of the solution pH on metal-peptide complex speciation. The [4Fe-4S]2(+/+)-IGA complex is both an excellent peptide-based synthetic analogue for natural ferredoxins and is flexible enough to accommodate mononuclear metal-ion binding. Incorporation of a single ferrous ion provides the FeII-IGA complex, a spectroscopic model of a reduced rubredoxin active site that possesses limited stability in aqueous buffers. As expected based on the Irving-Williams series and hard-soft acid-base theory, the Co(II) and Zn(II) complexes of IGA are significantly more stable than the Fe(II) complex. Direct proton competition experiments, coupled with determinations of the conditional dissociation constants over a range of pH values, fully define the thermodynamic stabilities and speciation of each MII-IGA complex. The

  3. Dinuclear nickel complexes modeling the structure and function of the acetyl CoA synthase active site

    OpenAIRE

    Ito, Mikinao; Kotera, Mai; Matsumoto, Tsuyoshi; Tatsumi, Kazuyuki

    2009-01-01

    A dinuclear nickel complex with methyl and thiolate ligands, Ni(dadtEt)Ni(Me)(SDmp) (2), has been synthesized as a dinuclear Nid–Nip-site model of acetyl-CoA synthase (ACS) (dadtEt is N,N′-diethyl-3,7-diazanonane-1,9-dithiolate; Dmp is 2,6-dimesitylphenyl). Complex 2 was prepared via 2 methods: (i) ligand substitution of a dinuclear Ni(II)–Ni(II) cation complex [Ni(dadtEt) Ni(tmtu)2] (OTf)2(1) with MeMgBr and KSDmp (tmtu is tetramethylthiourea), (ii) methyl transfer from methylcobaloxime Co(d...

  4. Three-Dimensional Model of Lanosterol 14α-Demethylase from Cryptococcus neoformans: Active-Site Characterization and Insights into Azole Binding ▿ †

    OpenAIRE

    Sheng, Chunquan; Miao, Zhenyuan; Ji, Haitao; Yao, Jianzhong; Wang, Wenya; Che, Xiaoying; Dong, Guoqiang; Lü, Jiaguo; Guo, Wei; Zhang, Wannian

    2009-01-01

    Cryptococcus neoformans is one of the most important causes of life-threatening fungal infections in immunocompromised patients. Lanosterol 14α-demethylase (CYP51) is the target of azole antifungal agents. This study describes, for the first time, the 3-dimensional model of CYP51 from Cryptococcus neoformans (CnCYP51). The model was further refined by energy minimization and molecular-dynamics simulations. The active site of CnCYP51 was well characterized by multiple-copy simultaneous-search ...

  5. Settings for Physical Activity – Developing a Site-specific Physical Activity Behavior Model based on Multi-level Intervention Studies

    DEFF Research Database (Denmark)

    Troelsen, Jens; Klinker, Charlotte Demant; Breum, Lars;

    activity (PA). The potential is shown by the fact that there has been a dramatic increase in application of ecological models in research and practice. One proposed core principle is that an ecological model is most powerful if the model is behavior-specific. However, based on multi-level interventions......-study is a comprehensive intervention in 7 local school districts (N=1,348). 2) The When Cities Move Children-study is investigating the effects of urban refurbishment on adolescents’ movement patterns (N=653) and 3) The Valuable Detours for PA-project is a intervention study in 9 municipalities measuring the effect...

  6. Forsmark - site descriptive model version 0

    International Nuclear Information System (INIS)

    During 2002, the Swedish Nuclear Fuel and Waste Management Company (SKB) is starting investigations at two potential sites for a deep repository in the Precambrian basement of the Fennoscandian Shield. The present report concerns one of those sites, Forsmark, which lies in the municipality of Oesthammar, on the east coast of Sweden, about 150 kilometres north of Stockholm. The site description should present all collected data and interpreted parameters of importance for the overall scientific understanding of the site, for the technical design and environmental impact assessment of the deep repository, and for the assessment of long-term safety. The site description will have two main components: a written synthesis of the site, summarising the current state of knowledge, as documented in the databases containing the primary data from the site investigations, and one or several site descriptive models, in which the collected information is interpreted and presented in a form which can be used in numerical models for rock engineering, environmental impact and long-term safety assessments. The site descriptive models are devised and stepwise updated as the site investigations proceed. The point of departure for this process is the regional site descriptive model, version 0, which is the subject of the present report. Version 0 is developed out of the information available at the start of the site investigation. This information, with the exception of data from tunnels and drill holes at the sites of the Forsmark nuclear reactors and the underground low-middle active radioactive waste storage facility, SFR, is mainly 2D in nature (surface data), and is general and regional, rather than site-specific, in content. For this reason, the Forsmark site descriptive model, version 0, as detailed in the present report, has been developed at a regional scale. It covers a rectangular area, 15 km in a southwest-northeast and 11 km in a northwest-southeast direction, around the

  7. Efficient oxygen electrocatalysis on special active sites

    DEFF Research Database (Denmark)

    Halck, Niels Bendtsen

    is used to explain the increase in activity observed for the OER catalyst ruthenium dioxide when it is mixed with nickel or cobalt. Manganese and cobalt oxides when in the vicinity of gold also display an increase in OER activity which can be explained by locally created special active sites. Density...

  8. Simpevarp - site descriptive model version 0

    International Nuclear Information System (INIS)

    , agricultural land, lakes and rivers, and sea, each further subdivided into appropriate entities (topography, vegetation, fauna, soil characteristics, sediments, etc). The main emphasis of the report is on the preparation of a site descriptive model, v. 0, for the geosphere, since data acquisition and processing in this area, in contrast to the biosphere, is sufficiently advanced for some initial modelling exercises. The available information on the geosphere in the Simpevarp regional model area is quite extensive, at least locally (especially Aespoe). In order to develop and test the modelling procedures, this information has been collected and transformed into appropriate formats under four separate headings: Geology, Rock mechanics, Hydrogeology, and Hydrogeochemistry. This first attempt to develop a 3D geological and geometrical framework for rock engineering and hydrogeological purposes, is accompanied by a discussion of how best to assess uncertainty in relation to geological data, depending on the scale of compilation, the level of knowledge and the interpretation of surface geometry. In the areas of rock engineering, hydrogeology and hydrogeochemistry, modelling activities were mainly confined to parametrisation exercises, using presently available data from the Simpevarp regional model area to put limits on, for instance, the in situ stress field, the mechanical properties of the rock mass, the hydraulic properties of the fracture zones and rock mass between them, and the hydrogeochemical evolution. The main results of the present project were to focus attention on the strengths and weaknesses in the available data coverage and data storage and processing systems, and to provide a basis for developing and testing ways of transform- ing diverse types of geoscientific information into a form appropriate for modelling. At the same time, the project provided concrete guidelines for the planning of the initial site invest

  9. Promoter proximal polyadenylation sites reduce transcription activity

    DEFF Research Database (Denmark)

    Andersen, Pia Kjølhede; Lykke-Andersen, Søren; Jensen, Torben Heick

    2012-01-01

    Gene expression relies on the functional communication between mRNA processing and transcription. We previously described the negative impact of a point-mutated splice donor (SD) site on transcription. Here we demonstrate that this mutation activates an upstream cryptic polyadenylation (CpA) site...

  10. Models for the active site in galactose oxidase: Structure, spectra and redox of copper(II) complexes of certain phenolate ligands

    Indian Academy of Sciences (India)

    Mathrubootham Vaidyanathan; Mallayan Palaniandavar

    2000-06-01

    Galactose oxidase (GOase) is a fungal enzyme which is unusual among metalloenzymes in appearing to catalyse the two electron oxidation of primary alcohols to aldehydes and H2O2. The crystal structure of the enzyme reveals that the coordination geometry of mononuclear copper(II) ion is square pyramidal, with two histidine imidazoles, a tyrosinate, and either H2O (H 7.0) or acetate (from buffer, H 4.5) in the equatorial sites and a tyrosinate ligand weakly bound in the axial position. This paper summarizes the results of our studies on the structure, spectral and redox properties of certain novel models for the active site of the inactive form of GOase. The monophenolato Cu(II) complexes of the type [Cu(L1)X][H(L1) = 2-(bis(pyrid-2-ylmethyl)aminomethyl)-4-nitrophenol and X-= Cl-1, NCS-2, CH3COO-3, ClO$_{4}^{-}$ 4] reveal a distorted square pyramidal geometry around Cu(II) with an unusual axial coordination of phenolate moiety. The coordination geometry of 3 is reminiscent of the active site of GOase with an axial phenolate and equatorial CH3COO- ligands. All the present complexes exhibit several electronic and EPR spectral features which are also similar to the enzyme. Further, to establish the structural and spectroscopic consequences of the coordination of two tyrosinates in GOase enzyme, we studied the monomeric copper(II) complexes containing two phenolates and imidazole/pyridine donors as closer structural models for GOase. N,Ndimethylethylenediamine and N,N -dimethylethylenediamine have been used as starting materials to obtain a variety of 2,4-disubstituted phenolate ligands. The X-ray crystal structures of the complexes [Cu(L5)(py)], (8) [H2 (L5) = N,N-dimethyl-N ,N -bis(2-hydroxy-4-nitrobenzyl) ethylenediamine, py = pyridine] and [Cu(L8)(H2O)] (11), [H2(L8) = N,N -dimethyl-N,N -bis(2-hydroxy-4-nitrobenzyl)ethylenediamine] reveal distorted square pyramidal geometries around Cu(II) with the axial tertiary amine nitrogen and water coordination respectively

  11. Forsmark - site descriptive model version 0

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2002-10-01

    During 2002, the Swedish Nuclear Fuel and Waste Management Company (SKB) is starting investigations at two potential sites for a deep repository in the Precambrian basement of the Fennoscandian Shield. The present report concerns one of those sites, Forsmark, which lies in the municipality of Oesthammar, on the east coast of Sweden, about 150 kilometres north of Stockholm. The site description should present all collected data and interpreted parameters of importance for the overall scientific understanding of the site, for the technical design and environmental impact assessment of the deep repository, and for the assessment of long-term safety. The site description will have two main components: a written synthesis of the site, summarising the current state of knowledge, as documented in the databases containing the primary data from the site investigations, and one or several site descriptive models, in which the collected information is interpreted and presented in a form which can be used in numerical models for rock engineering, environmental impact and long-term safety assessments. The site descriptive models are devised and stepwise updated as the site investigations proceed. The point of departure for this process is the regional site descriptive model, version 0, which is the subject of the present report. Version 0 is developed out of the information available at the start of the site investigation. This information, with the exception of data from tunnels and drill holes at the sites of the Forsmark nuclear reactors and the underground low-middle active radioactive waste storage facility, SFR, is mainly 2D in nature (surface data), and is general and regional, rather than site-specific, in content. For this reason, the Forsmark site descriptive model, version 0, as detailed in the present report, has been developed at a regional scale. It covers a rectangular area, 15 km in a southwest-northeast and 11 km in a northwest-southeast direction, around the

  12. Characterization of Reuse Activities at Contaminated Sites

    OpenAIRE

    Angela Vitulli; Charlotte Dougherty; Kimberly Bosworth

    2004-01-01

    Given the increased focus on reuse activity within EPA and state site cleanup programs, policy makers would benefit from looking across programs to better understand the extent and nature of reuse; examine site characteristics that influence reuse; leverage lessons learned; and coordinate reuse activities, data collection, and information management. This research paper begins to examine these issues. It reports the results of a preliminary review and analysis of available EPA and state progr...

  13. Fingerprinting differential active site constraints of ATPases

    OpenAIRE

    Hacker, Stephan M.; Hardt, Norman; Buntru, Alexander; Pagliarini, Dana; Möckel, Martin; Mayer, Thomas U; Scheffner, Martin; Hauck, Christof R.; Marx, Andreas

    2013-01-01

    The free energy provided by adenosine triphosphate (ATP) hydrolysis is central to many cellular processes and, therefore, the number of enzymes utilizing ATP as a substrate is almost innumerable. Modified analogues of ATP are a valuable means to understand the biological function of ATPases. Although these enzymes have evolved towards binding to ATP, large differences in active site architectures were found. In order to systematically access the specific active site constraints of different A...

  14. Bedrock hydrogeology Forsmark. Site descriptive modelling, SDM-Site Forsmark

    Energy Technology Data Exchange (ETDEWEB)

    Follin, Sven (SF GeoLogic AB, Taeby (Sweden))

    2008-12-15

    The Swedish Nuclear Fuel and Waste Management Company (SKB) has conducted site investigations at two different locations, the Forsmark and Laxemar-Simpevarp areas, with the objective of siting a final repository for spent nuclear fuel according to the KBS-3 concept. Site characterisation should provide all data required for an integrated evaluation of the suitability of the investigated site and an important component in the characterisation work is the development of a hydrogeological model. The hydrogeological model is used by repository engineering to design the underground facility and to develop a repository layout adapted to the site. It also provides input to the safety assessment. Another important use of the hydrogeological model is in the environmental impact assessment. This report presents the understanding of the hydrogeological conditions of the bedrock at Forsmark reached following the completion of the surface-based investigations and provides a summary of the bedrock hydrogeological model and the underlying data supporting its development. It constitutes the main reference on bedrock hydrogeology for the site descriptive model concluding the surface-based investigations at Forsmark, SDM-site, and is intended to describe the hydraulic properties and hydrogeological conditions of the bedrock at the site and to give the information essential for demonstrating understanding

  15. Bedrock hydrogeology Forsmark. Site descriptive modelling, SDM-Site Forsmark

    International Nuclear Information System (INIS)

    The Swedish Nuclear Fuel and Waste Management Company (SKB) has conducted site investigations at two different locations, the Forsmark and Laxemar-Simpevarp areas, with the objective of siting a final repository for spent nuclear fuel according to the KBS-3 concept. Site characterisation should provide all data required for an integrated evaluation of the suitability of the investigated site and an important component in the characterisation work is the development of a hydrogeological model. The hydrogeological model is used by repository engineering to design the underground facility and to develop a repository layout adapted to the site. It also provides input to the safety assessment. Another important use of the hydrogeological model is in the environmental impact assessment. This report presents the understanding of the hydrogeological conditions of the bedrock at Forsmark reached following the completion of the surface-based investigations and provides a summary of the bedrock hydrogeological model and the underlying data supporting its development. It constitutes the main reference on bedrock hydrogeology for the site descriptive model concluding the surface-based investigations at Forsmark, SDM-site, and is intended to describe the hydraulic properties and hydrogeological conditions of the bedrock at the site and to give the information essential for demonstrating understanding

  16. Geological discrete fracture network model for the Laxemar site. Site Descriptive Modelling. SDM-Site Laxemar

    Energy Technology Data Exchange (ETDEWEB)

    La Pointe, Paul; Fox, Aaron (Golder Associates Inc (United States)); Hermanson, Jan; Oehman, Johan (Golder Associates AB, Stockholm (Sweden))

    2008-12-15

    The Swedish Nuclear Fuel and Waste Management Company (SKB) is performing site characterization at two different locations, Forsmark and Laxemar, in order to locate a site for a final geologic repository for spent nuclear fuel. The program is built upon the development of Site Descriptive Models (SDMs) at specific timed data freezes. Each SDM is formed from discipline-specific reports from across the scientific spectrum. This report describes the methods, analyses, and conclusions of the modelling team in the production of the SDM-Site Laxemar geological discrete-fracture network (DFN) model. The DFN builds upon the work of other geological models, including the deformation zone and rock domain models. The geological DFN is a statistical model for stochastically simulating rock fractures and minor deformation zones at a scale of less than 1,000 m (the lower cut-off of the DZ models). The geological DFN is valid within six distinct fracture domains inside the Laxemar local model subarea: FSM{sub C}, FSM{sub E}W007, FSM{sub N}, FSM{sub N}E005, FSM{sub S}, and FSM{sub W}. The models are built using data from detailed surface outcrop maps, geophysical lineament maps, and the cored borehole record at Laxemar. The conceptual model for the SDM-Site Laxemar geological DFN model revolves around the identification of fracture domains based on relative fracture set intensities, orientation clustering, and the regional tectonic framework (including deformation zones). A single coupled fracture size/fracture intensity concept (the Base Model) based on a Pareto (power-law) distribution for fracture sizes was chosen as the recommended parameterisation. A slew of alternative size-intensity models were also carried through the fracture analyses and into the uncertainty and model verification analyses. Uncertainty is modelled by analysing the effects on fracture intensity (P32) that alternative model cases can have. Uncertainty is parameterised as a ratio between the P32 of the

  17. Mechanism of the Quorum-Quenching Lactonase (AiiA) from Bacillus thuringiensis. 2. Substrate Modeling and Active Site Mutations

    Energy Technology Data Exchange (ETDEWEB)

    Momb, Jessica; Wang, Canhui; Liu, Dali; Thomas, Pei W.; Petsko, Gregory A.; Guo, Hua; Ringe, Dagmar; Fast, Walter (UNM); (Brandeis); (Texas)

    2008-12-02

    The N-acyl-l-homoserine lactone hydrolases (AHL lactonases) have attracted considerable attention because of their ability to quench AHL-mediated quorum-sensing pathways in Gram-negative bacteria and because of their relation to other enzymes in the metallo-{beta}-lactamase superfamily. To elucidate the detailed catalytic mechanism of AHL lactonase, mutations are made on residues that presumably contribute to substrate binding and catalysis. Steady-state kinetic studies are carried out on both the wild-type and mutant enzymes using a spectrum of substrates. Two mutations, Y194F and D108N, present significant effects on the overall catalysis. On the basis of a high-resolution structural model of the enzyme-product complex, a hybrid quantum mechanical/molecular mechanical method is used to model the substrate binding orientation and to probe the effect of the Y194F mutation. Combining all experimental and computational results, we propose a detailed mechanism for the ring-opening hydrolysis of AHL substrates as catalyzed by the AHL lactonase from Bacillus thuringiensis. Several features of the mechanism that are also found in related enzymes are discussed and may help to define an evolutionary thread that connects the hydrolytic enzymes of this mechanistically diverse superfamily.

  18. Bedrock hydrogeochemistry Forsmark. Site descriptive modelling SDM-Site Forsmark

    Energy Technology Data Exchange (ETDEWEB)

    Laaksoharju, Marcus (Geopoint AB, Sollentuna (Sweden)); Smellie, John (Conterra AB, Partille (Sweden)); Tullborg, Eva-Lena (Terralogica, Graabo (Sweden)); Gimeno, Maria (Univ. of Zaragoza, Zaragoza (Spain)); Hallbeck, Lotta (Microbial Analytics, Goeteborg (Sweden)); Molinero, Jorge (Amphos XXI Consulting S.L., Barcelona (Spain)); Waber, Nick (Univ. of Bern, Bern (Switzerland))

    2008-12-15

    The overall objectives of the hydrogeochemical site description for Forsmark are to establish a detailed understanding of the hydrogeochemical conditions at the site, and to use this understanding to develop models that address the needs identified by the safety assessment groups during the site investigation phase. Issues of concern to safety assessment are radionuclide transport and technical barrier behaviour, both of which are dependent on the chemistry of groundwater and porewater and their evolution with time. The specific aims of the hydrogeochemical work were: To document the hydrogeochemistry at the Forsmark site with focus on the development of conceptual models to describe and visualise the site. To provide relevant parameter values to be used for safety assessment calculations. To provide the hydrogeochemical basis for the modelling work by other teams, in particular hydrogeology. To take account of the feedback from the SR-Can safety assessment work that bears relevance to the hydrogeochemical modelling work. The work has involved the development of descriptive and mathematical models for groundwaters in relation to rock domains, fracture domains and deformation zones. In this report, the groundwaters have been interpreted in relation to their origin, evolution and composition, which require close integration with geological, climatological and hydrogeological information. Past climate changes are one of the major driving forces for long-term hydrogeochemical changes (hundreds to thousands of years) and are, therefore, of fundamental importance for understanding the palaeohydrogeological, palaeohydrogeochemical and present evolution of groundwater in the Fennoscandian crystalline bedrock. In contrast, redox buffer capacity of the bedrock will minimise the effects on changes in alkalinity and redox at repository depths, therefore limiting the variations in pH and Eh significantly, regardless of major changes in groundwater composition. There is

  19. Bedrock hydrogeochemistry Forsmark. Site descriptive modelling SDM-Site Forsmark

    International Nuclear Information System (INIS)

    The overall objectives of the hydrogeochemical site description for Forsmark are to establish a detailed understanding of the hydrogeochemical conditions at the site, and to use this understanding to develop models that address the needs identified by the safety assessment groups during the site investigation phase. Issues of concern to safety assessment are radionuclide transport and technical barrier behaviour, both of which are dependent on the chemistry of groundwater and porewater and their evolution with time. The specific aims of the hydrogeochemical work were: To document the hydrogeochemistry at the Forsmark site with focus on the development of conceptual models to describe and visualise the site. To provide relevant parameter values to be used for safety assessment calculations. To provide the hydrogeochemical basis for the modelling work by other teams, in particular hydrogeology. To take account of the feedback from the SR-Can safety assessment work that bears relevance to the hydrogeochemical modelling work. The work has involved the development of descriptive and mathematical models for groundwaters in relation to rock domains, fracture domains and deformation zones. In this report, the groundwaters have been interpreted in relation to their origin, evolution and composition, which require close integration with geological, climatological and hydrogeological information. Past climate changes are one of the major driving forces for long-term hydrogeochemical changes (hundreds to thousands of years) and are, therefore, of fundamental importance for understanding the palaeohydrogeological, palaeohydrogeochemical and present evolution of groundwater in the Fennoscandian crystalline bedrock. In contrast, redox buffer capacity of the bedrock will minimise the effects on changes in alkalinity and redox at repository depths, therefore limiting the variations in pH and Eh significantly, regardless of major changes in groundwater composition. There is

  20. Biomolecular structure manipulation using tailored electromagnetic radiation: a proof of concept on a simplified model of the active site of bacterial DNA topoisomerase.

    Science.gov (United States)

    Jarukanont, Daungruthai; Coimbra, João T S; Bauerhenne, Bernd; Fernandes, Pedro A; Patel, Shekhar; Ramos, Maria J; Garcia, Martin E

    2014-10-21

    We report on the viability of breaking selected bonds in biological systems using tailored electromagnetic radiation. We first demonstrate, by performing large-scale simulations, that pulsed electric fields cannot produce selective bond breaking. Then, we present a theoretical framework for describing selective energy concentration on particular bonds of biomolecules upon application of tailored electromagnetic radiation. The theory is based on the mapping of biomolecules to a set of coupled harmonic oscillators and on optimal control schemes to describe optimization of temporal shape, the phase and polarization of the external radiation. We have applied this theory to demonstrate the possibility of selective bond breaking in the active site of bacterial DNA topoisomerase. For this purpose, we have focused on a model that was built based on a case study. Results are given as a proof of concept.

  1. Probabilistic prediction models for aggregate quarry siting

    Science.gov (United States)

    Robinson, G.R.; Larkins, P.M.

    2007-01-01

    Weights-of-evidence (WofE) and logistic regression techniques were used in a GIS framework to predict the spatial likelihood (prospectivity) of crushed-stone aggregate quarry development. The joint conditional probability models, based on geology, transportation network, and population density variables, were defined using quarry location and time of development data for the New England States, North Carolina, and South Carolina, USA. The Quarry Operation models describe the distribution of active aggregate quarries, independent of the date of opening. The New Quarry models describe the distribution of aggregate quarries when they open. Because of the small number of new quarries developed in the study areas during the last decade, independent New Quarry models have low parameter estimate reliability. The performance of parameter estimates derived for Quarry Operation models, defined by a larger number of active quarries in the study areas, were tested and evaluated to predict the spatial likelihood of new quarry development. Population density conditions at the time of new quarry development were used to modify the population density variable in the Quarry Operation models to apply to new quarry development sites. The Quarry Operation parameters derived for the New England study area, Carolina study area, and the combined New England and Carolina study areas were all similar in magnitude and relative strength. The Quarry Operation model parameters, using the modified population density variables, were found to be a good predictor of new quarry locations. Both the aggregate industry and the land management community can use the model approach to target areas for more detailed site evaluation for quarry location. The models can be revised easily to reflect actual or anticipated changes in transportation and population features. ?? International Association for Mathematical Geology 2007.

  2. Confidence assessment. Site-descriptive modelling SDM-Site Laxemar

    International Nuclear Information System (INIS)

    The objective of this report is to assess the confidence that can be placed in the Laxemar site descriptive model, based on the information available at the conclusion of the surface-based investigations (SDM-Site Laxemar). In this exploration, an overriding question is whether remaining uncertainties are significant for repository engineering design or long-term safety assessment and could successfully be further reduced by more surface-based investigations or more usefully by explorations underground made during construction of the repository. Procedures for this assessment have been progressively refined during the course of the site descriptive modelling, and applied to all previous versions of the Forsmark and Laxemar site descriptive models. They include assessment of whether all relevant data have been considered and understood, identification of the main uncertainties and their causes, possible alternative models and their handling, and consistency between disciplines. The assessment then forms the basis for an overall confidence statement. The confidence in the Laxemar site descriptive model, based on the data available at the conclusion of the surface based site investigations, has been assessed by exploring: - Confidence in the site characterization data base, - remaining issues and their handling, - handling of alternatives, - consistency between disciplines and - main reasons for confidence and lack of confidence in the model. Generally, the site investigation database is of high quality, as assured by the quality procedures applied. It is judged that the Laxemar site descriptive model has an overall high level of confidence. Because of the relatively robust geological model that describes the site, the overall confidence in the Laxemar Site Descriptive model is judged to be high, even though details of the spatial variability remain unknown. The overall reason for this confidence is the wide spatial distribution of the data and the consistency between

  3. Confidence assessment. Site-descriptive modelling SDM-Site Laxemar

    Energy Technology Data Exchange (ETDEWEB)

    2008-12-15

    The objective of this report is to assess the confidence that can be placed in the Laxemar site descriptive model, based on the information available at the conclusion of the surface-based investigations (SDM-Site Laxemar). In this exploration, an overriding question is whether remaining uncertainties are significant for repository engineering design or long-term safety assessment and could successfully be further reduced by more surface-based investigations or more usefully by explorations underground made during construction of the repository. Procedures for this assessment have been progressively refined during the course of the site descriptive modelling, and applied to all previous versions of the Forsmark and Laxemar site descriptive models. They include assessment of whether all relevant data have been considered and understood, identification of the main uncertainties and their causes, possible alternative models and their handling, and consistency between disciplines. The assessment then forms the basis for an overall confidence statement. The confidence in the Laxemar site descriptive model, based on the data available at the conclusion of the surface based site investigations, has been assessed by exploring: - Confidence in the site characterization data base, - remaining issues and their handling, - handling of alternatives, - consistency between disciplines and - main reasons for confidence and lack of confidence in the model. Generally, the site investigation database is of high quality, as assured by the quality procedures applied. It is judged that the Laxemar site descriptive model has an overall high level of confidence. Because of the relatively robust geological model that describes the site, the overall confidence in the Laxemar Site Descriptive model is judged to be high, even though details of the spatial variability remain unknown. The overall reason for this confidence is the wide spatial distribution of the data and the consistency between

  4. Part I. Cobalt thiolate complexes modeling the active site of cobalt nitrile hydratase. Part II. Formation of inorganic nanoparticles on protein scaffolding in Escherichia coli glutamine synthetase

    Science.gov (United States)

    Kung, Irene Yuk Man

    Part I. A series of novel cobalt dithiolate complexes with mixed imine/amine ligand systems is presented here as electronic and structural models for the active site in the bacterial enzyme class, nitrile hydratase (NHase). Pentadentate cobalt(II) complexes with S2N 3 ligand environments are first studied as precursors to the more relevant cobalt(III) complexes. Adjustment of the backbone length by removal of a methylene group increases the reactivity of the system; whereas reduction of the two backbone imine bonds to allow free rotation about those bonds may decrease reactivity. Reactivity change due to the replacement of the backbone amine proton with a more sterically challenging methyl group is not yet clear. Upon oxidation, the monocationic pentadentate cobalt(III) complex, 1b, shows promising reactivity similar to that of NHase. The metal's open coordination site allows reversible binding of the endogenous, monoanionic ligands, N 3- and NCS-. Oxygenation of the thiolate sulfur atoms by exposure to O2 and H2O 2 produces sulfenate and sulfinate ligands in complex 8, which resembles the crystal structure of "deactivated" Fe NHase. However, its lack of reactivity argues against the oxygenated enzyme structure as the active form. Six-coordinate cobalt(III) complexes with S2N4 amine/amine ligand systems are also presented as analogues of previously reported iron(III) compounds, which mimic the spectroscopic properties of Fe NHase. The cobalt complexes do not seem to similarly model Co NHase. However, the S = 0 cobalt(III) center can be spectroscopically silent and difficult to detect, making comparison with synthetic models using common techniques hard. Part II. Dodecameric Escherichia coli glutamine synthetase mutant, E165C, stacks along its six-fold axis to produce tubular nanostructures in the presence of some divalent metal ions, as does the wild type enzyme. The centrally located, engineered Cys-165 residues appear to bind to various species and may serve as

  5. Key messages from active CO2 storage sites

    Energy Technology Data Exchange (ETDEWEB)

    Wildenborg, T.; Wollenweber, J. [TNO, Princetonlaan 6, 3584 CB Utrecht (Netherlands); Chadwick, A. [BGS, Environmental Science Centre, Keyworth, Nottingham, NG12 5GG (United Kingdom); Deflandre, J.P. [IFP Energies nouvelles, 1-4 avenue de Bois Preau, 92852 Rueil-Malmaison (France); Eiken, O. [Statoil Research Centre, Rotvoll, Arkitekt Ebbells vei 10, 7005 Trondheim (Norway); Mathieson, A. [BP, Alternative Energy, Chertsey Road, Sunbury on Thames (United Kingdom); Metcalfe, R. [QUINTESSA, The Hub, 14 Station Road, Henley-on-Thames, Oxfordshire (United Kingdom); Schmidt Hattenberger, C. [GFZ German Research Centre for Geosciences, Centre for CO2Storage, Potsdam (Germany)

    2013-07-01

    An extensive programme of modelling, monitoring and verification activities was deployed at a set of active storage sites worldwide including Sleipner, In Salah, Ketzin, Weyburn, K12-B and Snoehvit (EU CO2ReMoVe project). All investigated storage sites were well managed and did not have a negative impact on humans or the environment. Time-lapse seismic and pressure monitoring are key in verifying the deep subsurface performance of the storage sites. Evidence gathered during the site characterisation and operational phases is key to handover responsibility of the storage site to governmental authorities after injection has definitely ceased, which is the focus of the follow-up EU project CO2CARE.

  6. Beyond the three-site Higgless model

    Energy Technology Data Exchange (ETDEWEB)

    Kurachi, Masafumi [Los Alamos National Laboratory; Belyaev, Alexander S [ENGLAND; Chivukula, R Sekhar [MSU; Christensen, Neil D [MSU; Simmon, Elizabeth H [MSU; He, Hong - Jian [TSINGHUA UNIV; Tanabashie, Masaharu [NAGOYA UNIV

    2009-01-01

    The three-site model has been offered as a benchmark or test case for studying the collider phenomenology of Higgs-less models. It is therefore appropriate to consider how well the three-site model performs as a general representative of Higgs-less models, and which modifications might remedy any shortcomings. We employ sum rules relating the masses and couplings of the Kaluza-Klein modes of the gauge fields in continuum and deconstructed Higgs-less models as a way to compare the different theories. These identities enable us to quantify how well a given theory performs at unitarizing the scattering of electroweak gauge bosons at a particular energy scale. We will see that the tendency of the sum rules to be saturated by contributions from the lowest-lying KK resonances provides a good measure of the extent to which a highly-deconstructed theory like the three-site model can accurately describe the low-energy physics. After comparing the three-site model to a pair of continuum models, we analyze extensions of the three-site model to a longer open linear model with an additional U(I) group and to a ring model with three sites and three links; both cases can be analyzed in the framework created by the sum rules. The hadron and lepton collider phenomenology of both extended models is discussed, with a focus on the complementary information to be gained from the different facilities.

  7. Site investigations: Strategy for rock mechanics site descriptive model

    International Nuclear Information System (INIS)

    As a part of the planning work for the Site Investigations, SKB has developed a Rock Mechanics Site Descriptive Modelling Strategy. Similar strategies are being developed for other disciplines. The objective of the strategy is that it should guide the practical implementation of evaluating site specific data during the Site Investigations. It is also understood that further development may be needed. This methodology enables the crystalline rock mass to be characterised in terms of the quality at different sites, for considering rock engineering constructability, and for providing the input to numerical models and performance assessment calculations. The model describes the initial stresses and the distribution of deformation and strength properties of the intact rock, of fractures and fracture zones, and of the rock mass. The rock mass mechanical properties are estimated by empirical relations and by numerical simulations. The methodology is based on estimation of mechanical properties using both empirical and heroretical/numerical approaches; and estimation of in situ rock stress using judgement and numerical modelling, including the influence of fracture zones. These approaches are initially used separately, and then combined to produce the required characterisation estimates. The methodology was evaluated with a Test Case at the Aespoe Hard Rock Laboratory in Sweden. The quality control aspects are an important feature of the methodology: these include Protocols to ensure the structure and coherence of the procedures used, regular meetings to enhance communication, feedback from internal and external reviewing, plus the recording of an audit trail of the development steps and decisions made. The strategy will be reviewed and, if required, updated as appropriate

  8. Site investigations: Strategy for rock mechanics site descriptive model

    Energy Technology Data Exchange (ETDEWEB)

    Andersson, Johan [JA Streamflow AB, Aelvsjoe (Sweden); Christiansson, Rolf [Swedish Nuclear Fuel and Waste Management Co., Stockholm (Sweden); Hudson, John [Rock Engineering Consultants, Welwyn Garden City (United Kingdom)

    2002-05-01

    As a part of the planning work for the Site Investigations, SKB has developed a Rock Mechanics Site Descriptive Modelling Strategy. Similar strategies are being developed for other disciplines. The objective of the strategy is that it should guide the practical implementation of evaluating site specific data during the Site Investigations. It is also understood that further development may be needed. This methodology enables the crystalline rock mass to be characterised in terms of the quality at different sites, for considering rock engineering constructability, and for providing the input to numerical models and performance assessment calculations. The model describes the initial stresses and the distribution of deformation and strength properties of the intact rock, of fractures and fracture zones, and of the rock mass. The rock mass mechanical properties are estimated by empirical relations and by numerical simulations. The methodology is based on estimation of mechanical properties using both empirical and heroretical/numerical approaches; and estimation of in situ rock stress using judgement and numerical modelling, including the influence of fracture zones. These approaches are initially used separately, and then combined to produce the required characterisation estimates. The methodology was evaluated with a Test Case at the Aespoe Hard Rock Laboratory in Sweden. The quality control aspects are an important feature of the methodology: these include Protocols to ensure the structure and coherence of the procedures used, regular meetings to enhance communication, feedback from internal and external reviewing, plus the recording of an audit trail of the development steps and decisions made. The strategy will be reviewed and, if required, updated as appropriate.

  9. Confidence assessment. Site descriptive modelling SDM-Site Forsmark

    Energy Technology Data Exchange (ETDEWEB)

    2008-09-15

    The objective of this report is to assess the confidence that can be placed in the Forsmark site descriptive model, based on the information available at the conclusion of the surface-based investigations (SDM-Site Forsmark). In this exploration, an overriding question is whether remaining uncertainties are significant for repository engineering design or long-term safety assessment and could successfully be further reduced by more surface based investigations or more usefully by explorations underground made during construction of the repository. The confidence in the Forsmark site descriptive model, based on the data available at the conclusion of the surface-based site investigations, have been assessed by exploring: Confidence in the site characterisation data base; Key remaining issues and their handling; Handling of alternative models; Consistency between disciplines; and, Main reasons for confidence and lack of confidence in the model. It is generally found that the key aspects of importance for safety assessment and repository engineering of the Forsmark site descriptive model are associated with a high degree of confidence. Because of the robust geological model that describes the site, the overall confidence in Forsmark site descriptive model is judged to be high. While some aspects have lower confidence this lack of confidence is handled by providing wider uncertainty ranges, bounding estimates and/or alternative models. Most, but not all, of the low confidence aspects have little impact on repository engineering design or for long-term safety. Poor precision in the measured data are judged to have limited impact on uncertainties on the site descriptive model, with the exceptions of inaccuracy in determining the position of some boreholes at depth in 3-D space, as well as the poor precision of the orientation of BIPS images in some boreholes, and the poor precision of stress data determined by overcoring at the locations where the pre

  10. Uncertainty and the Conceptual Site Model

    Science.gov (United States)

    Price, V.; Nicholson, T. J.

    2007-12-01

    Our focus is on uncertainties in the underlying conceptual framework upon which all subsequent steps in numerical and/or analytical modeling efforts depend. Experienced environmental modelers recognize the value of selecting an optimal conceptual model from several competing site models, but usually do not formally explore possible alternative models, in part due to incomplete or missing site data, as well as relevant regional data for establishing boundary conditions. The value in and approach for developing alternative conceptual site models (CSM) is demonstrated by analysis of case histories. These studies are based on reported flow or transport modeling in which alternative site models are formulated using data that were not available to, or not used by, the original modelers. An important concept inherent to model abstraction of these alternative conceptual models is that it is "Far better an approximate answer to the right question, which is often vague, than the exact answer to the wrong question, which can always be made precise." (Tukey, 1962) The case histories discussed here illustrate the value of formulating alternative models and evaluating them using site-specific data: (1) Charleston Naval Site where seismic characterization data allowed significant revision of the CSM and subsequent contaminant transport modeling; (2) Hanford 300-Area where surface- and ground-water interactions affecting the unsaturated zone suggested an alternative component to the site model; (3) Savannah River C-Area where a characterization report for a waste site within the modeled area was not available to the modelers, but provided significant new information requiring changes to the underlying geologic and hydrogeologic CSM's used; (4) Amargosa Desert Research Site (ADRS) where re-interpretation of resistivity sounding data and water-level data suggested an alternative geologic model. Simple 2-D spreadsheet modeling of the ADRS with the revised CSM provided an improved

  11. BET is active on Sellafield site

    International Nuclear Information System (INIS)

    Several companies, all part of BET Plant Services are carrying out work at the British Nuclear Fuels (BNFL) site at Sellafield, Cumbria, on one of the largest construction projects in Europe. The main development scheme is the THORP (Thermal Oxide Reprocessing Plant) buildings. One of the BET companies has the contract to paint the inside of the fuel storage ponds. It will also coat the surfaces of the MASWEP (Medium Active Solid Waste Encapsulation Plant) complex. Other work includes insulation and fire prevention installation. Scaffolding at the EARP (Enhanced Actinide Removal Plant) site is being provided on a common user basis so all the contractors can use the scaffolding and share the cost. Temporary office and living accommodation blocks have been provide by another BET company. (author)

  12. Site descriptive modelling - strategy for integrated evaluation

    International Nuclear Information System (INIS)

    The current document establishes the strategy to be used for achieving sufficient integration between disciplines in producing Site Descriptive Models during the Site Investigation stage. The Site Descriptive Model should be a multidisciplinary interpretation of geology, rock mechanics, thermal properties, hydrogeology, hydrogeochemistry, transport properties and ecosystems using site investigation data from deep bore holes and from the surface as input. The modelling comprise the following iterative steps, evaluation of primary data, descriptive and quantitative modelling (in 3D), overall confidence evaluation. Data are first evaluated within each discipline and then the evaluations are checked between the disciplines. Three-dimensional modelling (i.e. estimating the distribution of parameter values in space and its uncertainty) is made in a sequence, where the geometrical framework is taken from the geological model and in turn used by the rock mechanics, thermal and hydrogeological modelling etc. The three-dimensional description should present the parameters with their spatial variability over a relevant and specified scale, with the uncertainty included in this description. Different alternative descriptions may be required. After the individual discipline modelling and uncertainty assessment a phase of overall confidence evaluation follows. Relevant parts of the different modelling teams assess the suggested uncertainties and evaluate the feedback. These discussions should assess overall confidence by, checking that all relevant data are used, checking that information in past model versions is considered, checking that the different kinds of uncertainty are addressed, checking if suggested alternatives make sense and if there is potential for additional alternatives, and by discussing, if appropriate, how additional measurements (i.e. more data) would affect confidence. The findings as well as the modelling results are to be documented in a Site Description

  13. Simpevarp - site descriptive model version 0

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2002-11-01

    During 2002, SKB is starting detailed investigations at two potential sites for a deep repository in the Precambrian rocks of the Fennoscandian Shield. The present report concerns one of those sites, Simpevarp, which lies in the municipality of Oskarshamn, on the southeast coast of Sweden, about 250 kilometres south of Stockholm. The site description will have two main components: a written synthesis of the site, summarising the current state of knowledge, as documented in the databases containing the primary data from the site investigations, and one or several site descriptive models, in which the collected information is interpreted and presented in a form which can be used in numerical models for rock engineering, environmental impact and long-term safety assessments. SKB maintains two main databases at the present time, a site characterisation database called SICADA and a geographic information system called SKB GIS. The site descriptive model will be developed and presented with the aid of the SKB GIS capabilities, and with SKBs Rock Visualisation System (RVS), which is also linked to SICADA. The version 0 model forms an important framework for subsequent model versions, which are developed successively, as new information from the site investigations becomes available. Version 0 is developed out of the information available at the start of the site investigation. In the case of Simpevarp, this is essentially the information which was compiled for the Oskarshamn feasibility study, which led to the choice of that area as a favourable object for further study, together with information collected since its completion. This information, with the exception of the extensive data base from the nearby Aespoe Hard Rock Laboratory, is mainly 2D in nature (surface data), and is general and regional, rather than site-specific, in content. Against this background, the present report consists of the following components: an overview of the present content of the databases

  14. Hydrogeochemical site descriptive model - a strategy for the model development during site investigations

    International Nuclear Information System (INIS)

    overall aim of providing sufficient and reliable scientific knowledge to describe adequately and accurately the hydrogeochemical conditions at the site. In addition to these constraints, certain priorities have to be listed and addressed because of the size and complexity of the site investigation programme. Such priorities may be planned prior to field activities, whilst others will result from an on-going evaluation of field activities and scientific or modelling needs under the direction of the SKB Site Analysis Team. This team will liaise closely with those responsible field personnel. Based on past experience, identified priorities include: minimising groundwater contamination in the collected samples; sampling end member groundwater conditions (e.g. recharge/discharge conditions, or high/low topographic locations and shorelines) to define important boundary conditions for hydrogeochemical and hydrodynamic modelling; sampling of end member water compositions rather than groundwater mixtures; sampling groundwaters close to repository depth; understanding the spatial variation of chemical parameters closely integrated with hydrogeological conditions; measuring a large number of spatially strategic points (including time series measurements) distributed vertically and laterally over a large area; simultaneous sampling from many boreholes to produce accurate, time-related 3D interpolated snap shots of important groundwater parameters. Sampling of low permeable rocks and fracture zones of low transmissivities will be allocated greater priority. Some five classes of chemical analyses are available to characterise the collected groundwater samples. The choice of class will depend on the hydrogeochemical information required, the location to be sampled and the sampling method used. The major hydrogeochemical output data from a site characterisation will refer mainly to chemistry, isotopes, dissolved gas contents, redox potential conditions, presence of organic material

  15. Hydrogeochemical site descriptive model - a strategy for the model development during site investigations

    Energy Technology Data Exchange (ETDEWEB)

    Smellie, John [Conterra AB, Uppsala (Sweden); Laaksoharju, Marcus [GeoPoint AB, Sollentuna (Sweden); Tullborg, Eva-Lena [Terralogica AB, Graabo (Sweden)

    2002-12-01

    detrimentally affect the overall aim of providing sufficient and reliable scientific knowledge to describe adequately and accurately the hydrogeochemical conditions at the site. In addition to these constraints, certain priorities have to be listed and addressed because of the size and complexity of the site investigation programme. Such priorities may be planned prior to field activities, whilst others will result from an on-going evaluation of field activities and scientific or modelling needs under the direction of the SKB Site Analysis Team. This team will liaise closely with those responsible field personnel. Based on past experience, identified priorities include: minimising groundwater contamination in the collected samples; sampling end member groundwater conditions (e.g. recharge/discharge conditions, or high/low topographic locations and shorelines) to define important boundary conditions for hydrogeochemical and hydrodynamic modelling; sampling of end member water compositions rather than groundwater mixtures; sampling groundwaters close to repository depth; understanding the spatial variation of chemical parameters closely integrated with hydrogeological conditions; measuring a large number of spatially strategic points (including time series measurements) distributed vertically and laterally over a large area; simultaneous sampling from many boreholes to produce accurate, time-related 3D interpolated snap shots of important groundwater parameters. Sampling of low permeable rocks and fracture zones of low transmissivities will be allocated greater priority. Some five classes of chemical analyses are available to characterise the collected groundwater samples. The choice of class will depend on the hydrogeochemical information required, the location to be sampled and the sampling method used. The major hydrogeochemical output data from a site characterisation will refer mainly to chemistry, isotopes, dissolved gas contents, redox potential conditions, presence of

  16. Geology Laxemar. Site descriptive modelling SDM-Site Laxemar

    Energy Technology Data Exchange (ETDEWEB)

    Wahlgren, Carl-Henric (Geological Survey of Sweden, Uppsala (Sweden)); Curtis, Philip; Hermanson, Jan; Forssberg, Ola; Oehman, Johan (Golder Associates AB (Sweden)); Fox, Aaron; La Pointe, Paul (Golder Associates Inc (United States)); Drake, Henrik (Dept. of Earth Sciences, Univ. of Goeteborg, Goeteborg (Sweden)); Triumf, Carl-Axel; Mattsson, Haakan; Thunehed, Hans (GeoVista AB, Luleaa (Sweden)); Juhlin, Christopher (Dept. of Earth Sciences, Uppsala Univ., Uppsala (Sweden))

    2008-11-15

    The geological work during the SDM Site Laxemar modelling stage has involved the continued development of deterministic models for rock domains (RSM) and deformation zones (ZSM), the identification and deterministic modelling of fracture domains (FSM), and the development of statistical models for fractures and minor deformation zones (geological discrete fracture network (DFN) modelling). The geological DFN model addresses fractures/structures with a size of less than 1 km, which is the lower cut-off of structures included in the deterministic modelling of deformation zones. In order to take account of variability in data resolution, deterministic models for rock domains and deformation zones are presented in both regional and local scale model volumes, while the geological DFN model is valid only within specific fracture domains inside the Laxemar local model volume. The geological and geophysical data that constitute the basis for the SDM-Site Laxemar modelling work comprise all data that have been acquired from Laxemar, i.e. all data that were available at the data freeze for SDM-Site Laxemar at August 31, 2007. Selected quality controlled data from the complementary cored borehole KLX27A have also been utilised in the modelling work. Data from the following investigations were acquired during the complete site investigation between the data freezes for Laxemar 1.2 and SDM-Site Laxemar as defined above: A revised bedrock geological map at the ground surface. Geological and geophysical data from 40 new cored boreholes and 14 percussion boreholes. Sampling and subsequent modal and geochemical analytical work of bedrock samples taken in connection with excavations in southern Laxemar. Detailed mapping of fractures and rock units along 10 trench excavations and 2 large surface exposures (drill sites for KLX09 and KLX11A/KLX20A). Special studies involving more detailed characterisation of deformation zones identified in the geological single-hole interpretation

  17. Site-Scale Saturated Zone Flow Model

    Energy Technology Data Exchange (ETDEWEB)

    G. Zyvoloski

    2003-12-17

    The purpose of this model report is to document the components of the site-scale saturated-zone flow model at Yucca Mountain, Nevada, in accordance with administrative procedure (AP)-SIII.lOQ, ''Models''. This report provides validation and confidence in the flow model that was developed for site recommendation (SR) and will be used to provide flow fields in support of the Total Systems Performance Assessment (TSPA) for the License Application. The output from this report provides the flow model used in the ''Site-Scale Saturated Zone Transport'', MDL-NBS-HS-000010 Rev 01 (BSC 2003 [162419]). The Site-Scale Saturated Zone Transport model then provides output to the SZ Transport Abstraction Model (BSC 2003 [164870]). In particular, the output from the SZ site-scale flow model is used to simulate the groundwater flow pathways and radionuclide transport to the accessible environment for use in the TSPA calculations. Since the development and calibration of the saturated-zone flow model, more data have been gathered for use in model validation and confidence building, including new water-level data from Nye County wells, single- and multiple-well hydraulic testing data, and new hydrochemistry data. In addition, a new hydrogeologic framework model (HFM), which incorporates Nye County wells lithology, also provides geologic data for corroboration and confidence in the flow model. The intended use of this work is to provide a flow model that generates flow fields to simulate radionuclide transport in saturated porous rock and alluvium under natural or forced gradient flow conditions. The flow model simulations are completed using the three-dimensional (3-D), finite-element, flow, heat, and transport computer code, FEHM Version (V) 2.20 (software tracking number (STN): 10086-2.20-00; LANL 2003 [161725]). Concurrently, process-level transport model and methodology for calculating radionuclide transport in the saturated zone at Yucca

  18. Site-Scale Saturated Zone Flow Model

    International Nuclear Information System (INIS)

    The purpose of this model report is to document the components of the site-scale saturated-zone flow model at Yucca Mountain, Nevada, in accordance with administrative procedure (AP)-SIII.lOQ, ''Models''. This report provides validation and confidence in the flow model that was developed for site recommendation (SR) and will be used to provide flow fields in support of the Total Systems Performance Assessment (TSPA) for the License Application. The output from this report provides the flow model used in the ''Site-Scale Saturated Zone Transport'', MDL-NBS-HS-000010 Rev 01 (BSC 2003 [162419]). The Site-Scale Saturated Zone Transport model then provides output to the SZ Transport Abstraction Model (BSC 2003 [164870]). In particular, the output from the SZ site-scale flow model is used to simulate the groundwater flow pathways and radionuclide transport to the accessible environment for use in the TSPA calculations. Since the development and calibration of the saturated-zone flow model, more data have been gathered for use in model validation and confidence building, including new water-level data from Nye County wells, single- and multiple-well hydraulic testing data, and new hydrochemistry data. In addition, a new hydrogeologic framework model (HFM), which incorporates Nye County wells lithology, also provides geologic data for corroboration and confidence in the flow model. The intended use of this work is to provide a flow model that generates flow fields to simulate radionuclide transport in saturated porous rock and alluvium under natural or forced gradient flow conditions. The flow model simulations are completed using the three-dimensional (3-D), finite-element, flow, heat, and transport computer code, FEHM Version (V) 2.20 (software tracking number (STN): 10086-2.20-00; LANL 2003 [161725]). Concurrently, process-level transport model and methodology for calculating radionuclide transport in the saturated zone at Yucca Mountain using FEHM V 2.20 are being

  19. Ligand K-edge x-ray adsorption spectroscopic studies of the electronic structure of inorganic model complexes and metalloprotein active sites

    Science.gov (United States)

    Shadle, S. E.

    1994-08-01

    Ligand K-edge X-ray absorption spectroscopy (XAS) has been developed as a technique for the investigation of ligand-metal bonding and has been applied to the study of electronic structure in organic model complexes and metalloprotein active sites. Ligand K-edge XAS has been measured at the chloride K-edge for a series of complexes containing chloride ligands bound to open shell d(sup 9) copper ions. The intensity of the pre-edge feature in these spectra reflects the covalency in the half-occupied d(sub x)2(sub -y)2-derived molecular orbital (HOMO) of the complex. The energy of the pre-edge feature is related to both the charge on the ligand and the HOMO energy. An analysis of the intensity and energy of the pre-edge feature as well as the energy of the rising edge absorption provides quantitative information about the covalency of the ligand-metal interaction, the charge donated by the chloride, and the energy of the copper d-manifold. The results demonstrate that ligand K-edge XAS features can be used to obtain quantitative information about ligand-metal bonding. The results also identify the chemical basis for trends in the XAS data for the complexes: D(sub 4h)CuCl4(sup 2-), D(sub 2d)CuCl4(sup 2-), planar, trans-CuCl2(pdmp)(sub 2) (pdmp=N-phenyl-3,5-dimethylpyrazole), square pyramidal CuCl5(sup 3-), the planar dimer KCuCl3, the distorted tetrahedral dimer (Ph4P)CuCl3, and two dimers with mixed ligation, one containing a bridging chloride, and the other, terminally bound chloride. A geometric distortion from square planar to distorted tetrahedral results in a decrease in the chloride-copper HOMO covalency but an increase in the total charge donation by the chlorides. Thus, while the geometry can maximize the overlap for a highly covalent HOMO, this does not necessarily reflect the overall charge donation. The Cl-Cu(II) bonding interactions are dependent on the nature of the other coordinating ligands.

  20. Surface system Forsmark. Site descriptive modelling SDM-Site Forsmark

    International Nuclear Information System (INIS)

    SKB has undertaken site characterization of two different areas, Forsmark and Laxemar-Simpevarp, in order to find a suitable location for a geological repository for spent nuclear fuel. This report focuses on the site descriptive modelling of the surface system at Forsmark. The characterization of the surface system at the site was primarily made by identifying and describing important properties in different parts of the surface system, properties concerning e.g. hydrology and climate, Quaternary deposits and soils, hydrochemistry, vegetation, ecosystem functions, but also current and historical land use. The report presents available input data, methodology for data evaluation and modelling, and resulting models for each of the different disciplines. Results from the modelling of the surface system are also integrated with results from modelling of the deep bedrock system. The Forsmark site is located within the municipality of Oesthammar, about 120 km north of Stockholm. The investigated area is located along the shoreline of Oeregrundsgrepen, a funnel-shaped bay of the Baltic Sea. The area is characterized by small-scale topographic variations and is almost entirely located at altitudes lower than 20 metres above sea level. The Quaternary deposits in the area are dominated by till, characterized by a rich content of calcite which was transported by the glacier ice to the area from the sedimentary bedrock of Gaevlebukten about 100 km north of Forsmark. As a result, the surface waters and shallow groundwater at Forsmark are characterized by high pH values and high concentrations of certain major constituents, especially calcium and bicarbonate. The annual precipitation and runoff are 560 and 150 mm, respectively. The lakes are small and shallow, with mean and maximum depths ranging from approximately 0.1 to 1 m and 0.4 to 2 m. Sea water flows into the most low-lying lakes during events giving rise to very high sea levels. Wetlands are frequent and cover 25 to 35

  1. Importance Sampling for the Infinite Sites Model*

    OpenAIRE

    Hobolth, Asger; Uyenoyama, Marcy K; Wiuf, Carsten

    2008-01-01

    Importance sampling or Markov Chain Monte Carlo sampling is required for state-of-the-art statistical analysis of population genetics data. The applicability of these sampling-based inference techniques depends crucially on the proposal distribution. In this paper, we discuss importance sampling for the infinite sites model. The infinite sites assumption is attractive because it constraints the number of possible genealogies, thereby allowing for the analysis of larger data sets. We recall th...

  2. N-relaxion (N-site model)

    Energy Technology Data Exchange (ETDEWEB)

    Fonseca, N. [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); Sao Paulo Univ. (Brazil). Inst. de Fisica; Lima, L. de [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); Univ. Estadual Paulista, Sao Paulo (Brazil). Inst. de Fisica Teorica; Machado, C.S. [Univ. Estadual Paulista, Sao Paulo (Brazil). Inst. de Fisica Teorica; CERN, Geneva (Switzerland). Theoretical Physics Dept.; Matheus, R.D. [Univ. Estadual Paulista, Sao Paulo (Brazil). Inst. de Fisica Teorica

    2016-01-15

    Relaxion models are an interesting new avenue to explain the radiative stability of the Standard Model scalar sector. They require very large field excursions, which are difficult to generate in a consistent UV completion and to reconcile with the compact field space of the relaxion. We propose an N-site model which naturally generates the large decay constant needed to address these issues. Our model offers distinct advantages with respect to previous proposals: the construction involves non-abelian fields, allowing for controlled high energy behaviour and more model building possibilities, both in particle physics and inflationary models, and also admits a continuum limit when the number of sites is large, which may be interpreted as a warped extra dimension.

  3. Exploiting Innocuous Activity for Correlating Users Across Sites

    OpenAIRE

    Goga, Oana; Lei, Howard; Parthasarathi, Sree Hari Krishnan; Friedland, Gerald; Sommer, Robin; Teixeira, Renata

    2013-01-01

    International audience We study how potential attackers can identify accounts on different social network sites that all belong to the same user, exploiting only innocuous activity that inherently comes with posted content. We examine three specific features on Yelp, Flickr, and Twitter: the geo-location attached to a user's posts, the timestamp of posts, and the user's writing style as captured by language models. We show that among these three features the location of posts is the most po...

  4. Watershed modeling at the Savannah River Site.

    Energy Technology Data Exchange (ETDEWEB)

    Vache, Kellie [Oregon State University

    2015-04-29

    The overall goal of the work was the development of a watershed scale model of hydrological function for application to the US Department of Energy’s (DOE) Savannah River Site (SRS). The primary outcomes is a grid based hydrological modeling system that captures near surface runoff as well as groundwater recharge and contributions of groundwater to streams. The model includes a physically-based algorithm to capture both evaporation and transpiration from forestland.

  5. Simpevarp - site descriptive model version 0

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2002-11-01

    During 2002, SKB is starting detailed investigations at two potential sites for a deep repository in the Precambrian rocks of the Fennoscandian Shield. The present report concerns one of those sites, Simpevarp, which lies in the municipality of Oskarshamn, on the southeast coast of Sweden, about 250 kilometres south of Stockholm. The site description will have two main components: a written synthesis of the site, summarising the current state of knowledge, as documented in the databases containing the primary data from the site investigations, and one or several site descriptive models, in which the collected information is interpreted and presented in a form which can be used in numerical models for rock engineering, environmental impact and long-term safety assessments. SKB maintains two main databases at the present time, a site characterisation database called SICADA and a geographic information system called SKB GIS. The site descriptive model will be developed and presented with the aid of the SKB GIS capabilities, and with SKBs Rock Visualisation System (RVS), which is also linked to SICADA. The version 0 model forms an important framework for subsequent model versions, which are developed successively, as new information from the site investigations becomes available. Version 0 is developed out of the information available at the start of the site investigation. In the case of Simpevarp, this is essentially the information which was compiled for the Oskarshamn feasibility study, which led to the choice of that area as a favourable object for further study, together with information collected since its completion. This information, with the exception of the extensive data base from the nearby Aespoe Hard Rock Laboratory, is mainly 2D in nature (surface data), and is general and regional, rather than site-specific, in content. Against this background, the present report consists of the following components: an overview of the present content of the databases

  6. 3D modeling of buildings outstanding sites

    CERN Document Server

    Héno, Rapha?le

    2014-01-01

    Conventional topographic databases, obtained by capture on aerial or spatial images provide a simplified 3D modeling of our urban environment, answering the needs of numerous applications (development, risk prevention, mobility management, etc.). However, when we have to represent and analyze more complex sites (monuments, civil engineering works, archeological sites, etc.), these models no longer suffice and other acquisition and processing means have to be implemented. This book focuses on the study of adapted lifting means for "notable buildings". The methods tackled in this book cover las

  7. Surface system Forsmark. Site descriptive modelling SDM-Site Forsmark

    Energy Technology Data Exchange (ETDEWEB)

    Lindborg, Tobias (ed.)

    2008-12-15

    SKB has undertaken site characterization of two different areas, Forsmark and Laxemar-Simpevarp, in order to find a suitable location for a geological repository for spent nuclear fuel. This report focuses on the site descriptive modelling of the surface system at Forsmark. The characterization of the surface system at the site was primarily made by identifying and describing important properties in different parts of the surface system, properties concerning e.g. hydrology and climate, Quaternary deposits and soils, hydrochemistry, vegetation, ecosystem functions, but also current and historical land use. The report presents available input data, methodology for data evaluation and modelling, and resulting models for each of the different disciplines. Results from the modelling of the surface system are also integrated with results from modelling of the deep bedrock system. The Forsmark site is located within the municipality of Oesthammar, about 120 km north of Stockholm. The investigated area is located along the shoreline of Oeregrundsgrepen, a funnel-shaped bay of the Baltic Sea. The area is characterized by small-scale topographic variations and is almost entirely located at altitudes lower than 20 metres above sea level. The Quaternary deposits in the area are dominated by till, characterized by a rich content of calcite which was transported by the glacier ice to the area from the sedimentary bedrock of Gaevlebukten about 100 km north of Forsmark. As a result, the surface waters and shallow groundwater at Forsmark are characterized by high pH values and high concentrations of certain major constituents, especially calcium and bicarbonate. The annual precipitation and runoff are 560 and 150 mm, respectively. The lakes are small and shallow, with mean and maximum depths ranging from approximately 0.1 to 1 m and 0.4 to 2 m. Sea water flows into the most low-lying lakes during events giving rise to very high sea levels. Wetlands are frequent and cover 25 to 35

  8. Site occupancy models with heterogeneous detection probabilities

    Science.gov (United States)

    Royle, J. Andrew

    2006-01-01

    Models for estimating the probability of occurrence of a species in the presence of imperfect detection are important in many ecological disciplines. In these ?site occupancy? models, the possibility of heterogeneity in detection probabilities among sites must be considered because variation in abundance (and other factors) among sampled sites induces variation in detection probability (p). In this article, I develop occurrence probability models that allow for heterogeneous detection probabilities by considering several common classes of mixture distributions for p. For any mixing distribution, the likelihood has the general form of a zero-inflated binomial mixture for which inference based upon integrated likelihood is straightforward. A recent paper by Link (2003, Biometrics 59, 1123?1130) demonstrates that in closed population models used for estimating population size, different classes of mixture distributions are indistinguishable from data, yet can produce very different inferences about population size. I demonstrate that this problem can also arise in models for estimating site occupancy in the presence of heterogeneous detection probabilities. The implications of this are discussed in the context of an application to avian survey data and the development of animal monitoring programs.

  9. Hydrogeochemical site descriptive model - a strategy for the model development during site investigations

    Energy Technology Data Exchange (ETDEWEB)

    Smellie, John [Conterra AB, Uppsala (Sweden); Laaksoharju, Marcus [GeoPoint AB, Sollentuna (Sweden); Tullborg, Eva-Lena [Terralogica AB, Graabo (Sweden)

    2002-12-01

    detrimentally affect the overall aim of providing sufficient and reliable scientific knowledge to describe adequately and accurately the hydrogeochemical conditions at the site. In addition to these constraints, certain priorities have to be listed and addressed because of the size and complexity of the site investigation programme. Such priorities may be planned prior to field activities, whilst others will result from an on-going evaluation of field activities and scientific or modelling needs under the direction of the SKB Site Analysis Team. This team will liaise closely with those responsible field personnel. Based on past experience, identified priorities include: minimising groundwater contamination in the collected samples; sampling end member groundwater conditions (e.g. recharge/discharge conditions, or high/low topographic locations and shorelines) to define important boundary conditions for hydrogeochemical and hydrodynamic modelling; sampling of end member water compositions rather than groundwater mixtures; sampling groundwaters close to repository depth; understanding the spatial variation of chemical parameters closely integrated with hydrogeological conditions; measuring a large number of spatially strategic points (including time series measurements) distributed vertically and laterally over a large area; simultaneous sampling from many boreholes to produce accurate, time-related 3D interpolated snap shots of important groundwater parameters. Sampling of low permeable rocks and fracture zones of low transmissivities will be allocated greater priority. Some five classes of chemical analyses are available to characterise the collected groundwater samples. The choice of class will depend on the hydrogeochemical information required, the location to be sampled and the sampling method used. The major hydrogeochemical output data from a site characterisation will refer mainly to chemistry, isotopes, dissolved gas contents, redox potential conditions, presence of

  10. Surface system Forsmark. Site descriptive modelling SDM-Site Forsmark

    Energy Technology Data Exchange (ETDEWEB)

    Lindborg, Tobias (ed.)

    2008-12-15

    SKB has undertaken site characterization of two different areas, Forsmark and Laxemar-Simpevarp, in order to find a suitable location for a geological repository for spent nuclear fuel. This report focuses on the site descriptive modelling of the surface system at Forsmark. The characterization of the surface system at the site was primarily made by identifying and describing important properties in different parts of the surface system, properties concerning e.g. hydrology and climate, Quaternary deposits and soils, hydrochemistry, vegetation, ecosystem functions, but also current and historical land use. The report presents available input data, methodology for data evaluation and modelling, and resulting models for each of the different disciplines. Results from the modelling of the surface system are also integrated with results from modelling of the deep bedrock system. The Forsmark site is located within the municipality of Oesthammar, about 120 km north of Stockholm. The investigated area is located along the shoreline of Oeregrundsgrepen, a funnel-shaped bay of the Baltic Sea. The area is characterized by small-scale topographic variations and is almost entirely located at altitudes lower than 20 metres above sea level. The Quaternary deposits in the area are dominated by till, characterized by a rich content of calcite which was transported by the glacier ice to the area from the sedimentary bedrock of Gaevlebukten about 100 km north of Forsmark. As a result, the surface waters and shallow groundwater at Forsmark are characterized by high pH values and high concentrations of certain major constituents, especially calcium and bicarbonate. The annual precipitation and runoff are 560 and 150 mm, respectively. The lakes are small and shallow, with mean and maximum depths ranging from approximately 0.1 to 1 m and 0.4 to 2 m. Sea water flows into the most low-lying lakes during events giving rise to very high sea levels. Wetlands are frequent and cover 25 to 35

  11. 无限个吸收态方点阵模型中激活位的临界扩散%Critical Spreading of Active Site in a square lattice Model Possessing Infinite Absorbing States

    Institute of Scientific and Technical Information of China (English)

    乔文华

    2008-01-01

    The spreading of active sites of the square lattice model is simulated. Finite-time scaling behaviors are observed in the vicinity of the critical point.%采用计算机模拟了方点阵模型中激活位的扩散.观察和讨论了临界点附近的有限时间的扩散行为.

  12. Comparison of Transcription Factor Binding Site Models

    KAUST Repository

    Bhuyan, Sharifulislam

    2012-05-01

    Modeling of transcription factor binding sites (TFBSs) and TFBS prediction on genomic sequences are important steps to elucidate transcription regulatory mechanism. Dependency of transcription regulation on a great number of factors such as chemical specificity, molecular structure, genomic and epigenetic characteristics, long distance interaction, makes this a challenging problem. Different experimental procedures generate evidence that DNA-binding domains of transcription factors show considerable DNA sequence specificity. Probabilistic modeling of TFBSs has been moderately successful in identifying patterns from a family of sequences. In this study, we compare performances of different probabilistic models and try to estimate their efficacy over experimental TFBSs data. We build a pipeline to calculate sensitivity and specificity from aligned TFBS sequences for several probabilistic models, such as Markov chains, hidden Markov models, Bayesian networks. Our work, containing relevant statistics and evaluation for the models, can help researchers to choose the most appropriate model for the problem at hand.

  13. Active sites in char gasification: Final technical report

    Energy Technology Data Exchange (ETDEWEB)

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

    1987-09-01

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

  14. WebCom: A Model for Understanding Web Site Communication

    DEFF Research Database (Denmark)

    Godsk, Mikkel; Petersen, Anja Bechmann

    2008-01-01

    This chapter presents a model (WebCom) for understanding and analyzing Web site-mediated communication, also referred to as Web site communication. The model combines three theoretical approaches - communication, medium, and activity theory - into one generic model that benefits from each...... of the approaches' strengths. Furthermore, it is discussed and shortly demonstrated how WebCom can be used for analytical and design purposes with YouTube as an example. The chapter concludes that WebCom is able to serve as a theoretically-based model for understanding complex Web site communication situations...... in their entirety, and that such thoroughly approach is required for successful computer mediated communication (CMC) when communicating across cultures and contexts....

  15. Crystallographic B factor of critical residues at enzyme active site

    Institute of Scientific and Technical Information of China (English)

    张海龙; 宋时英; 林政炯

    1999-01-01

    Thirty-seven sets of crystallographic enzyme data were selected from Protein Data Bank (PDB, 1995). The average temperature factors (B) of the critical residues at the active site and the whole molecule of those enzymes were calculated respectively. The statistical results showed that the critical residues at the active site of most of the enzymes had lower B factors than did the whole molecules, indicating that in the crystalline state the critical residues at the active site of the natural enzymes possess more stable conformation than do the whole molecules. The flexibility of the active site during the unfolding by denaturing was also discussed.

  16. Site-Specific Seismic Site Response Model for the Waste Treatment Plant, Hanford, Washington

    International Nuclear Information System (INIS)

    This interim report documents the collection of site-specific geologic and geophysical data characterizing the Waste Treatment Plant site and the modeling of the site-specific structure response to earthquake ground motions

  17. Site-Specific Seismic Site Response Model for the Waste Treatment Plant, Hanford, Washington

    Energy Technology Data Exchange (ETDEWEB)

    Rohay, Alan C.; Reidel, Steve P.

    2005-02-24

    This interim report documents the collection of site-specific geologic and geophysical data characterizing the Waste Treatment Plant site and the modeling of the site-specific structure response to earthquake ground motions.

  18. Savannah River Site prioritization of transition activities

    International Nuclear Information System (INIS)

    Effective management of SRS conversion from primarily a production facility to other missions (or Decontamination and Decommissioning (D ampersand D)) requires a systematic and consistent method of prioritizing the transition activities. This report discusses the design of a prioritizing method developed to achieve systematic and consistent methods of prioritizing these activities

  19. Savannah River Site prioritization of transition activities

    Energy Technology Data Exchange (ETDEWEB)

    Finley, R.H.

    1993-11-01

    Effective management of SRS conversion from primarily a production facility to other missions (or Decontamination and Decommissioning (D&D)) requires a systematic and consistent method of prioritizing the transition activities. This report discusses the design of a prioritizing method developed to achieve systematic and consistent methods of prioritizing these activities.

  20. Safety Oversight of Decommissioning Activities at DOE Nuclear Sites

    International Nuclear Information System (INIS)

    The Defense Nuclear Facilities Safety Board (Board) is an independent federal agency established by Congress in 1988 to provide nuclear safety oversight of activities at U.S. Department of Energy (DOE) defense nuclear facilities. The activities under the Board's jurisdiction include the design, construction, startup, operation, and decommissioning of defense nuclear facilities at DOE sites. This paper reviews the Board's safety oversight of decommissioning activities at DOE sites, identifies the safety problems observed, and discusses Board initiatives to improve the safety of decommissioning activities at DOE sites. The decommissioning of former defense nuclear facilities has reduced the risk of radioactive material contamination and exposure to the public and site workers. In general, efforts to perform decommissioning work at DOE defense nuclear sites have been successful, and contractors performing decommissioning work have a good safety record. Decommissioning activities have recently been completed at sites identified for closure, including the Rocky Flats Environmental Technology Site, the Fernald Closure Project, and the Miamisburg Closure Project (the Mound site). The Rocky Flats and Fernald sites, which produced plutonium parts and uranium materials for defense needs (respectively), have been turned into wildlife refuges. The Mound site, which performed R and D activities on nuclear materials, has been converted into an industrial and technology park called the Mound Advanced Technology Center. The DOE Office of Legacy Management is responsible for the long term stewardship of these former EM sites. The Board has reviewed many decommissioning activities, and noted that there are valuable lessons learned that can benefit both DOE and the contractor. As part of its ongoing safety oversight responsibilities, the Board and its staff will continue to review the safety of DOE and contractor decommissioning activities at DOE defense nuclear sites

  1. Study the active site of flavonoid applying radiation chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Wu Jilan; Sun Gang; Zhang Fugen; He Yongke; Li Jiuqiang [Department of Technical Physics, Peking Univ., Beijing (China)

    2000-03-01

    Flavonoid are a large and important class of naturally occurring, low molecular weight benzo-{gamma}-pyrone derivatives which are reported to have a myriad of biological activities, but the study on the active sites of flavonoids is still ambiguous. In this paper, rutin, quercetin and baicalin have been selected as model compounds. It is well known that rutin is used in inhibiting arteriosclerosis and baicalin is antibacterial and antiviral. They have similar basic structure, but their medicinal properties are so different, why? As most flavonoids contain carbonyl group, which can capture electron effectively, we predict that flavonoids can capture electron to form radical anion. The formation of anion radical may have influence on the mitochondrial electron transport chain. The difference in the ability of forming anion radical may cause the difference in their medicinal effects. (author)

  2. Hydrogeological Site Descriptive Model - a strategy for its development during Site Investigations

    Energy Technology Data Exchange (ETDEWEB)

    Rhen, Ingvar [SWECO VIAK AB, Goeteborg (Sweden); Follin, Sven [SF GeoLogic AB, Stockholm (Sweden); Hermanson, Jan [Golder Associates, Stockholm (Sweden)

    2003-04-01

    The report is to present a strategy for the development of the Site Descriptive Hydrogeological Model within the SKB Site Investigation Programme. The report, and similar reports from the Geology, Rock Mechanics, Thermal properties, Hydrogeochemistry, Transport Properties and Surface Ecosystem disciplines are intended to guide SKB Site Descriptive Modelling but also to provide the authorities with an overview of how the modelling should be performed. Thus the objectives of this report are to: provide guidelines for the modelling of different sites resulting in consistent handling of modelling issues during the Site Investigations, provide a structure for the modelling sequence that is suitable for the establishment of a Site Descriptive model and provide some necessary details that should be considered in a Site Descriptive model.

  3. The Surface Groups and Active Site of Fibrous Mineral Materials

    Institute of Scientific and Technical Information of China (English)

    DONG Fa-qin; WAN Pu; FENG Qi-ming; SONG Gong-bao; PENG Tong-jiang; LI Ping; LI Guo-wu

    2004-01-01

    The exposed and transformed groups of fibrous brucite,wollastonite,chrysotile asbestos,sepiolite,palygorskite,clinoptilolite,crocidolite and diatomaceous earth mineral materials are analyzed by IR spectra after acid and alikali etching,strong mechanical and polarity molecular interaction.The results show the active sites concentrate on the ends in stick mineral materials and on the defect or hole edge in pipe mineral materials.The inside active site of mineral materials plays a main role in small molecular substance.The shape of minerals influence their distribution and density of active site.The strong mechanical impulsion and weak chemical force change the active site feature of minerals,the powder process enables minerals exposed more surface group and more combined types.The surface processing with the small polarity molecular or the brand of middle molecular may produce ionation and new coordinate bond,and change the active properties and level of original mineral materials.

  4. Geological Site Descriptive Model. A strategy for the model development during site investigations

    Energy Technology Data Exchange (ETDEWEB)

    Munier, Raymond; Stenberg, Leif [Swedish Nuclear Fuel and Waste Management Co., Stockholm (Sweden); Stanfors, Roy [Roy Stanfors Consulting, Lund (Sweden); Milnes, Allan Geoffrey [GEA Consulting, Uppsala (Sweden); Hermanson, Jan [Golder Associates, Stockholm (Sweden); Triumf, Carl-Axel [Geovista, Luleaa (Sweden)

    2003-04-01

    The Swedish Nuclear Fuel and Waste Management Company (SKB) is at present conducting site investigations as a preliminary to building an underground nuclear waste disposal facility in Sweden. This report presents a methodology for constructing, visualising and presenting 3-dimensional geological models, based on data from the site investigations. The methodology integrates with the overall work-flow of the site investigations, from the collection of raw data to the complete site description, as proposed in several earlier technical reports. Further, it is specifically designed for interaction with SICADA - SKB's Site Characterisation Database - and RVS - SKB's Rock Visualisation System. This report is one in a series of strategy documents intended to demonstrate how modelling is to be performed within each discipline. However, it also has a wider purpose, since the geological site descriptive model provides the basic geometrical framework for all the other disciplines. Hence, the wider aim is to present a practical and clear methodology for the analysis and interpretation of input data for use in the construction of the geology-based 3D geometrical model. In addition to the various aspects of modelling described above, the methodology presented here should therefore also provide: guidelines and directives on how systematic interpretation and integration of geo-scientific data from the different investigation methods should be carried out; guidelines on how different geometries should be created in the geological models; guidelines on how the assignment of parameters to the different geological units in RVS should be accomplished; guidelines on the handling of uncertainty at different points in the interpretation process. In addition, it should clarify the relation between the geological model and other models used in the processes of site characterisation, repository layout and safety analysis. In particular, integration and transparency should be

  5. Residents’ Environmental Conservation Behaviors at Tourist Sites: Broadening the Norm Activation Framework by Adopting Environment Attachment

    OpenAIRE

    Yuling Zhang; Jie Zhang; Yuyao Ye; Qitao Wu; Lixia Jin; Hongou Zhang

    2016-01-01

    Understanding the factors that affect residents’ environmental conservation behaviors help in managing the environment of tourist sites. This research provides an integrative understanding of how residents near tourist sites form their environmental conservation behaviors by merging the norm-activation model and cognitive-affective model into one theoretical framework. Results of the structural analysis from a sample of 642 residents showed that this study’s proposed composite model includes ...

  6. Fluorescence energy transfer studies on the active site of papain

    OpenAIRE

    Henes, Jill B.; Briggs, Martha S.; Sligar, Stephen G.; Fruton, Joseph S.

    1980-01-01

    Measurements have been performed of the excited-state lifetimes and fluorescence yields of papain tryptophan units when acyl derivatives of Phe-glycinal are bound at the active site of the enzyme. The enhancement of tryptophan fluorescence in complexes of papain with the acetyl or benzyloxycarbonyl derivatives is not stereospecific with respect to the configuration of the phenylalanyl residue, and the L and D isomers are equally effective as active-site-directed inhibitors of papain action. E...

  7. Effects of Folding on Metalloprotein Active Sites

    Science.gov (United States)

    Winkler, Jay R.; Wittung-Stafshede, Pernilla; Leckner, Johan; Malmstrom, Bo G.; Gray, Harry B.

    1997-04-01

    Experimental data for the unfolding of cytochrome c and azurin by guanidinium chloride (GuHCl) are used to construct free-energy diagrams for the folding of the oxidized and reduced proteins. With cytochrome c, the driving force for folding the reduced protein is larger than that for the oxidized form. Both the oxidized and the reduced folded forms of yeast cytochrome c are less stable than the corresponding states of the horse protein. Due to the covalent attachment of the heme and its fixed tetragonal coordination geometry, cytochrome c folding can be described by a two-state model. A thermodynamic cycle leads to an expression for the difference in self-exchange reorganization energies for the folded and unfolded proteins. The reorganization energy for electron exchange in the folded protein is approximately 0.5 eV smaller than that for a heme in aqueous solution. The finding that reduced azurin unfolds at lower GuHCl concentrations than the oxidized protein suggests that the coordination structure of copper is different in oxidized and reduced unfolded states: it is likely that the geometry of CuI in the unfolded protein is linear or trigonal, whereas CuII prefers to be tetragonal. The evidence indicates that protein folding lowers the azurin reorganization energy by roughly 1.7 eV relative to an aqueous Cu(1,10-phenanthroline)2{}2+/+ reference system.

  8. Hydrological Interpretation of ERT Monitoring Data on active landslides by implementation of numerical modelling at sites of the LAMOND Long-Term Landslide Monitoring Network

    Science.gov (United States)

    Hoyer, Stefan; Ottowitz, David; Supper, Robert; Jochum, Birgit; Riegler, Monika; Scolobig, Anna; Pfeiler, Stefan

    2016-04-01

    Five landslides are monitored in the framework of the LAMOND Network using Electrical Resistivity Tomography (ERT), three of these are located in Austria, one in Italy and one in France. Hydrological interpretation of the collected ERT data is typically carried out qualitatively on a visual basis. In this study, numerical modelling in combination with parameter estimation is implemented to build a basis for an enhanced interpretation. Parameter estimation is carried out by Comsol Multiphysics using Richard's equation and the Optimization module. The result of the forward model (water saturation) is compared to the ERT section (resistivity) using Archies law. The study LAMOND is funded by the Austrian Academy of sciences.

  9. Evaluation models for contaminated sites – biological system at risk

    OpenAIRE

    Golomeova, Mirjana; Krstev, Boris; Golomeov, Blagoj; Zendelska, Afrodita; Krstev, Aleksandar

    2009-01-01

    The paper presents the different methods that can be used correspond to three types of approaches, testing, monitoring, and modeling: experimental models, in situ indicators and mathematical models, and choice of model for contaminated sites – biological system at risk.

  10. Gunnison sage-grouse lek site suitability modeling

    Science.gov (United States)

    Ouren, Douglas S.; Ignizio, Drew A.; Siders, Melissa; Childers, Theresa; Tucker, Karen; Seward, Nathan

    2014-01-01

    suite of spatial data, geographic information system tools, and maximum entropy species distribution tools. Based on expert knowledge and landscape variables, the modeling process evolved into a hybrid approach for delineating areas that would have a significant probability for supporting GUSG lekking activities. Based on model results, a sampling protocol was developed for model verification. The results of this project provide wildlife managers with a more sophisticated methodology to evaluate GUSG habitat for potential lekking sites.

  11. Metalloprotein-inhibitor binding: human carbonic anhydrase II as a model for probing metal-ligand interactions in a metalloprotein active site.

    Science.gov (United States)

    Martin, David P; Hann, Zachary S; Cohen, Seth M

    2013-11-01

    An ever-increasing number of metalloproteins are being discovered that play essential roles in physiological processes. Inhibitors of these proteins have significant potential for the treatment of human disease, but clinical success of these compounds has been limited. Herein, zinc(II)-dependent metalloprotein inhibitors in clinical use are reviewed, and the potential for using novel metal-binding groups (MBGs) in the design of these inhibitors is discussed. By using human carbonic anhydrase II as a model system, the nuances of MBG-metal interactions in the context of a protein environment can be probed. Understanding how metal coordination influences inhibitor binding may help in the design of new therapeutics targeting metalloproteins.

  12. Dashboard applications to monitor experiment activities at sites

    Science.gov (United States)

    Andreeva, Julia; Belforte, Stefano; Boehm, Max; Casajus, Adrian; Flix, Josep; Gaidioz, Benjamin; Grigoras, Costin; Kokoszkiewicz, Lukasz; Lanciotti, Elisa; Rocha, Ricardo; Saiz, Pablo; Santinelli, Roberto; Sidorova, Irina; Sciabà, Andrea; Tsaregorodtsev, Andrei

    2010-04-01

    In the framework of a distributed computing environment, such as WLCG, monitoring has a key role in order to keep under control activities going on in sites located in different countries and involving people based in many different sites. To be able to cope with such a large scale heterogeneous infrastructure, it is necessary to have monitoring tools providing a complete and reliable view of the overall performance of the sites. Moreover, the structure of a monitoring system critically depends on the object to monitor and on the users it is addressed to. In this article we will describe two different monitoring systems both aimed to monitor activities and services provided in the WLCG framework, but designed in order to meet the requirements of different users: Site Status Board has an overall view of the services available in all the sites supporting an experiment, whereas Siteview provides a complete view of all the activities going on at a site, for all the experiments supported by the site.

  13. Dashboard applications to monitor experiment activities at sites

    CERN Document Server

    Andreeva, J; Boehm, M; Casajus, A; Flix, J; Gaidioz, B; Grigoras, C; Kokoszkiewicz, L; Lanciotti, E; Rocha, R; Saiz, P; Santinelli, R; Sidorova, I; Sciabà, A; Tsaregorodtsev, A

    2010-01-01

    In the framework of a distributed computing environment, such as WLCG, monitoring has a key role in order to keep under control activities going on in sites located in different countries and involving people based in many different sites. To be able to cope with such a large scale heterogeneous infrastructure, it is necessary to have monitoring tools providing a complete and reliable view of the overall performance of the sites. Moreover, the structure of a monitoring system critically depends on the object to monitor and on the users it is addressed to. In this article we will describe two different monitoring systems both aimed to monitor activities and services provided in the WLCG framework, but designed in order to meet the requirements of different users: Site Status Board has an overall view of the services available in all the sites supporting an experiment, whereas Siteview provides a complete view of all the activities going on at a site, for all the experiments supported by the site.

  14. Dashboard applications to monitor experiment activities at sites

    International Nuclear Information System (INIS)

    In the framework of a distributed computing environment, such as WLCG, monitoring has a key role in order to keep under control activities going on in sites located in different countries and involving people based in many different sites. To be able to cope with such a large scale heterogeneous infrastructure, it is necessary to have monitoring tools providing a complete and reliable view of the overall performance of the sites. Moreover, the structure of a monitoring system critically depends on the object to monitor and on the users it is addressed to. In this article we will describe two different monitoring systems both aimed to monitor activities and services provided in the WLCG framework, but designed in order to meet the requirements of different users: Site Status Board has an overall view of the services available in all the sites supporting an experiment, whereas Siteview provides a complete view of all the activities going on at a site, for all the experiments supported by the site.

  15. Methanopyrus kandleri topoisomerase V contains three distinct AP lyase active sites in addition to the topoisomerase active site.

    Science.gov (United States)

    Rajan, Rakhi; Osterman, Amy; Mondragón, Alfonso

    2016-04-20

    Topoisomerase V (Topo-V) is the only topoisomerase with both topoisomerase and DNA repair activities. The topoisomerase activity is conferred by a small alpha-helical domain, whereas the AP lyase activity is found in a region formed by 12 tandem helix-hairpin-helix ((HhH)2) domains. Although it was known that Topo-V has multiple repair sites, only one had been mapped. Here, we show that Topo-V has three AP lyase sites. The atomic structure and Small Angle X-ray Scattering studies of a 97 kDa fragment spanning the topoisomerase and 10 (HhH)2 domains reveal that the (HhH)2 domains extend away from the topoisomerase domain. A combination of biochemical and structural observations allow the mapping of the second repair site to the junction of the 9th and 10th (HhH)2 domains. The second site is structurally similar to the first one and to the sites found in other AP lyases. The 3rd AP lyase site is located in the 12th (HhH)2 domain. The results show that Topo-V is an unusual protein: it is the only known protein with more than one (HhH)2 domain, the only known topoisomerase with dual activities and is also unique by having three AP lyase repair sites in the same polypeptide.

  16. Biomimetic oxidation studies. 9. Mechanistic aspects of the oxidation of alcohols with functional,active site methane monooxygenase enzyme models in aqueous solution

    Energy Technology Data Exchange (ETDEWEB)

    Rabion, A. [Lawrence Berkeley National Lab., CA (United States)]|[Univ. of California, Berkeley, CA (United States)]|[Groupement de Recherche de Lacq, Artix (France); Chen, S.; Wang, J.; Buchanan, R.M. [Univ. of Louisville, KY (United States); Seris, J.L. [Groupement de recherche de Lacq, Artix (France); Fish, R.H. [Lawrence Berkeley National Lab., CA (United States)]|[Univ. of California, Berkeley, CA (United States)

    1995-12-13

    The syntheses of biomimetic complexes that mimic the major structural features of the hydroxylase component of methane monooxygenase enzyme (MMO) and, more importantly, that provide similar alkane functionalization activity, in the presence of an oxidant, have been of great interest to the discipline of bioinorganic chemistry. In this communication, we will demonstrate the feasibility of conducting biomimetic oxidation studies in H{sub 2}O with soluble substrates, i.e., alcohols (cyclohexanol, benzyl alcohol), using H{sub 2}O-stable MMO mimics at pH 4.2, and the oxidant, tert-butyl hydroperoxide (TBHP). Both the Mitusunobu procedure and the mesylate displacement reaction proceeded with complete inversion of the stereo-center and provided optically pure penultimate intermediate (>99.9% ee). The synthesis was completed by reduction of the nitro group under standard conditions to deliver LY300164 in 87%. In summary, we have developed an efficient and environmentally benign synthesis of the 5H-2,3-benzodiazepine LY300164 that provides the optically pure compound in 51% overall yield. Intramolecular hydrazone alkylation led to a remarkably facile and selective formation of the benzodiazepine. Furthermore, the application of resins to whole-cell-based biotransformations should find general utility for similar reactions that are complicated by component inhibition and product isolation. 11 refs., 1 fig.

  17. Oxidation of butane and butene on the (100) face of (VO) sub 2 P sub 2 O sub 7 : A dynamic view in terms of the crystallochemical model of active sites

    Energy Technology Data Exchange (ETDEWEB)

    Ziolkowski, J. (Institute of Catalysis and Surface Chemistry, Krakow (Poland)); Bordes, E.; Courtine, P. (Universite de Technologie de Compiegne (France))

    1990-03-01

    The structure of the (100) face of (VO){sub 2}P{sub 2}O{sub 7} and its performance in the oxidation of n-butane and butenes to maleic anhydride have been analyzed in terms of the crystallochemical model of active sites (CMAS). Analysis involves the heats of adsorption of oxygen, hydrogen (as a component of OH), and water as well as the heats of their movement along the surface, which allows determination of the energetically easiest pathways of elementary steps and gives insight into the reaction dynamics. The catalyst (100) (VO){sub 2}P{sub 2}O{sub 7} is found to work in a surface-oxidized state, all cations being covered with oxygen. The active site for the direct oxidation of n-butane to maleic anhydride is found to be situated between four protruding, undersaturated oxygens (2 {times} V-O, 2 {times} P-O). The reaction is thought to be initiated by H bonding at both terminal carbons. The desorption of water and migration of surface oxygen (which produces the pairs of adjacent vacancies to be filled by O{sub 2} molecules) that constitute a substep of the concerted reoxidation seem to be rate determining. Oxidation of butenes on (100) (VO){sub 2}P{sub 2}O{sub 7} is thought to be initiated by adsorption of C{double bond}C over unsaturated oxygens. In view of the surface structure, this adsorption limits the number of active oxygens with which the hydrocarbon may interact and favors a mild and nonselective oxidation to epoxybutanes, crotonaldehyde, hydrofuran, furan, and acetaldehyde. Minor yields are expected due to difficult reoxidation and competitive adsorption. Theoretical predictions are shown to agree with experimental data.

  18. Gideaa study site. Scope of activities and main results

    International Nuclear Information System (INIS)

    During the period from 1977-1986 SKB (Swedish Nuclear Fuel and Waste Management Co) performed surface and borehole investigations of 14 study sites for the purpose of assessing their suitability for a repository of spent nuclear fuel. The next phase in the SKB site selection programme will be to perform detailed characterization, including characterization from shafts and/or tunnels, of two or three sites. The detailed investigations will continue over several years to provide all the data needed for a licensing application to build a repository. Such an application is foreseen to be given to the authorities around the year 2003. It is presently not clear if anyone of the study sites will be selected as a site for detailed characterization. Other site with geological and/or socio-economical characteristics judged more favourable may very well be the ones selected. However, as a part of the background documentation needed for the site selection studies to come, summary reports will be prepared for most study sites. These reports will include scope of activities, main results, uncertainties and need of complementary investigations. This report concerns the Gideaa study site. (au)

  19. Optimization model for air quality analysis in energy facility siting

    Energy Technology Data Exchange (ETDEWEB)

    Emanuel, W. R.; Murphy, B. D.; Huff, D. D.; Begovich, C. L.; Hurt, J. F.

    1977-09-01

    The siting of energy facilities on a regional scale is discussed with particular attention to environmental planning criteria. A multiple objective optimization model is proposed as a framework for the analysis of siting problems. Each planning criterion (e.g., air quality, water quality, or power demand) is treated as an objective function to be minimized or maximized subject to constraints in this optimization procedure. The formulation of the objective functions is illustrated by the development of a siting model for the minimization of human exposure to air pollutants. This air quality siting model takes the form of a linear programming problem. A graphical analysis of this type of problem, which provides insight into the nature of the siting model, is given. The air quality siting model is applied to an illustrative siting example for the Tennessee Valley area.

  20. Proposal Of Landfill Site Model In The Particular Territory

    Directory of Open Access Journals (Sweden)

    Stopka Ondrej

    2015-12-01

    Full Text Available Nowadays, waste logistics is a relevant element within the worldwide logistics system. This paper is focused on the proposal of the appropriate model of landfill site for disposal of municipal waste. This issue refers to waste logistics in urban areas. In this regard, three different alternative models of landfill sites are considered. Landfill site model can significantly influence the waste management productivity and effectiveness of the enterprise. In the paper, one of the decision-making problem methods is utilized. This particular method enables to assess each model of landfill site in relation to each of the specified criterion and order the models according to the achieved results.

  1. 'Unconventional' coordination chemistry by metal chelating fragments in a metalloprotein active site.

    Science.gov (United States)

    Martin, David P; Blachly, Patrick G; Marts, Amy R; Woodruff, Tessa M; de Oliveira, César A F; McCammon, J Andrew; Tierney, David L; Cohen, Seth M

    2014-04-01

    The binding of three closely related chelators: 5-hydroxy-2-methyl-4H-pyran-4-thione (allothiomaltol, ATM), 3-hydroxy-2-methyl-4H-pyran-4-thione (thiomaltol, TM), and 3-hydroxy-4H-pyran-4-thione (thiopyromeconic acid, TPMA) to the active site of human carbonic anhydrase II (hCAII) has been investigated. Two of these ligands display a monodentate mode of coordination to the active site Zn(2+) ion in hCAII that is not recapitulated in model complexes of the enzyme active site. This unprecedented binding mode in the hCAII-thiomaltol complex has been characterized by both X-ray crystallography and X-ray spectroscopy. In addition, the steric restrictions of the active site force the ligands into a 'flattened' mode of coordination compared with inorganic model complexes. This change in geometry has been shown by density functional computations to significantly decrease the strength of the metal-ligand binding. Collectively, these data demonstrate that the mode of binding by small metal-binding groups can be significantly influenced by the protein active site. Diminishing the strength of the metal-ligand bond results in unconventional modes of metal coordination not found in typical coordination compounds or even carefully engineered active site models, and understanding these effects is critical to the rational design of inhibitors that target clinically relevant metalloproteins.

  2. 'Unconventional' coordination chemistry by metal chelating fragments in a metalloprotein active site.

    Science.gov (United States)

    Martin, David P; Blachly, Patrick G; Marts, Amy R; Woodruff, Tessa M; de Oliveira, César A F; McCammon, J Andrew; Tierney, David L; Cohen, Seth M

    2014-04-01

    The binding of three closely related chelators: 5-hydroxy-2-methyl-4H-pyran-4-thione (allothiomaltol, ATM), 3-hydroxy-2-methyl-4H-pyran-4-thione (thiomaltol, TM), and 3-hydroxy-4H-pyran-4-thione (thiopyromeconic acid, TPMA) to the active site of human carbonic anhydrase II (hCAII) has been investigated. Two of these ligands display a monodentate mode of coordination to the active site Zn(2+) ion in hCAII that is not recapitulated in model complexes of the enzyme active site. This unprecedented binding mode in the hCAII-thiomaltol complex has been characterized by both X-ray crystallography and X-ray spectroscopy. In addition, the steric restrictions of the active site force the ligands into a 'flattened' mode of coordination compared with inorganic model complexes. This change in geometry has been shown by density functional computations to significantly decrease the strength of the metal-ligand binding. Collectively, these data demonstrate that the mode of binding by small metal-binding groups can be significantly influenced by the protein active site. Diminishing the strength of the metal-ligand bond results in unconventional modes of metal coordination not found in typical coordination compounds or even carefully engineered active site models, and understanding these effects is critical to the rational design of inhibitors that target clinically relevant metalloproteins. PMID:24635441

  3. Validation of coastal oceanographic models at Forsmark. Site descriptive modelling SDM-Site Forsmark

    Energy Technology Data Exchange (ETDEWEB)

    Engqvist, Anders (A och I Engqvist Konsult HB, Vaxholm (SE)); Andrejev, Oleg (Finnish Inst. of Marine Research, Helsinki (FI))

    2008-01-15

    The Swedish Nuclear Fuel and Waste Management Company (SKB) is undertaking site characterisation at two different locations, the Forsmark and the Simpevarp areas, with the objective of siting a geological repository for spent nuclear fuel. The characterisation work is divided into an initial site investigation phase and a complete site investigation phase. In this context, the water exchange of the coastal zone is one link of the chain of possible nuclide transport mechanisms that must be assessed in the site description of potential repository areas. For the purpose of validating the pair of nested 3D-models employed to simulate the water exchange in the near-shore coastal zone in the Forsmark area, an encompassing measurement program entailing six stations has been performed. The design of this program was to first assess to what degree the forcing of the fine resolution (FR) model of the Forsmark study area at its interfacial boundary to the coarse resolution (CR) model of the entire Baltic was reproduced. In addition to this scrutiny it is of particular interest how the time-varying density-determining properties, salinity and temperature, at the borders are propagated into the FR-domain, since this corresponds to the most efficient mode of water exchange. An important part of the validation process has been to carefully evaluate which measurement data that can be considered reliable. The result was that several periods of foremost near-surface salinity data had to be discarded due to growth of algae on the conductivity sensors. Lack of thorough absolute calibration of the salinity meters also necessitates dismissal of measurement data. Relative the assessed data that can be accepted as adequate, the outcome of the validation can be summarized in five points: (i) The surface-most salinity of the CR-model drifts downward a little less than one practical salinity unit (psu) per year, requiring that the ensuing correlation analysis be subdivided into periods of a

  4. Active chemisorption sites in functionalized ionic liquids for carbon capture.

    Science.gov (United States)

    Cui, Guokai; Wang, Jianji; Zhang, Suojiang

    2016-07-25

    Development of novel technologies for the efficient and reversible capture of CO2 is highly desired. In the last decade, CO2 capture using ionic liquids has attracted intensive attention from both academia and industry, and has been recognized as a very promising technology. Recently, a new approach has been developed for highly efficient capture of CO2 by site-containing ionic liquids through chemical interaction. This perspective review focuses on the recent advances in the chemical absorption of CO2 using site-containing ionic liquids, such as amino-based ionic liquids, azolate ionic liquids, phenolate ionic liquids, dual-functionalized ionic liquids, pyridine-containing ionic liquids and so on. Other site-containing liquid absorbents such as amine-based solutions, switchable solvents, and functionalized ionic liquid-amine blends are also investigated. Strategies have been discussed for how to activate the existent reactive sites and develop novel reactive sites by physical and chemical methods to enhance CO2 absorption capacity and reduce absorption enthalpy. The carbon capture mechanisms of these site-containing liquid absorbents are also presented. Particular attention has been paid to the latest progress in CO2 capture in multiple-site interactions by amino-free anion-functionalized ionic liquids. In the last section, future directions and prospects for carbon capture by site-containing ionic liquids are outlined.

  5. Active chemisorption sites in functionalized ionic liquids for carbon capture.

    Science.gov (United States)

    Cui, Guokai; Wang, Jianji; Zhang, Suojiang

    2016-07-25

    Development of novel technologies for the efficient and reversible capture of CO2 is highly desired. In the last decade, CO2 capture using ionic liquids has attracted intensive attention from both academia and industry, and has been recognized as a very promising technology. Recently, a new approach has been developed for highly efficient capture of CO2 by site-containing ionic liquids through chemical interaction. This perspective review focuses on the recent advances in the chemical absorption of CO2 using site-containing ionic liquids, such as amino-based ionic liquids, azolate ionic liquids, phenolate ionic liquids, dual-functionalized ionic liquids, pyridine-containing ionic liquids and so on. Other site-containing liquid absorbents such as amine-based solutions, switchable solvents, and functionalized ionic liquid-amine blends are also investigated. Strategies have been discussed for how to activate the existent reactive sites and develop novel reactive sites by physical and chemical methods to enhance CO2 absorption capacity and reduce absorption enthalpy. The carbon capture mechanisms of these site-containing liquid absorbents are also presented. Particular attention has been paid to the latest progress in CO2 capture in multiple-site interactions by amino-free anion-functionalized ionic liquids. In the last section, future directions and prospects for carbon capture by site-containing ionic liquids are outlined. PMID:27243042

  6. Using the conceptual site model approach to characterize groundwater quality

    International Nuclear Information System (INIS)

    To understand groundwater quality, the first step is to develop a conceptual site model (CSM) that describes the site history, describes the geology and the hydrogeology of the site, identifies potential release areas or sources, and evaluates the fate and transport of site related compounds. After the physical site setting is understood and potential release areas are identified, appropriate and representative groundwater monitoring wells may be used to evaluate groundwater quality at a site and provide a network to assess impacts from potential future releases. To develop the CSM, the first step to understand the different requirements from each of the regulatory stakeholders. Each regulatory agency may have different approaches to site characterization and closure (i.e., different groundwater and soil remediation criteria). For example, the United States Environmental Protection Agency (EPA) and state governments have published guidance documents that proscribe the required steps and information needed to develop a CSM. The Nuclear Regulatory Commission (NRC) has a proscriptive model for the Historical Site Assessment under the Multi-Agency Radiation Survey and Site Investigation Manual (MARSSIM), and contains requirements for developing a conceptual site model in NUREG 1757. Federal and state agencies may also have different closure criteria for potential contaminants of concern. Understanding these differences before starting a groundwater monitoring program is important because the minimum detectable activity (MDA), lowest limit detection (LLD), and sample quantitation limit (SQL) must be low enough so that data may be evaluated under each of the programs. After a Historical Site Assessment is completed a work plan is developed and executed to not only collect physical data that describes the geology and hydrogeology, but to also characterize the soil, groundwater, sediments, and surface water quality of each potentially impacted areas. Although the primary

  7. Probing the active sites for CO dissociation on ruthenium nanoparticles

    DEFF Research Database (Denmark)

    Strebel, Christian Ejersbo; Murphy, Shane; Nielsen, Rasmus Munksgård;

    2012-01-01

    The active sites for CO dissociation were probed on mass-selected Ru nanoparticles on a HOPG support by temperature programmed desorption spectroscopy using isotopically labelled CO. Combined with transmission electron microscopy we gain insight on how the size and morphology of the nanoparticles...... microscopy. Surprisingly, it was found that larger particles were more active per surface area for CO dissociation. It is suggested that this is due to larger particles exposing a more rough surface than the smaller particles, giving rise to a higher relative amount of under-coordinated adsorption sites...

  8. Thermal site descriptive model. A strategy for the model development during site investigations - version 2

    Energy Technology Data Exchange (ETDEWEB)

    Back, Paer-Erik; Sundberg, Jan [Geo Innova AB (Sweden)

    2007-09-15

    This report presents a strategy for describing, predicting and visualising the thermal aspects of the site descriptive model. The strategy is an updated version of an earlier strategy applied in all SDM versions during the initial site investigation phase at the Forsmark and Oskarshamn areas. The previous methodology for thermal modelling did not take the spatial correlation fully into account during simulation. The result was that the variability of thermal conductivity in the rock mass was not sufficiently well described. Experience from earlier thermal SDMs indicated that development of the methodology was required in order describe the spatial distribution of thermal conductivity in the rock mass in a sufficiently reliable way, taking both variability within rock types and between rock types into account. A good description of the thermal conductivity distribution is especially important for the lower tail. This tail is important for the design of a repository because it affects the canister spacing. The presented approach is developed to be used for final SDM regarding thermal properties, primarily thermal conductivity. Specific objectives for the strategy of thermal stochastic modelling are: Description: statistical description of the thermal conductivity of a rock domain. Prediction: prediction of thermal conductivity in a specific rock volume. Visualisation: visualisation of the spatial distribution of thermal conductivity. The thermal site descriptive model should include the temperature distribution and thermal properties of the rock mass. The temperature is the result of the thermal processes in the repository area. Determination of thermal transport properties can be made using different methods, such as laboratory investigations, field measurements, modelling from mineralogical composition and distribution, modelling from density logging and modelling from temperature logging. The different types of data represent different scales, which has to be

  9. Validation of coastal oceanographic models at Laxemar-Simpevarp. Site descriptive modelling SDM-Site Laxemar

    Energy Technology Data Exchange (ETDEWEB)

    Engqvist, Anders (A och I Engqvist Konsult HB, Vaxholm (SE)); Andrejev, Oleg (Finnish Inst. of Marine Research, Helsinki (FI))

    2008-12-15

    The Swedish Nuclear Fuel and Waste Management Company (SKB) is undertaking site characterization at two different locations, the Forsmark and the Laxemar-Simpevarp areas, with the objective of siting a geological repository for spent nuclear fuel. The characterization work is divided into an initial site investigation phase and a complete site investigation phase. In this context, the water exchange of the coastal zone is one link of the chain of possible nuclide transport mechanisms that must be assessed in the site description of potential repository areas. For the purpose of validating the pair of nested 3D-models and the coupled discrete basin (CDB-) model employed to simulate the water exchange in the near-shore coastal zone in the Laxemar-Simpevarp area, an encompassing measurement program entailing data from six stations (of which two are close) has been performed. The design of this program was to first assess to what degree the forcing of the fine resolution (FR-) model of the Laxemar- Simpevarp study area at its interfacial boundary to the coarse resolution (CR-) model of the entire Baltic was reproduced. In addition to this, it is of particular interest how the time-varying density-determining properties, salinity and temperature, at the borders are propagated into the FR-domain and further influence the water exchange with the interior, more secluded, basins. An important part of the validation process has been to carefully evaluate which measurement data that can be considered reliable. The result was that some periods of foremost near-surface salinity data had to be discarded due to growth of algae on the conductivity sensors. Interference with ship traffic and lack of absolute calibration of the salinity meters necessitated dismissal of measurement data too. In this study so-called Mesan data have been consistently used for the meteorological forcing of the 3D-models. Relative the assessed data that can be accepted as adequate, the outcome of the

  10. Activation of phenylalanine hydroxylase by phenylalanine does not require binding in the active site.

    Science.gov (United States)

    Roberts, Kenneth M; Khan, Crystal A; Hinck, Cynthia S; Fitzpatrick, Paul F

    2014-12-16

    Phenylalanine hydroxylase (PheH), a liver enzyme that catalyzes the hydroxylation of excess phenylalanine in the diet to tyrosine, is activated by phenylalanine. The lack of activity at low levels of phenylalanine has been attributed to the N-terminus of the protein's regulatory domain acting as an inhibitory peptide by blocking substrate access to the active site. The location of the site at which phenylalanine binds to activate the enzyme is unknown, and both the active site in the catalytic domain and a separate site in the N-terminal regulatory domain have been proposed. Binding of catecholamines to the active-site iron was used to probe the accessibility of the active site. Removal of the regulatory domain increases the rate constants for association of several catecholamines with the wild-type enzyme by ∼2-fold. Binding of phenylalanine in the active site is effectively abolished by mutating the active-site residue Arg270 to lysine. The k(cat)/K(phe) value is down 10⁴ for the mutant enzyme, and the K(m) value for phenylalanine for the mutant enzyme is >0.5 M. Incubation of the R270K enzyme with phenylalanine also results in a 2-fold increase in the rate constants for catecholamine binding. The change in the tryptophan fluorescence emission spectrum seen in the wild-type enzyme upon activation by phenylalanine is also seen with the R270K mutant enzyme in the presence of phenylalanine. Both results establish that activation of PheH by phenylalanine does not require binding of the amino acid in the active site. This is consistent with a separate allosteric site, likely in the regulatory domain.

  11. Active Sites Environmental Monitoring Program: FY 1990 annual report

    Energy Technology Data Exchange (ETDEWEB)

    Wickliff, D.S.; Morrissey, C.M.; Ashwood, T.L.

    1991-10-01

    Chapter 3 of US Department of Energy (DOE) Order 5820.2A (DOE 1988) sets forth requirements for environmental monitoring of active low-level waste (LLW) disposal sites. Active sites are defined as those LLW facilities that were in use on or after the date of the order (September 1988). The transuranic (TRU) waste storage areas in Solid Waste Storage Area (SWSA) 5 North are covered by Chap. 2 of the order. In both chapters, monitoring is required to provide for early warning of leaks before those leaks pose a threat to human health or the environment. Chapter 3 also requires that monitoring be conducted to evaluate the short- and long-term performance of LLW disposal facilities. In accordance with this order, the Solid Waste Operations Department at Oak Ridge National Laboratory (ORNL) has established an Active Sites Environmental Monitoring Program (ASEMP) that is implemented by staff of the Environmental Sciences Division (ESD) at ORNL. This report summarizes data from ASEMP monitoring activities for the final 6 months of FY 1990. A brief summary of the monitoring methodology for each site is presented also.

  12. Chemical Modification of Papain and Subtilisin: An Active Site Comparison

    Science.gov (United States)

    St-Vincent, Mireille; Dickman, Michael

    2004-01-01

    An experiment using methyle methanethiosulfonate (MMTS) and phenylmethylsulfonyl flouride (PMSF) to specifically modify the cysteine and serine residues in the active sites of papain and subtilism respectively is demonstrated. The covalent modification of these enzymes and subsequent rescue of papain shows the beginning biochemist that proteins…

  13. The nature of the active site in heterogeneous metal catalysis

    DEFF Research Database (Denmark)

    Nørskov, Jens Kehlet; Bligaard, Thomas; Larsen, Britt Hvolbæk;

    2008-01-01

    This tutorial review, of relevance for the surface science and heterogeneous catalysis communities, provides a molecular-level discussion of the nature of the active sites in metal catalysis. Fundamental concepts such as "Bronsted-Evans-Polanyi relations'' and "volcano curves'' are introduced...

  14. A Bayesian belief network approach for assessing uncertainty in conceptual site models at contaminated sites

    DEFF Research Database (Denmark)

    Thomsen, Nanna Isbak; Binning, Philip John; McKnight, Ursula S.;

    2016-01-01

    A key component in risk assessment of contaminated sites is in the formulation of a conceptual site model (CSM). A CSM is a simplified representation of reality and forms the basis for the mathematical modeling of contaminant fate and transport at the site. The CSM should therefore identify...... opinion at different knowledge levels. The developed BBNs combine data from desktop studies and initial site investigations with expert opinion to assess which of the CSMs are more likely to reflect the actual site conditions. The method is demonstrated on a Danish field site, contaminated...... with chlorinated ethenes. Four different CSMs are developed by combining two contaminant source zone interpretations (presence or absence of a separate phase contamination) and two geological interpretations (fractured or unfractured clay till). The beliefs in each of the CSMs are assessed sequentially based...

  15. Thermal site descriptive model. A strategy for the model development during site investigations - version 2

    Energy Technology Data Exchange (ETDEWEB)

    Back, Paer-Erik; Sundberg, Jan [Geo Innova AB (Sweden)

    2007-09-15

    This report presents a strategy for describing, predicting and visualising the thermal aspects of the site descriptive model. The strategy is an updated version of an earlier strategy applied in all SDM versions during the initial site investigation phase at the Forsmark and Oskarshamn areas. The previous methodology for thermal modelling did not take the spatial correlation fully into account during simulation. The result was that the variability of thermal conductivity in the rock mass was not sufficiently well described. Experience from earlier thermal SDMs indicated that development of the methodology was required in order describe the spatial distribution of thermal conductivity in the rock mass in a sufficiently reliable way, taking both variability within rock types and between rock types into account. A good description of the thermal conductivity distribution is especially important for the lower tail. This tail is important for the design of a repository because it affects the canister spacing. The presented approach is developed to be used for final SDM regarding thermal properties, primarily thermal conductivity. Specific objectives for the strategy of thermal stochastic modelling are: Description: statistical description of the thermal conductivity of a rock domain. Prediction: prediction of thermal conductivity in a specific rock volume. Visualisation: visualisation of the spatial distribution of thermal conductivity. The thermal site descriptive model should include the temperature distribution and thermal properties of the rock mass. The temperature is the result of the thermal processes in the repository area. Determination of thermal transport properties can be made using different methods, such as laboratory investigations, field measurements, modelling from mineralogical composition and distribution, modelling from density logging and modelling from temperature logging. The different types of data represent different scales, which has to be

  16. Concept for calculating dose rates from activated groundwater at accelerator sites

    CERN Document Server

    Prolingheuer, N; Vanderborght, J; Schlögl, B; Nabbi, R; Moormann, R

    Licensing of particle accelerators requires the proof that the groundwater outside of the site will not be significantly contaminated by activation products formed below accelerator and target. In order to reduce the effort for this proof, a site independent simplified but conservative method is under development. The conventional approach for calculation of activation of soil and groundwater is shortly described on example of a site close to Forschungszentrum Juelich, Germany. Additionally an updated overview of a data library for partition coefficients for relevant nuclides transported in the aquifer at the site is presented. The approximate model for transport of nuclides with ground water including exemplary results on nuclide concentrations outside of the site boundary and of resulting effective doses is described. Further applications and developments are finally outlined.

  17. Numerical modelling of surface hydrology and near-surface hydrogeology at Forsmark. Site descriptive modelling SDM. Site Forsmark

    Energy Technology Data Exchange (ETDEWEB)

    Bosson, Emma (Swedish Nuclear Fuel and Waste Management Co., Stockholm (Sweden)); Gustafsson, Lars-Goeran; Sassner, Mona (DHI Sverige AB, Stockholm (Sweden))

    2008-09-15

    SKB is currently performing site investigations at two potential sites for a final repository for spent nuclear fuel. This report presents results of water flow and solute transport modelling of the Forsmark site. The modelling reported in this document focused on the near-surface groundwater, i.e. groundwater in Quaternary deposits and shallow rock, and surface water systems, and was performed using the MIKE SHE tool. The most recent site data used in the modelling were delivered in the Forsmark 2.3 dataset, which had its 'data freeze' on March 31, 2007. The present modelling is performed in support of the final version of the Forsmark site description that is produced during the site investigation phase. In this work, the hydrological modelling system MIKE SHE has been used to describe near-surface groundwater flow and the contact between groundwater and surface water at the Forsmark site. The surface water system at Forsmark is described with the one-dimensional 'channel flow' modelling tool MIKE 11, which is fully and dynamically integrated with MIKE SHE. The MIKE SHE model was updated with data from the F2.3 data freeze. The main updates concerned the geological description of the saturated zone and the time series data on water levels and surface water discharges. The time series data used as input data and for calibration and validation was extended until the Forsmark 2.3 data freeze (March 31, 2007). The present work can be subdivided into the following four parts: 1. Update of the numerical flow model. 2. Sensitivity analysis and calibration of the model parameters. 3. Validation of the calibrated model, followed by evaluation and identification of discrepancies between measurements and model results. 4. Additional sensitivity analysis and calibration in order to resolve the problems identified in point three above. The main actions taken during the calibration can be summarised as follows: 1. The potential evapotranspiration was

  18. Computational approaches to the determination of active site structures and reaction mechanisms in heterogeneous catalysts.

    Science.gov (United States)

    Catlow, C R A; French, S A; Sokol, A A; Thomas, J M

    2005-04-15

    We apply quantum chemical methods to the study of active site structures and reaction mechanisms in mesoporous silica and metal oxide catalysts. Our approach is based on the use of both molecular cluster and embedded cluster (QM/MM) techniques, where the active site and molecular complex are described using density functional theory (DFT) and the embedding matrix simulated by shell model potentials. We consider three case studies: alkene epoxidation over the microporous TS-1 catalyst; methanol synthesis on ZnO and Cu/ZnO and C-H bond activation over Li-doped MgO. PMID:15901543

  19. Mapping the active site of vaccinia virus RNA triphosphatase

    International Nuclear Information System (INIS)

    The RNA triphosphatase component of vaccinia virus mRNA capping enzyme (the product of the viral D1 gene) belongs to a family of metal-dependent phosphohydrolases that includes the RNA triphosphatases of fungi, protozoa, Chlorella virus, and baculoviruses. The family is defined by two glutamate-containing motifs (A and C) that form the metal-binding site. Most of the family members resemble the fungal and Chlorella virus enzymes, which have a complex active site located within the hydrophilic interior of a topologically closed eight-stranded β barrel (the so-called ''triphosphate tunnel''). Here we queried whether vaccinia virus capping enzyme is a member of the tunnel subfamily, via mutational mapping of amino acids required for vaccinia triphosphatase activity. We identified four new essential side chains in vaccinia D1 via alanine scanning and illuminated structure-activity relationships by conservative substitutions. Our results, together with previous mutational data, highlight a constellation of six acidic and three basic amino acids that likely compose the vaccinia triphosphatase active site (Glu37, Glu39, Arg77, Lys107, Glu126, Asp159, Lys161, Glu192, and Glu194). These nine essential residues are conserved in all vertebrate and invertebrate poxvirus RNA capping enzymes. We discerned no pattern of clustering of the catalytic residues of the poxvirus triphosphatase that would suggest structural similarity to the tunnel proteins (exclusive of motifs A and C). We infer that the poxvirus triphosphatases are a distinct lineage within the metal-dependent RNA triphosphatase family. Their unique active site, which is completely different from that of the host cell's capping enzyme, recommends the poxvirus RNA triphosphatase as a molecular target for antipoxviral drug discovery

  20. M{\\"o}ssbauer characterization of an unusual high-spin side-on peroxo-Fe3+ species in the active site of superoxide reductase from Desulfoarculus Baarsii. Density functional calculations on related models

    CERN Document Server

    Horner, Olivier; Oddou, Jean-Louis; Jeandey, Claudine; Nivière, Vincent; Mattioli, Tony A; Mathé, Christelle; Fontecave, Marc; Maldivi, Pascale; Bonville, Pierre; Halfen, Jason A; Latour, Jean-Marc

    2014-01-01

    Superoxide reductase (SOR) is an Fe protein that catalyzes the reduction of superoxide to give H(2)O(2). Recently, the mutation of the Glu47 residue into alanine (E47A) in the active site of SOR from Desulfoarculus baarsii has allowed the stabilization of an iron-peroxo species when quickly reacted with H(2)O(2) [Math{\\'e} et al. (2002) J. Am. Chem. Soc. 124, 4966-4967]. To further investigate this non-heme peroxo-iron species, we have carried out a M{\\"o}ssbauer study of the (57)Fe-enriched E47A SOR from D. baarsii reacted quickly with H(2)O(2). Considering the M{\\"o}ssbauer data, we conclude, in conjunction with the other spectroscopic data available and with the results of density functional calculations on related models, that this species corresponds to a high-spin side-on peroxo-Fe(3+) complex. This is one of the first examples of such a species in a biological system for which M{\\"o}ssbauer parameters are now available: delta(/Fe) = 0.54 (1) mm/s, DeltaE(Q) = -0.80 (5) mm/s, and the asymmetry parameter...

  1. Explorative analysis of microbes, colloids and gases together with microbial modelling. Site description model SDM-Site Laxemar

    Energy Technology Data Exchange (ETDEWEB)

    Hallbeck, Lotta; Pedersen, Karsten (Microbial Analytics Sweden AB, Goeteborg (Sweden))

    2008-08-15

    The work has involved the development of descriptive and mathematical models for groundwaters in relation to rock domains, fracture domains and deformation zones. Past climate changes are the major driving force for hydrogeochemical changes and therefore of fundamental importance for understanding the palaeohydrogeological, palaeohydrogeochemical and present evolution of groundwater in the crystalline bedrock of the Fennoscandian Shield. Understanding current undisturbed hydrochemical conditions at the proposed repository site is important when predicting future changes in groundwater chemistry. The causes of copper corrosion and/or bentonite degradation are of particular interest as they may jeopardise the long-term integrity of the planned SKB repository system. Thus, the following variables are considered for the hydrogeochemical site descriptive modelling: pH, Eh, sulphur species, iron, manganese, carbonate, phosphate, nitrogen species, total dissolved solids (TDS), isotopes, colloids, fulvic and humic acids and microorganisms. In addition, dissolved gases (e.g. carbon dioxide, methane and hydrogen) are of interest because of their likely participation in microbial reactions. In this series of reports, the final hydrogeochemical evaluation work of the site investigation at the Laxemar site, is presented. The work was conducted by SKB's hydrogeochemical project group, ChemNet, which consists of independent consultants and Univ. researchers with expertise in geochemistry, hydrochemistry, hydrogeochemistry, microbiology, geomicrobiology, analytical chemistry etc. The resulting site descriptive model version, mainly based on available primary data from the extended data freeze L2.3 (Nov 2007). This report focuses on microbiology, colloids and gases. Several methods must be used to characterise active microbial communities in groundwater. Microbial parameters of interest are the total number of cells (TNC) and the presence of various metabolic groups of

  2. Decommissioning and decontamination activity, Gnome Site, Eddy County, New Mexico

    International Nuclear Information System (INIS)

    The purpose of this assessment is to present a brief description of the proposed activity and its potential impacts on the environment. This assessment will constitute an evaluation as to whether or not a formal Environmental Statement need be prepared. As background to the proposed activity, Project Gnome was an underground nuclear test conducted in December 1961 as part of the PLOWSHARE Program. The project site is located about 25 miles southeast of Carlsbad, New Mexico. By means of an excavated shaft and tunnel, a 3-kiloton nuclear explosive was emplaced and detonated in a salt bed about 1200 feet below the surface. The uncontaminated rock and salt muck from the original excavation and subsequent contaminated muck and minor construction debris from reentry activities into the nuclear cavity is commingled and stored in a pile near the Gnome/Coach Shaft. Other areas on the site are known to have been contaminated. In 1969, a program was conducted to cleanup and dispose of all surface contamination to whatever depth it occurred in excess of 0.1 mR/hr. Contaminated materials and soil were collected and disposed into the Gnome shaft, which was filled and sealed. Since then, NV has proposed to DOE/HQ much lower criteria for residual radioactive contamination for the Gnome Site. These proposed criteria were to collect and dispose of surficial materials which contain more than 2 x 10-5 microcuries per gram of soil for beta/gamma emitters and 3 x 10-2 microcuries per milliliter of tritium in soil moisture. According to the latest reconnaissance in 1972, low concentrations of Cs-137, Sr-90 and tritium were present at various locations on the site in excess of these proposed guidelines. Other operational areas within the site are suspected of containing radioactive contamination in much lesser volume, which are to be determined by careful probing and monitoring, as described in the next section

  3. Extension of Hopfield's Electron Transfer Model To Accommodate Site-Site Correlation.

    Science.gov (United States)

    Newton, Marshall D

    2015-11-19

    Extension of the Förster analogue for the ET rate constant (based on virtual intermediate electron detachment or attachment states) with inclusion of site-site correlation due to coulomb terms associated with solvent reorganization energy and the driving force, has been developed and illustrated for a simple three-state, two-mode model. The model is applicable to charge separation (CS), recombination (CR), and shift (CSh) ET processes, with or without an intervening bridge. The model provides a unified perspective on the role of virtual intermediate states in accounting for the thermal Franck-Condon weighted density of states (FCWD), the gaps controlling superexchange coupling, and mean absolute redox potentials, with full accommodation of site-site coulomb interactions. Two types of correlation have been analyzed: aside from the site-site correlation due to coulomb interactions, we have emphasized the intrinsic "nonorthogonality" which generally pertains to reaction coordinates (RCs) for different ET processes involving multiple electronic states, as may be expressed by suitably defined direction cosines (cos(θ)). A pair of RCs may be nonorthogonal even when the site-site coulomb correlations are absent. While different RCs are linearly independent in the mathematical sense for all θ ≠ 0°, they are independent in the sense of being "uncorrelated" only in the limit of orthogonality (θ = 90°). Application to more than two coordinates is straightforward and may include both discrete and continuum contributions.

  4. Extension of Hopfield's Electron Transfer Model To Accommodate Site-Site Correlation.

    Science.gov (United States)

    Newton, Marshall D

    2015-11-19

    Extension of the Förster analogue for the ET rate constant (based on virtual intermediate electron detachment or attachment states) with inclusion of site-site correlation due to coulomb terms associated with solvent reorganization energy and the driving force, has been developed and illustrated for a simple three-state, two-mode model. The model is applicable to charge separation (CS), recombination (CR), and shift (CSh) ET processes, with or without an intervening bridge. The model provides a unified perspective on the role of virtual intermediate states in accounting for the thermal Franck-Condon weighted density of states (FCWD), the gaps controlling superexchange coupling, and mean absolute redox potentials, with full accommodation of site-site coulomb interactions. Two types of correlation have been analyzed: aside from the site-site correlation due to coulomb interactions, we have emphasized the intrinsic "nonorthogonality" which generally pertains to reaction coordinates (RCs) for different ET processes involving multiple electronic states, as may be expressed by suitably defined direction cosines (cos(θ)). A pair of RCs may be nonorthogonal even when the site-site coulomb correlations are absent. While different RCs are linearly independent in the mathematical sense for all θ ≠ 0°, they are independent in the sense of being "uncorrelated" only in the limit of orthogonality (θ = 90°). Application to more than two coordinates is straightforward and may include both discrete and continuum contributions. PMID:26501566

  5. A Bayesian belief network approach for assessing uncertainty in conceptual site models at contaminated sites

    Science.gov (United States)

    Thomsen, Nanna I.; Binning, Philip J.; McKnight, Ursula S.; Tuxen, Nina; Bjerg, Poul L.; Troldborg, Mads

    2016-05-01

    A key component in risk assessment of contaminated sites is in the formulation of a conceptual site model (CSM). A CSM is a simplified representation of reality and forms the basis for the mathematical modeling of contaminant fate and transport at the site. The CSM should therefore identify the most important site-specific features and processes that may affect the contaminant transport behavior at the site. However, the development of a CSM will always be associated with uncertainties due to limited data and lack of understanding of the site conditions. CSM uncertainty is often found to be a major source of model error and it should therefore be accounted for when evaluating uncertainties in risk assessments. We present a Bayesian belief network (BBN) approach for constructing CSMs and assessing their uncertainty at contaminated sites. BBNs are graphical probabilistic models that are effective for integrating quantitative and qualitative information, and thus can strengthen decisions when empirical data are lacking. The proposed BBN approach facilitates a systematic construction of multiple CSMs, and then determines the belief in each CSM using a variety of data types and/or expert opinion at different knowledge levels. The developed BBNs combine data from desktop studies and initial site investigations with expert opinion to assess which of the CSMs are more likely to reflect the actual site conditions. The method is demonstrated on a Danish field site, contaminated with chlorinated ethenes. Four different CSMs are developed by combining two contaminant source zone interpretations (presence or absence of a separate phase contamination) and two geological interpretations (fractured or unfractured clay till). The beliefs in each of the CSMs are assessed sequentially based on data from three investigation stages (a screening investigation, a more detailed investigation, and an expert consultation) to demonstrate that the belief can be updated as more information

  6. A Bayesian belief network approach for assessing uncertainty in conceptual site models at contaminated sites.

    Science.gov (United States)

    Thomsen, Nanna I; Binning, Philip J; McKnight, Ursula S; Tuxen, Nina; Bjerg, Poul L; Troldborg, Mads

    2016-05-01

    A key component in risk assessment of contaminated sites is in the formulation of a conceptual site model (CSM). A CSM is a simplified representation of reality and forms the basis for the mathematical modeling of contaminant fate and transport at the site. The CSM should therefore identify the most important site-specific features and processes that may affect the contaminant transport behavior at the site. However, the development of a CSM will always be associated with uncertainties due to limited data and lack of understanding of the site conditions. CSM uncertainty is often found to be a major source of model error and it should therefore be accounted for when evaluating uncertainties in risk assessments. We present a Bayesian belief network (BBN) approach for constructing CSMs and assessing their uncertainty at contaminated sites. BBNs are graphical probabilistic models that are effective for integrating quantitative and qualitative information, and thus can strengthen decisions when empirical data are lacking. The proposed BBN approach facilitates a systematic construction of multiple CSMs, and then determines the belief in each CSM using a variety of data types and/or expert opinion at different knowledge levels. The developed BBNs combine data from desktop studies and initial site investigations with expert opinion to assess which of the CSMs are more likely to reflect the actual site conditions. The method is demonstrated on a Danish field site, contaminated with chlorinated ethenes. Four different CSMs are developed by combining two contaminant source zone interpretations (presence or absence of a separate phase contamination) and two geological interpretations (fractured or unfractured clay till). The beliefs in each of the CSMs are assessed sequentially based on data from three investigation stages (a screening investigation, a more detailed investigation, and an expert consultation) to demonstrate that the belief can be updated as more information

  7. A Bayesian belief network approach for assessing uncertainty in conceptual site models at contaminated sites.

    Science.gov (United States)

    Thomsen, Nanna I; Binning, Philip J; McKnight, Ursula S; Tuxen, Nina; Bjerg, Poul L; Troldborg, Mads

    2016-05-01

    A key component in risk assessment of contaminated sites is in the formulation of a conceptual site model (CSM). A CSM is a simplified representation of reality and forms the basis for the mathematical modeling of contaminant fate and transport at the site. The CSM should therefore identify the most important site-specific features and processes that may affect the contaminant transport behavior at the site. However, the development of a CSM will always be associated with uncertainties due to limited data and lack of understanding of the site conditions. CSM uncertainty is often found to be a major source of model error and it should therefore be accounted for when evaluating uncertainties in risk assessments. We present a Bayesian belief network (BBN) approach for constructing CSMs and assessing their uncertainty at contaminated sites. BBNs are graphical probabilistic models that are effective for integrating quantitative and qualitative information, and thus can strengthen decisions when empirical data are lacking. The proposed BBN approach facilitates a systematic construction of multiple CSMs, and then determines the belief in each CSM using a variety of data types and/or expert opinion at different knowledge levels. The developed BBNs combine data from desktop studies and initial site investigations with expert opinion to assess which of the CSMs are more likely to reflect the actual site conditions. The method is demonstrated on a Danish field site, contaminated with chlorinated ethenes. Four different CSMs are developed by combining two contaminant source zone interpretations (presence or absence of a separate phase contamination) and two geological interpretations (fractured or unfractured clay till). The beliefs in each of the CSMs are assessed sequentially based on data from three investigation stages (a screening investigation, a more detailed investigation, and an expert consultation) to demonstrate that the belief can be updated as more information

  8. Modeling atmospheric CO2 concentration profiles and fluxes above sloping terrain at a boreal site

    Directory of Open Access Journals (Sweden)

    T. Aalto

    2006-01-01

    Full Text Available CO2 fluxes and concentrations were simulated in the planetary boundary layer above subarctic hilly terrain using a three dimensional model. The model solves the transport equations in the local scale and includes a vegetation sub-model. A WMO/GAW background concentration measurement site and an ecosystem flux measurement site are located inside the modeled region at a hilltop and above a mixed boreal forest, respectively. According to model results, the concentration measurement at the hill site was representative for continental background. However, this was not the case for the whole model domain. Concentration at few meters above active vegetation represented mainly local variation. Local variation became inseparable from the regional signal at about 60-100 m above ground. Flow over hills changed profiles of environmental variables and height of inversion layer, however CO2 profiles were more affected by upwind land use than topography. The hill site was above boundary layer during night and inside boundary layer during daytime. The CO2 input from model lateral boundaries dominated in both cases. Daily variation in the CO2 assimilation rate was clearly seen in the CO2 profiles. Concentration difference between the hill site and the forest site was about 5ppm during afternoon according to both model and measurements. The average modeled flux to the whole model region was about 40% of measured and modeled local flux at the forest site.

  9. Active serine involved in the stabilization of the active site loop in the Humicola lanuginosa lipase

    DEFF Research Database (Denmark)

    Peters, Günther H.j.; Svendsen, A.; Langberg, H.;

    1998-01-01

    reveal that the hinges of the active site lid are more flexible in the wild-type Hll than in S146A. In contrast, larger fluctuations are observed in the middle region of the active site loop in S 146A than in Hll. These findings reveal that the single mutation (S146A) of the active site serine leads......We have investigated the binding properties of and dynamics in Humicola lanuginosa lipase (HII) and the inactive mutant S146A (active Ser146 substituted with Ala) using fluorescence spectroscopy and molecular dynamics simulations, respectively. Hll and S146A show significantly different binding......, whereas only small changes are observed for I-Ill suggesting that the active site Lid in the latter opens more easily and hence more lipase molecules are bound to the liposomes. These observations are in agreement with molecular dynamics simulations and subsequent essential dynamics analyses. The results...

  10. Effects of resource activities upon repository siting and waste containment with reference to bedded salt

    International Nuclear Information System (INIS)

    The primary consideration for the suitability of a nuclear waste repository site is the overall ability of the repository to safely contain radioactive waste. This report is a discussion of the past, present, and future effects of resource activities on waste containment. Past and present resource activities which provide release pathways (i.e., leaky boreholes, adjacent mines) will receive initial evaluation during the early stages of any repository site study. However, other resource activities which may have subtle effects on containment (e.g., long-term pumping causing increased groundwater gradients, invasion of saline water causing lower retardation) and all potential future resource activities must also be considered during the site evaluation process. Resource activities will affect both the siting and the designing of repositories. Ideally, sites should be located in areas of low resource activity and low potential for future activity, and repository design should seek to eliminate or minimize the adverse effects of any resource activity. Buffer zones should be created to provide areas in which resource activities that might adversely affect containment can be restricted or curtailed. This could mean removing large areas of land from resource development. The impact of these frozen assets should be assessed in terms of their economic value and of their effect upon resource reserves. This step could require a major effort in data acquisition and analysis followed by extensive numerical modeling of regional fluid flow and mass transport. Numerical models should be used to assess the effects of resource activity upon containment and should include the cumulative effects of different resource activities. Analysis by other methods is probably not possible except for relatively simple cases

  11. The purification of affinity-labelled active-site peptides

    International Nuclear Information System (INIS)

    The isolation of the labelled peptide from the protein digest, following the affinity labelling of the active sites of enzymes or antibodies, is described. Single-step affinity chromatography utilises the affinity of the native enzymes or antibody for the ligand used to label the same protein. The labelled peptide is the only one in the digest that displays affinity for the immobilised protein and can be released with eluants that dissociate the protein-ligand complex. (Auth.)

  12. Structural and Kinetic Analyses of Macrophage Migration Inhibitory Factor Active Site Interactions

    Energy Technology Data Exchange (ETDEWEB)

    Crichlow, G.; Lubetsky, J; Leng, L; Bucala, R; Lolis, E

    2009-01-01

    Macrophage migration inhibitory factor (MIF) is a secreted protein expressed in numerous cell types that counters the antiinflammatory effects of glucocorticoids and has been implicated in sepsis, cancer, and certain autoimmune diseases. Interestingly, the structure of MIF contains a catalytic site resembling the tautomerase/isomerase sites of microbial enzymes. While bona fide physiological substrates remain unknown, model substrates have been identified. Selected compounds that bind in the tautomerase active site also inhibit biological functions of MIF. It had previously been shown that the acetaminophen metabolite, N-acetyl-p-benzoquinone imine (NAPQI), covalently binds to the active site of MIF. In this study, kinetic data indicate that NAPQI inhibits MIF both covalently and noncovalently. The structure of MIF cocrystallized with NAPQI reveals that the NAPQI has undergone a chemical alteration forming an acetaminophen dimer (bi-APAP) and binds noncovalently to MIF at the mouth of the active site. We also find that the commonly used protease inhibitor, phenylmethylsulfonyl fluoride (PMSF), forms a covalent complex with MIF and inhibits the tautomerase activity. Crystallographic analysis reveals the formation of a stable, novel covalent bond for PMSF between the catalytic nitrogen of the N-terminal proline and the sulfur of PMSF with complete, well-defined electron density in all three active sites of the MIF homotrimer. Conclusions are drawn from the structures of these two MIF-inhibitor complexes regarding the design of novel compounds that may provide more potent reversible and irreversible inhibition of MIF.

  13. Site characterization alternatives for numerical models of a deep excavation

    OpenAIRE

    Sau, Núria; Arroyo Alvarez de Toledo, Marcos; Gens Solé, Antonio

    2012-01-01

    A cut-and-cover railway tunnel site on the outskirts of Barcelona benefited from an extensive site investigation campaign. During the construction of the tunnel, the displacement of the wall as well as the of soil beneath was recorded. A 2D numerical model of the excavation sequence was established. The large amount of site investigation data allowed a systematic comparative approach. Four different soil characterization strategies were mimicked, deliberately ignoring one or another subset...

  14. Preliminary examination of the impacts of repository site characterization activities and facility construction and operation activities on Hanford air quality

    Energy Technology Data Exchange (ETDEWEB)

    Glantz, C.S.; Ramsdell, J.V.

    1986-04-01

    Air quality impacts that would result from site characterization activities and from the construction and operation of a high-level nuclear wste repository at Hanford are estimated using two simple atmospheric dispersion models, HANCHI and CHISHORT. Model results indicate that pollutant concentrations would not exceed ambient air quality standards at any point outside the Hanford fenceline or at any publicly accessible location within the Hanford Site. The increase in pollutant concentrations in nearby communities due to site activities would be minimal. HANCHI and CHISHORT are documented in the appendices of this document. Further study of the repository's impact on air quality will be conducted when more detailed project plans and work schedules are available.

  15. Seismic activity parameters of the Finnish potential repository sites

    Energy Technology Data Exchange (ETDEWEB)

    Saari, J. [Fortum Engineering Oy, Vantaa (Finland)

    2000-10-01

    Posiva Oy has started a project for estimating the possible earthquake induced rock movements on the deposition holes containing canisters of spent nuclear fuel. These estimates will be made for the four investigation sites, Romuvaara, Kivetty, Olkiluoto and Haestholmen. This study deals with the current and future seismicity associated with the above mentioned sites. Seismic belts that participate the seismic behaviour of the studied sites have been identified and the magnitude-frequency distributions of these belts have been estimated. The seismic activity parameters of the sites have been deduced from the characteristics of the seismic belts in order to forecast the seismicity during the next 100,000 years. The report discusses the possible earthquakes induced by future glaciation. The seismic interpretation seems to indicate that the previous postglacial faults in Finnish Lapland have been generated in compressional environment. The orientation of the rather uniform compression has been NW-SE, which coincide with the current stress field. It seems that, although the impact of postglacial crustal rebound must have been significant, the impact of plate tectonics has been dominant. A major assumption of this study has been that future seismicity will generally resemble the current seismicity. However, when the postglacial seismicity is concerned, the magnitude-frequency distribution is likely different and the expected maximum magnitude will be higher. Maximum magnitudes of future postglacial earthquakes have been approximated by strain release examinations. Seismicity has been examined within the framework of the lineament maps, in order to associate the future significant earthquakes with active fault zones in the vicinity of the potential repository sites. (orig.)

  16. Event-Based Activity Modeling

    DEFF Research Database (Denmark)

    Bækgaard, Lars

    2004-01-01

    We present and discuss a modeling approach that supports event-based modeling of information and activity in information systems. Interacting human actors and IT-actors may carry out such activity. We use events to create meaningful relations between information structures and the related activit...

  17. Fixed site neutralization model programmer's manual. Volume II

    International Nuclear Information System (INIS)

    This report relates to protection of nuclear materials at nuclear facilities. This volume presents the source listings for the Fixed Site Neutralization Model and its supporting modules, the Plex Preprocessor and the Data Preprocessor

  18. HDAC Inhibitors without an Active Site Zn2+-Binding Group

    DEFF Research Database (Denmark)

    Vickers, Chris J.; Olsen, Christian Adam; Leman, Luke J.;

    2012-01-01

    potency against class 1 HDACs and are active in tissue culture against various human cancer cell lines. Importantly, enzymological analysis of 26 indicates that the cyclic α3β-tetrapeptide is a fast-on/ off competitive inhibitor of HDACs 1−3 with Ki values of 49, 33, and 37 nM, respectively. Our proof......Natural and synthetic histone deacetylase (HDAC) inhibitors generally derive their strong binding affinity and high potency from a key functional group that binds to the Zn2+ ion within the enzyme active site. However, this feature is also thought to carry the potential liability of undesirable off......-target interactions with other metalloenzymes. As a step toward mitigating this issue, here, we describe the design, synthesis, and structure−activity characterizations of cyclic α3β-tetrapeptide HDAC inhibitors that lack the presumed indispensable Zn2+-binding group. The lead compounds (e.g., 15 and 26) display good...

  19. Calibration of the Site-Scale Saturated Zone Flow Model

    International Nuclear Information System (INIS)

    The purpose of the flow calibration analysis work is to provide Performance Assessment (PA) with the calibrated site-scale saturated zone (SZ) flow model that will be used to make radionuclide transport calculations. As such, it is one of the most important models developed in the Yucca Mountain project. This model will be a culmination of much of our knowledge of the SZ flow system. The objective of this study is to provide a defensible site-scale SZ flow and transport model that can be used for assessing total system performance. A defensible model would include geologic and hydrologic data that are used to form the hydrogeologic framework model; also, it would include hydrochemical information to infer transport pathways, in-situ permeability measurements, and water level and head measurements. In addition, the model should include information on major model sensitivities. Especially important are those that affect calibration, the direction of transport pathways, and travel times. Finally, if warranted, alternative calibrations representing different conceptual models should be included. To obtain a defensible model, all available data should be used (or at least considered) to obtain a calibrated model. The site-scale SZ model was calibrated using measured and model-generated water levels and hydraulic head data, specific discharge calculations, and flux comparisons along several of the boundaries. Model validity was established by comparing model-generated permeabilities with the permeability data from field and laboratory tests; by comparing fluid pathlines obtained from the SZ flow model with those inferred from hydrochemical data; and by comparing the upward gradient generated with the model with that observed in the field. This analysis is governed by the Office of Civilian Radioactive Waste Management (OCRWM) Analysis and Modeling Report (AMR) Development Plan ''Calibration of the Site-Scale Saturated Zone Flow Model'' (CRWMS M and O 1999a)

  20. Current activities handbook: formerly utilized sites remedial action program

    Energy Technology Data Exchange (ETDEWEB)

    None

    1981-02-27

    This volume is one of a series produced under contract with the DOE, by Politech Corporation to develop a legislative and regulatory data base to assist the FUSRAP management in addressing the institutional and socioeconomic issues involved in carrying out the Formerly Utilized Sites Remedial Action Program. This Information Handbook series contains information about all relevant government agencies at the Federal and state levels, the pertinent programs they administer, each affected state legislature, and current Federal and state legislative and regulatory initiatives. This volume is a compilation of information about the activities each of the thirteen state legislatures potentially affected by the Formerly Utilized Sites Remedial Action Program. It contains a description of the state legislative procedural rules and a schedule of each legislative session; a summary of pending relevant legislation; the name and telephone number of legislative and state agency contacts; and the full text of all bills identified.

  1. Overview of the activities carried out at the FEBEX site

    Energy Technology Data Exchange (ETDEWEB)

    Missana, T.; Buil, B.; Garralon, A.; Gomez, P. [CIEMAT, Dept. de Medioambien te, 28040 Madrid (Spain); Perez-Estaun, A.; Carbonell, R. [Inst. Jaume Almera, CSIC (Spain); Suso, J.; Carretero, G.; Bueno, J.; Martinez, L. [AITEMIN (Spain) ; Hernan, P. [ENRESA (Spain)

    2007-06-15

    One of the main aim of WP 4.1 and 4.2 is to study solute migration mechanisms in crystalline host-rock in realistic conditions. Many organisations are participating in a joint study that is being performed in the FEBEX gallery (NAGRA's Grimsel Test Site, GTS, Switzerland). The FEBEX experiment reproduces at a real scale a high-level waste repository in granite and was installed more than 9 years ago. At moment, it represents the most realistic environment where the processes affecting radionuclide migration from the bentonite to granite can be studied. This paper summarises the main activities carried out at the FEBEX site during the second year of the project.

  2. Current activities handbook: formerly utilized sites remedial action program

    International Nuclear Information System (INIS)

    This volume is one of a series produced under contract with the DOE, by Politech Corporation to develop a legislative and regulatory data base to assist the FUSRAP management in addressing the institutional and socioeconomic issues involved in carrying out the Formerly Utilized Sites Remedial Action Program. This Information Handbook series contains information about all relevant government agencies at the Federal and state levels, the pertinent programs they administer, each affected state legislature, and current Federal and state legislative and regulatory initiatives. This volume is a compilation of information about the activities each of the thirteen state legislatures potentially affected by the Formerly Utilized Sites Remedial Action Program. It contains a description of the state legislative procedural rules and a schedule of each legislative session; a summary of pending relevant legislation; the name and telephone number of legislative and state agency contacts; and the full text of all bills identified

  3. The Ohio River Basin Energy Facility siting model. Volume 2: Sites and on-line dates

    Science.gov (United States)

    Fowler, G. L.; Bailey, R. E.; Jansen, S. D.; Randolph, J. C.; Jones, W. W.; Gordon, S. I.

    1981-09-01

    The siting model developed for the Ohio River Basin Energy Study, and specifically designed for regional policy analysis is included. The region includes 423 counties in an area that consists of all of Kentucky and substantial portions of Illinois, Indiana, Ohio, Pennsylvania, and West Virginia. Detailed schedules of county-level sites and on-line dates for coal-fired and nuclear-fueled generating unit additions for each ORBES scenario are included.

  4. Screening Approach to the Activation of Soil and Contamination of Groundwater at Linear Proton Accelerator Sites

    CERN Document Server

    Otto, Thomas

    The activation of soil and the contamination of groundwater at proton accelerator sites with the radionuclides 3H and 22Na are estimated with a Monte-Carlo calculation and a conservative soil- and ground water model. The obtained radionuclide concentrations show that the underground environment of future accelerators must be adequately protected against a migration of activation products. This study is of particular importance for the proton driver accelerator in the planned EURISOL facility.

  5. Wind resource modelling for micro-siting - Validation at a 60-MW wind farm site

    Energy Technology Data Exchange (ETDEWEB)

    Hansen, J.C.; Gylling Mortensen, N. [Risoe National Lab., Wind Energy and Atmospheric Physics Dept., Roskilde (Denmark); Said, U.S. [New and Renewable Energy Authority, Cairo (Egypt)

    1999-03-01

    This paper investigates and validates the applicability of the WAsP-model for layout optimization and micro-siting of wind turbines at a given site for a 60-MW wind farm at Zafarana at the Gulf of Suez in Egypt. Previous investigations show large gradients in the wind climate within the area. For the design and optimization of the wind farm it was found necessary to verify the WAsP extrapolation of wind atlas results from 2 existing meteorological masts located 5 and 10 km, respectively, from the wind farm site. On-site measurements at the 3.5 x 3.5 km{sup 2} wind farm site in combination with 7 years of near-site wind atlas measurements offer significant amounts of data for verification of wind conditions for micro-siting. Wind speeds, wind directions, turbulence intensities and guests in 47.5 m a.g.l. have been measured at 9 locations across the site. Additionally, one of the site masts is equipped as a reference mast, measuring both vertical profiles of wind speed and temperature as well as air pressure and temperature. The exercise is further facilitated by the fact that winds are highly uni-directional; the north direction accounting for 80-90% of the wind resource. The paper presents comparisons of 5 months of on-site measurements and modeled predictions from 2 existing meteorological masts located at distances of 5 and 10 km, respectively, from the wind farm site. Predictions based on terrain descriptions of the Wind Atlas for the Gulf of Suez 1991-95 showed over-predictions of wind speeds of 4-10%. With calibrated terrain descriptions, made based on measured data and a re-visit to critical parts of the terrain, the average prediction error of wind speeds was reduced to about 1%. These deviations are smaller than generally expected for such wind resource modeling, clearly documenting the validity of using WAsP modeling for micro-siting and layout optimization of the wind farm. (au)

  6. Fixed site neutralization model programmer's manual. Volume 1

    International Nuclear Information System (INIS)

    The Fixed Site Neutralization Model (FSNM) is a stochastic, time-stepped simulation of an engagement process whereby an adversary force attempts to steal or sabotage sensitive (e.g., nuclear) materials being guarded by a security force on a fixed site and a response force that is off-site. FSNM will assist regulatory bodies of the US Government in evaluating fixed site physical protection systems at various installations in a variety of scenarios. Most data input to the Fixed Site Neutralization Model are in binary form. The user's data are transformed into binary form by two supporting modules, the Data Preprocessor (DPP) and the Plex Preprocessor (PPP). Both preprocessors and the FSNM itself are written in FORTRAN. This volume of the program maintenance program contains: introduction, logic descriptions, PLEX data structure, PLEX records, dictionaries, and error conditions and comments

  7. Insight into the mechanism of phosphoenolpyruvate mutase catalysis derived from site-directed mutagenesis studies of active site residues.

    Science.gov (United States)

    Jia, Y; Lu, Z; Huang, K; Herzberg, O; Dunaway-Mariano, D

    1999-10-26

    PEP mutase catalyzes the conversion of phosphoenolpyruvate (PEP) to phosphonopyruvate in biosynthetic pathways leading to phosphonate secondary metabolites. A recent X-ray structure [Huang, K., Li, Z., Jia, Y., Dunaway-Mariano, D., and Herzberg, O. (1999) Structure (in press)] of the Mytilus edulis enzyme complexed with the Mg(II) cofactor and oxalate inhibitor reveals an alpha/beta-barrel backbone-fold housing an active site in which Mg(II) is bound by the two carboxylate groups of the oxalate ligand and the side chain of D85 and, via bridging water molecules, by the side chains of D58, D85, D87, and E114. The oxalate ligand, in turn, interacts with the side chains of R159, W44, and S46 and the backbone amide NHs of G47 and L48. Modeling studies identified two feasible PEP binding modes: model A in which PEP replaces oxalate with its carboxylate group interacting with R159 and its phosphoryl group positioned close to D58 and Mg(II) shifting slightly from its original position in the crystal structure, and model B in which PEP replaces oxalate with its phosphoryl group interacting with R159 and Mg(II) retaining its original position. Site-directed mutagenesis studies of the key mutase active site residues (R159, D58, D85, D87, and E114) were carried out in order to evaluate the catalytic roles predicted by the two models. The observed retention of low catalytic activity in the mutants R159A, D85A, D87A, and E114A, coupled with the absence of detectable catalytic activity in D58A, was interpreted as evidence for model A in which D58 functions in nucleophilic catalysis (phosphoryl transfer), R159 functions in PEP carboxylate group binding, and the carboxylates of D85, D87 and E114 function in Mg(II) binding. These results also provide evidence against model B in which R159 serves to mediate the phosphoryl transfer. A catalytic motif, which could serve both the phosphoryl transfer and the C-C cleavage enzymes of the PEP mutase superfamily, is proposed. PMID:10571990

  8. Penetration Testing Model for Web sites Hosted in Nuclear Malaysia

    International Nuclear Information System (INIS)

    Nuclear Malaysia web sites has been very crucial in providing important and useful information and services to the clients as well as the users worldwide. Furthermore, a web site is important as it reflects the organisation image. To ensure the integrity of the content of web site, a study has been made and a penetration testing model has been implemented to test the security of several web sites hosted at Nuclear Malaysia for malicious attempts. This study will explain how the security was tested in the detailed condition and measured. The result determined the security level and the vulnerability of several web sites. This result is important for improving and hardening the security of web sites in Nuclear Malaysia. (author)

  9. Active control: Wind turbine model

    DEFF Research Database (Denmark)

    Bindner, H.

    1999-01-01

    validation as well as parameter estimation. The model includes a simple model of the structure of the turbine including tower and flapwise blade bending,a detailed model of the gear box and induction generator, a linearized aerodynamic model including modelling of induction lag and actuator and sensor models......This report is a part of the reporting of the work done in the project 'Active Control of Wind Turbines'. This project aim is to develop a simulation model for design of control systems for turbines with pitch control and to use that model to designcontrollers. This report describes the model...... developed for controller design and analysis. Emphasis has been put on establishment of simple models describing the dynamic behavior of the wind turbine in adequate details for controller design. This hasbeen done with extensive use of measurements as the basis for selection of model complexity and model...

  10. Ground-water monitoring and modeling at the Hanford Site

    International Nuclear Information System (INIS)

    The ground-water monitoring program at the Hanford Site in southeastern Washington State is continually evolving in response to changing operations at the site, changes in the ground-water flow system, movement of the constituents in the aquifers, and regulatory requirements. Sampling and analysis of ground water, along with ground-water flow and solute transport modeling are used to evaluate the movement and resulting distributions of radionuclides and hazardous chemical constituents in the unconfined aquifer. Evaluation of monitoring results, modeling, and information on waste management practices are being combined to continually improve the network of ground-water monitoring wells at the site

  11. Ground-water monitoring and modeling at the Hanford Site

    International Nuclear Information System (INIS)

    The ground-water monitoring program at the Hanford Site in southeastern Washington State is continually evolving in response to changing operations at the site, changes in the ground-water flow system, movement of the constituents in the aquifers, and regulatory requirements. Sampling and analysis of ground water, along with ground-water flow and solute transport modeling are used ito evaluate the movement and resulting distributions of radionuclides and hazardous chemical constituents in the unconfined aquifer. Evaluation of monitoring results, modeling, and information on waste management practices are being combined to continually improve the network of ground-water monitoring wells at the site

  12. Prediction of functional sites based on the fuzzy oil drop model.

    Directory of Open Access Journals (Sweden)

    Michał Bryliński

    2007-05-01

    Full Text Available A description of many biological processes requires knowledge of the 3-D structure of proteins and, in particular, the defined active site responsible for biological function. Many proteins, the genes of which have been identified as the result of human genome sequencing, and which were synthesized experimentally, await identification of their biological activity. Currently used methods do not always yield satisfactory results, and new algorithms need to be developed to recognize the localization of active sites in proteins. This paper describes a computational model that can be used to identify potential areas that are able to interact with other molecules (ligands, substrates, inhibitors, etc.. The model for active site recognition is based on the analysis of hydrophobicity distribution in protein molecules. It is shown, based on the analyses of proteins with known biological activity and of proteins of unknown function, that the region of significantly irregular hydrophobicity distribution in proteins appears to be function related.

  13. Human population and activities in Forsmark. Site description

    Energy Technology Data Exchange (ETDEWEB)

    Miliander, Sofia; Punakivi, Mari; Kylaekorpi, Lasse; Rydgren, Bernt [SwedPower AB, Stockholm (Sweden)

    2004-12-01

    The Swedish Nuclear Fuel and Waste Management Co (SKB) is in the process of selecting a safe and environmentally acceptable location for a deep repository of radioactive waste. Two alternative locations are under investigation. These are Forsmark, Oesthammars kommun (kommun = municipality) and Simpevarp/Laxemar, Oskarshamns kommun. SKB has expressed the importance of describing the humans and their activities in these areas and therefore has this synthesis concerning the human population in Forsmark been produced.The description is a statistical synthesis, mainly based upon statistical data from SCB (Statistics Sweden) that has been collected, processed and analysed. The statistical data has not been verified through site inspections and interviews. When using statistical data, it is advisable to note that the data becomes more unreliable if the areas are small, with small populations.The data in this description is essential for future evaluations of the impact on the environment and its human population (Environmental Impact Assessments). The data is also important when modelling the potential flows of radio nuclides and calculating the risk of exposure in future safety assessments.The actual area for the study is in this report called 'the Forsmark area', an area of 19.5 km{sup 2} near Forsmark nuclear power plant. The land use in the Forsmark area differs notably from the land use in Uppsala laen (laen = county). Only 0.04% of the total area is developed (built-up) compared to 4.9% in Uppsala laen and only 4% is agricultural land compared to 25% in the county. Furthermore, there are far more forest, wetlands and water areas in the Forsmark area. The forest area represents as much as 72.5% of the total area.The Forsmark area is uninhabited, and its surroundings are very sparsely populated. In 2002, the population density in Forsmark was 1.8 inhabitants per square kilometre, which was 24 times lower than in Uppsala laen. The population density in the

  14. Human population and activities in Forsmark. Site description

    International Nuclear Information System (INIS)

    The Swedish Nuclear Fuel and Waste Management Co (SKB) is in the process of selecting a safe and environmentally acceptable location for a deep repository of radioactive waste. Two alternative locations are under investigation. These are Forsmark, Oesthammars kommun (kommun = municipality) and Simpevarp/Laxemar, Oskarshamns kommun. SKB has expressed the importance of describing the humans and their activities in these areas and therefore has this synthesis concerning the human population in Forsmark been produced.The description is a statistical synthesis, mainly based upon statistical data from SCB (Statistics Sweden) that has been collected, processed and analysed. The statistical data has not been verified through site inspections and interviews. When using statistical data, it is advisable to note that the data becomes more unreliable if the areas are small, with small populations.The data in this description is essential for future evaluations of the impact on the environment and its human population (Environmental Impact Assessments). The data is also important when modelling the potential flows of radio nuclides and calculating the risk of exposure in future safety assessments.The actual area for the study is in this report called 'the Forsmark area', an area of 19.5 km2 near Forsmark nuclear power plant. The land use in the Forsmark area differs notably from the land use in Uppsala laen (laen = county). Only 0.04% of the total area is developed (built-up) compared to 4.9% in Uppsala laen and only 4% is agricultural land compared to 25% in the county. Furthermore, there are far more forest, wetlands and water areas in the Forsmark area. The forest area represents as much as 72.5% of the total area.The Forsmark area is uninhabited, and its surroundings are very sparsely populated. In 2002, the population density in Forsmark was 1.8 inhabitants per square kilometre, which was 24 times lower than in Uppsala laen. The population density in the parish has been

  15. Sphingosine-1-phosphate receptor 1 reporter mice reveal receptor activation sites in vivo

    OpenAIRE

    Kono, Mari; Tucker, Ana E.; Tran, Jennifer; Bergner, Jennifer B.; Turner, Ewa M; Proia, Richard L.

    2014-01-01

    Activation of the GPCR sphingosine-1-phosphate receptor 1 (S1P1) by sphingosine-1-phosphate (S1P) regulates key physiological processes. S1P1 activation also has been implicated in pathologic processes, including autoimmunity and inflammation; however, the in vivo sites of S1P1 activation under normal and disease conditions are unclear. Here, we describe the development of a mouse model that allows in vivo evaluation of S1P1 activation. These mice, known as S1P1 GFP signaling mice, produce a ...

  16. Oxygen reduction and evolution at single-metal active sites

    DEFF Research Database (Denmark)

    Calle-Vallejo, F.; Martínez, J.I.; García Lastra, Juan Maria;

    2013-01-01

    A worldwide spread of clean technologies such as low-temperature fuel cells and electrolyzers depends strictly on their technical reliability and economic affordability. Currently, both conditions are hardly fulfilled mainly due to the same reason: the oxygen electrode, which has large overpotent...... may be improved by careful selections of the support and the ligand properties close to the active sites and/or the ramifications near them, so that charge is transferred back and forth during adsorption and selective hydrogen bonds are formed....

  17. From site measurements to spatial modelling - multi-criteria model evaluation

    Science.gov (United States)

    Gottschalk, Pia; Roers, Michael; Wechsung, Frank

    2015-04-01

    Hydrological models are traditionally evaluated at gauge stations for river runoff which is assumed to be the valid and global test for model performance. One model output is assumed to reflect the performance of all implemented processes and parameters. It neglects the complex interactions of landscape processes which are actually simulated by the model but not tested. The application of a spatial hydrological model however offers a vast potential of evaluation aspects which shall be presented here with the example of the eco-hydrological model SWIM. We present current activities to evaluate SWIM at the lysimeter site Brandis, the eddy-co-variance site Gebesee and with spatial crop yields of Germany to constrain model performance additionally to river runoff. The lysimeter site is used to evaluate actuall evapotranspiration, total runoff below the soil profile and crop yields. The eddy-covariance site Gebesee offers data to study crop growth via net-ecosystem carbon exchange and actuall evapotranspiration. The performance of the vegetation module is tested via spatial crop yields at county level of Germany. Crop yields are an indirect measure of crop growth which is an important driver of the landscape water balance and therefore eventually determines river runoff as well. First results at the lysimeter site show that simulated soil water dynamics are less sensitive to soil type than measured soil water dynamics. First results from the simulation of actuall evapotranspiration and carbon exchange at Gebesee show a satisfactorily model performance with however difficulties to capture initial vegetation growth in spring. The latter is a hint at problems capturing winter growth conditions and subsequent impacts on crop growth. This is also reflected in the performance of simulated crop yields for Germany where the model reflects crop yields of silage maize much better than of winter wheat. With the given approach we would like to highlight the advantages and

  18. 10 CFR 63.16 - Review of site characterization activities. 2

    Science.gov (United States)

    2010-01-01

    ... 10 Energy 2 2010-01-01 2010-01-01 false Review of site characterization activities. 2 63.16... site characterization activities. 2 2 In addition to the review of site characterization activities... investigation and site characterization, to allow early identification of potential licensing issues for...

  19. 77 FR 39508 - Commercial Wind Lease Issuance and Site Assessment Activities on the Atlantic Outer Continental...

    Science.gov (United States)

    2012-07-03

    ... characterization activities (geophysical, geotechnical, archaeological, and biological surveys needed to develop..., site characterization, and site assessment in and around the Call Area (76 FR 51391). The Call Area...

  20. A single-site multipole model for liquid water

    Science.gov (United States)

    Tran, Kelly N.; Tan, Ming-Liang; Ichiye, Toshiko

    2016-07-01

    Accurate and efficient empirical potential energy models that describe the atomistic interactions between water molecules in the liquid phase are essential for computer simulations of many problems in physics, chemistry, and biology, especially when long length or time scales are important. However, while models with non-polarizable partial charges at four or five sites in a water molecule give remarkably good values for certain properties, deficiencies have been noted in other properties and increasing the number of sites decreases computational efficiency. An alternate approach is to utilize a multipole expansion of the electrostatic potential due to the molecular charge distribution, which is exact outside the charge distribution in the limits of infinite distances or infinite orders of multipoles while partial charges are a qualitative representation of electron density as point charges. Here, a single-site multipole model of water is presented, which is as fast computationally as three-site models but is also more accurate than four- and five-site models. The dipole, quadrupole, and octupole moments are from quantum mechanical-molecular mechanical calculations so that they account for the average polarization in the liquid phase, and represent both the in-plane and out-of-plane electrostatic potentials of a water molecule in the liquid phase. This model gives accurate thermodynamic, dynamic, and dielectric properties at 298 K and 1 atm, as well as good temperature and pressure dependence of these properties.

  1. Probing the putative active site of YjdL

    DEFF Research Database (Denmark)

    Jensen, Johanne Mørch; Ismat, Fouzia; Szakonyi, Gerda;

    2012-01-01

    YjdL from E. coli is an unusual proton-coupled oligopeptide transporter (POT). Unlike prototypical POTs, dipeptides are preferred over tripeptides, in particular dipeptides with a positively charged C-terminal residue. To further understand this difference in peptide specificity, the sequences...... of YjdL and YdgR, a prototypical E. coli POT, were compared in light of the crystal structure of a POT from Shewanella oneidensis. Several residues found in the putative active site were mutated and the activities of the mutated variants were assessed in terms of substrate uptake assays, and changes...... pocket that opens towards the extracellular space. The C-terminal side chain faces in the opposite direction into a sub pocket that faces the cytoplasm. These data indicated a stabilizing effect on a bulky N-terminal residue by an Ala281Phe variant and on the dipeptide backbone by Trp278...

  2. SITE-DIRECTED MUTAGENESIS OF PROPOSED ACTIVE-SITE RESIDUES OF PENICILLIN-BINDING PROTEIN-5 FROM ESCHERICHIA-COLI

    NARCIS (Netherlands)

    VANDERLINDEN, MPG; DEHAAN, L; DIDEBERG, O; KECK, W

    1994-01-01

    Alignment of the amino acid sequence of penicillin-binding protein 5 (PBP5) with the sequences of other members of the family of active-site-serine penicillin-interacting enzymes predicted the residues playing a role in the catalytic mechanism of PBP5. Apart from the active-site (Ser(44)), Lys(47),

  3. Polarizability of the active site of cytochrome c reduces the activation barrier for electron transfer

    Science.gov (United States)

    Dinpajooh, Mohammadhasan; Martin, Daniel R.; Matyushov, Dmitry V.

    2016-06-01

    Enzymes in biology’s energy chains operate with low energy input distributed through multiple electron transfer steps between protein active sites. The general challenge of biological design is how to lower the activation barrier without sacrificing a large negative reaction free energy. We show that this goal is achieved through a large polarizability of the active site. It is polarized by allowing a large number of excited states, which are populated quantum mechanically by electrostatic fluctuations of the protein and hydration water shells. This perspective is achieved by extensive mixed quantum mechanical/molecular dynamics simulations of the half reaction of reduction of cytochrome c. The barrier for electron transfer is consistently lowered by increasing the number of excited states included in the Hamiltonian of the active site diagonalized along the classical trajectory. We suggest that molecular polarizability, in addition to much studied electrostatics of permanent charges, is a key parameter to consider in order to understand how enzymes work.

  4. Examination of compensatory model application in site selection.

    Science.gov (United States)

    Zaredar, Narges; Kheirkhah Zarkesh, Mir Masoud

    2012-01-01

    Nowadays, usage of compensatory models in land evaluation process and site selection is broadly observed. Meanwhile, methods such as analytical hierarchy process are used more than the others. Whether the usage of compensatory model methods in site selection studies is essentially correct or not is an issue that should be hesitated. In this model, inefficiency of a factor, to be offset by strength of others, means that in urban development site selection, if somewhere has unsuitable aspect but suitable slope, the aspect deficiency will be compensated by the slope. But quodlibet reflection is that in this model, sometimes, deficiency of proximity to fault can be compensated by other parameters strength. And finally, a place is diagnosed as a suitable area for urban development that is close to the fault. This research aims at examination of compensatory models application in urban development site selection of Taleghan Basin using analytical hierarchy process as one of the compensatory model methods. Among this the weaknesses and strengths of compensatory model were analyzed carefully. Results indicate that despite usefulness of this model in being fast, easy, and low expense, it has some weaknesses like very high sensitivity to decision maker's idea. PMID:21442190

  5. Perchlorate Reductase Is Distinguished by Active Site Aromatic Gate Residues.

    Science.gov (United States)

    Youngblut, Matthew D; Tsai, Chi-Lin; Clark, Iain C; Carlson, Hans K; Maglaqui, Adrian P; Gau-Pan, Phonchien S; Redford, Steven A; Wong, Alan; Tainer, John A; Coates, John D

    2016-04-22

    Perchlorate is an important ion on both Earth and Mars. Perchlorate reductase (PcrAB), a specialized member of the dimethylsulfoxide reductase superfamily, catalyzes the first step of microbial perchlorate respiration, but little is known about the biochemistry, specificity, structure, and mechanism of PcrAB. Here we characterize the biophysics and phylogeny of this enzyme and report the 1.86-Å resolution PcrAB complex crystal structure. Biochemical analysis revealed a relatively high perchlorate affinity (Km = 6 μm) and a characteristic substrate inhibition compared with the highly similar respiratory nitrate reductase NarGHI, which has a relatively much lower affinity for perchlorate (Km = 1.1 mm) and no substrate inhibition. Structural analysis of oxidized and reduced PcrAB with and without the substrate analog SeO3 (2-) bound to the active site identified key residues in the positively charged and funnel-shaped substrate access tunnel that gated substrate entrance and product release while trapping transiently produced chlorate. The structures suggest gating was associated with shifts of a Phe residue between open and closed conformations plus an Asp residue carboxylate shift between monodentate and bidentate coordination to the active site molybdenum atom. Taken together, structural and mutational analyses of gate residues suggest key roles of these gate residues for substrate entrance and product release. Our combined results provide the first detailed structural insight into the mechanism of biological perchlorate reduction, a critical component of the chlorine redox cycle on Earth.

  6. Maxey Flats low-level waste disposal site closure activities

    International Nuclear Information System (INIS)

    The Maxey Flats Radioactive Waste Disposal Facility in Fleming County, Kentucky is in the process of being closed. The facility opened for commercial business in the spring of 1963 and received approximately 4.75 million cubic feet of radioactive waste by the time it was closed in December of 1977. During fourteen years of operation approximately 2.5 million curies of by-product material, 240,000 kilograms of source material, and 430 kilograms of special nuclear material were disposed. The Commonwealth purchased the lease hold estate and rights in May 1978 from the operating company. This action was taken to stabilize the facility and prepare it for closure consisting of passive care and monitoring. To prepare the site for closure, a number of remedial activities had to be performed. The remediation activities implemented have included erosion control, surface drainage modifications, installation of a temporary plastic surface cover, leachate removal, analysis, treatment and evaporation, US DOE funded evaporator concentrates solidification project and their on-site disposal in an improved disposal trench with enhanced cover for use in a humid environment situated in a fractured geology, performance evaluation of a grout injection demonstration, USGS subsurface geologic investigation, development of conceptual closure designs, and finally being added to the US EPA National Priority List for remediation and closure under Superfund. 13 references, 3 figures

  7. Identification of covalent active site inhibitors of dengue virus protease

    Directory of Open Access Journals (Sweden)

    Koh-Stenta X

    2015-12-01

    Full Text Available Xiaoying Koh-Stenta,1 Joma Joy,1 Si Fang Wang,1 Perlyn Zekui Kwek,1 John Liang Kuan Wee,1 Kah Fei Wan,2 Shovanlal Gayen,1 Angela Shuyi Chen,1 CongBao Kang,1 May Ann Lee,1 Anders Poulsen,1 Subhash G Vasudevan,3 Jeffrey Hill,1 Kassoum Nacro11Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR, Singapore; 2Novartis Institute for Tropical Diseases, Singapore; 3Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, SingaporeAbstract: Dengue virus (DENV protease is an attractive target for drug development; however, no compounds have reached clinical development to date. In this study, we utilized a potent West Nile virus protease inhibitor of the pyrazole ester derivative class as a chemical starting point for DENV protease drug development. Compound potency and selectivity for DENV protease were improved through structure-guided small molecule optimization, and protease-inhibitor binding interactions were validated biophysically using nuclear magnetic resonance. Our work strongly suggests that this class of compounds inhibits flavivirus protease through targeted covalent modification of active site serine, contrary to an allosteric binding mechanism as previously described.Keywords: flavivirus protease, small molecule optimization, covalent inhibitor, active site binding, pyrazole ester derivatives

  8. Coarse-Grained Model for Water Involving a Virtual Site.

    Science.gov (United States)

    Deng, Mingsen; Shen, Hujun

    2016-02-01

    In this work, we propose a new coarse-grained (CG) model for water by combining the features of two popular CG water models (BMW and MARTINI models) as well as by adopting a topology similar to that of the TIP4P water model. In this CG model, a CG unit, representing four real water molecules, consists of a virtual site, two positively charged particles, and a van der Waals (vdW) interaction center. Distance constraint is applied to the bonds formed between the vdW interaction center and the positively charged particles. The virtual site, which carries a negative charge, is determined by the locations of the two positively charged particles and the vdW interaction center. For the new CG model of water, we coined the name "CAVS" (charge is attached to a virtual site) due to the involvment of the virtual site. After being tested in molecular dynamic (MD) simulations of bulk water at various time steps, under different temperatures and in different salt (NaCl) concentrations, the CAVS model offers encouraging predictions for some bulk properties of water (such as density, dielectric constant, etc.) when compared to experimental ones. PMID:26747089

  9. Large field excursions from a few site relaxion model

    Science.gov (United States)

    Fonseca, N.; de Lima, L.; Machado, C. S.; Matheus, R. D.

    2016-07-01

    Relaxion models are an interesting new avenue to explain the radiative stability of the Standard Model scalar sector. They require very large field excursions, which are difficult to generate in a consistent UV completion and to reconcile with the compact field space of the relaxion. We propose an N -site model which naturally generates the large decay constant needed to address these issues. Our model offers distinct advantages with respect to previous proposals: the construction involves non-Abelian fields, allowing for controlled high-energy behavior and more model building possibilities, both in particle physics and inflationary models, and also admits a continuum limit when the number of sites is large, which may be interpreted as a warped extra dimension.

  10. Number of active transcription factor binding sites is essential for the Hes7 oscillator

    Directory of Open Access Journals (Sweden)

    de Angelis Martin

    2006-02-01

    Full Text Available Abstract Background It is commonly accepted that embryonic segmentation of vertebrates is regulated by a segmentation clock, which is induced by the cycling genes Hes1 and Hes7. Their products form dimers that bind to the regulatory regions and thereby repress the transcription of their own encoding genes. An increase of the half-life of Hes7 protein causes irregular somite formation. This was shown in recent experiments by Hirata et al. In the same work, numerical simulations from a delay differential equations model, originally invented by Lewis, gave additional support. For a longer half-life of the Hes7 protein, these simulations exhibited strongly damped oscillations with, after few periods, severely attenuated the amplitudes. In these simulations, the Hill coefficient, a crucial model parameter, was set to 2 indicating that Hes7 has only one binding site in its promoter. On the other hand, Bessho et al. established three regulatory elements in the promoter region. Results We show that – with the same half life – the delay system is highly sensitive to changes in the Hill coefficient. A small increase changes the qualitative behaviour of the solutions drastically. There is sustained oscillation and hence the model can no longer explain the disruption of the segmentation clock. On the other hand, the Hill coefficient is correlated with the number of active binding sites, and with the way in which dimers bind to them. In this paper, we adopt response functions in order to estimate Hill coefficients for a variable number of active binding sites. It turns out that three active transcription factor binding sites increase the Hill coefficient by at least 20% as compared to one single active site. Conclusion Our findings lead to the following crucial dichotomy: either Hirata's model is correct for the Hes7 oscillator, in which case at most two binding sites are active in its promoter region; or at least three binding sites are active, in which

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

    Science.gov (United States)

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

    2015-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Yu Zhang

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

  13. Immobilized low-activity waste site borehole 299-E17-21

    Energy Technology Data Exchange (ETDEWEB)

    Reidel, S.P.; Reynolds, K.D.; Horton, D.G.

    1998-08-01

    The Tank Waste Remediation System (TWRS) is the group at the Hanford Site responsible for the safe underground storage of liquid waste from previous Hanford Site operations, the storage and disposal of immobilized tank waste, and closure of underground tanks. The current plan is to dispose of immobilized low-activity tank waste (ILAW) in new facilities in the southcentral part of 200-East Area and in four existing vaults along the east side of 200-East Area. Boreholes 299-E17-21, B8501, and B8502 were drilled at the southwest corner of the ILAW site in support of the Performance Assessment activities for the disposal options. This report summarizes the initial geologic findings, field tests conducted on those boreholes, and ongoing studies. One deep (480 feet) borehole and two shallow (50 feet) boreholes were drilled at the southwest corner of the ILAW site. The primary factor dictating the location of the boreholes was their characterization function with respect to developing the geohydrologic model for the site and satisfying associated Data Quality Objectives. The deep borehole was drilled to characterize subsurface conditions beneath the ILAW site, and two shallow boreholes were drilled to support an ongoing environmental tracer study. The tracer study will supply information to the Performance Assessment. All the boreholes provide data on the vadose zone and saturated zone in a previously uncharacterized area.

  14. Three-dimensional representations of salt-dome margins at four active strategic petroleum reserve sites.

    Energy Technology Data Exchange (ETDEWEB)

    Rautman, Christopher Arthur; Stein, Joshua S.

    2003-01-01

    Existing paper-based site characterization models of salt domes at the four active U.S. Strategic Petroleum Reserve sites have been converted to digital format and visualized using modern computer software. The four sites are the Bayou Choctaw dome in Iberville Parish, Louisiana; the Big Hill dome in Jefferson County, Texas; the Bryan Mound dome in Brazoria County, Texas; and the West Hackberry dome in Cameron Parish, Louisiana. A new modeling algorithm has been developed to overcome limitations of many standard geological modeling software packages in order to deal with structurally overhanging salt margins that are typical of many salt domes. This algorithm, and the implementing computer program, make use of the existing interpretive modeling conducted manually using professional geological judgement and presented in two dimensions in the original site characterization reports as structure contour maps on the top of salt. The algorithm makes use of concepts of finite-element meshes of general engineering usage. Although the specific implementation of the algorithm described in this report and the resulting output files are tailored to the modeling and visualization software used to construct the figures contained herein, the algorithm itself is generic and other implementations and output formats are possible. The graphical visualizations of the salt domes at the four Strategic Petroleum Reserve sites are believed to be major improvements over the previously available two-dimensional representations of the domes via conventional geologic drawings (cross sections and contour maps). Additionally, the numerical mesh files produced by this modeling activity are available for import into and display by other software routines. The mesh data are not explicitly tabulated in this report; however an electronic version in simple ASCII format is included on a PC-based compact disk.

  15. Molecular dioxygen enters the active site of 12/15-lipoxygenase via dynamic oxygen access channels.

    Science.gov (United States)

    Saam, Jan; Ivanov, Igor; Walther, Matthias; Holzhütter, Hermann-Georg; Kuhn, Hartmut

    2007-08-14

    Cells contain numerous enzymes that use molecular oxygen for their reactions. Often, their active sites are buried deeply inside the protein, which raises the question whether there are specific access channels guiding oxygen to the site of catalysis. Choosing 12/15-lipoxygenase as a typical example for such oxygen-dependent enzymes, we determined the oxygen distribution within the protein and defined potential routes for oxygen access. For this purpose, we have applied an integrated strategy of structural modeling, molecular dynamics simulations, site-directed mutagenesis, and kinetic measurements. First, we computed the 3D free-energy distribution for oxygen, which led to identification of four oxygen channels in the protein. All channels connect the protein surface with a region of high oxygen affinity at the active site. This region is localized opposite to the nonheme iron providing a structural explanation for the reaction specificity of this lipoxygenase isoform. The catalytically most relevant path can be obstructed by L367F exchange, which leads to a strongly increased Michaelis constant for oxygen. The blocking mechanism is explained in detail by reordering the hydrogen-bonding network of water molecules. Our results provide strong evidence that the main route for oxygen access to the active site of the enzyme follows a channel formed by transiently interconnected cavities whereby the opening and closure are governed by side chain dynamics. PMID:17675410

  16. Metals in the active site of native protein phosphatase-1.

    Science.gov (United States)

    Heroes, Ewald; Rip, Jens; Beullens, Monique; Van Meervelt, Luc; De Gendt, Stefan; Bollen, Mathieu

    2015-08-01

    Protein phosphatase-1 (PP1) is a major protein Ser/Thr phosphatase in eukaryotic cells. Its activity depends on two metal ions in the catalytic site, which were identified as manganese in the bacterially expressed phosphatase. However, the identity of the metal ions in native PP1 is unknown. In this study, total reflection X-ray fluorescence (TXRF) was used to detect iron and zinc in PP1 that was purified from rabbit skeletal muscle. Metal exchange experiments confirmed that the distinct substrate specificity of recombinant and native PP1 is determined by the nature of their associated metals. We also found that the iron level associated with native PP1 is decreased by incubation with inhibitor-2, consistent with a function of inhibitor-2 as a PP1 chaperone. PMID:25890482

  17. Hydrogeological modeling of prb for remediation of a contaminated site

    Science.gov (United States)

    Yang, Y. S.; McGeogh, K. L.; Kalin, R. M.

    2003-04-01

    In recent decades great effort has been spent on restoration of contaminated environment and considerable progress has been made in improving environmental quality. However, challenges still exist in some areas, such as remediation of contaminated land and groundwater. To provide sufficient remediation and protection for land and groundwater underneath, minimize environmental risk in infrastructure maintenance and urban re-development in terms of contamination remediation, it is necessary to incorporate understanding of the sub-surface conditions in the decision-making process. Characterization of regional and site-specific hydrogeological systems plays an important role in remediation of contaminated sites. Advanced modeling techniques can realize and improve characterization of complex hydrogeological systems. Numerical models can provide straightforward approaches for remediation designs. In this paper, a case study on hydrogeologic modeling of Permeable Reactive Barriers (PRB) for remediation of a contaminated site in the dockland area of Dublin, Ireland, is presented. The groundwater modeling maneuvers were carried out in three strands: regional characterization, zoom-in model in a smaller area; and detailed site-specific study. The regional hydrogeology and groundwater systems were characterized to form a regional conceptual model; a more detailed zoom-in 3-D model was further constructed in the quayside area to simulate the impact of adjacent remedial action and diurnally tidal fluctuation; finally, a site-specific model was built to study the detailed flow field and design the best remediation option. This site model was calibrated with field-monitored data under natural condition; hydraulic parameter, time varying river boundary and head-dependant boundary conditions were calibrated to achieve best fits between modeled and observed groundwater heads. The calibrated model then was used to carry out a remediation plan design using Permeable Reactive Barriers

  18. Site-scale groundwater flow modelling of Beberg

    International Nuclear Information System (INIS)

    The Swedish Nuclear Fuel and Waste Management Company (SKB) Safety Report for 1997 (SR 97) study is a comprehensive performance assessment illustrating the results for three hypothetical repositories in Sweden. In support of SR 97, this study examines the hydrogeologic modelling of the hypothetical site called Beberg, which adopts input parameters from the SKB study site near Finnsjoen, in central Sweden. This study uses a nested modelling approach, with a deterministic regional model providing boundary conditions to a site-scale stochastic continuum model. The model is run in Monte Carlo fashion to propagate the variability of the hydraulic conductivity to the advective travel paths from representative canister positions. A series of variant cases addresses uncertainties in the inference of parameters and the boundary conditions. The study uses HYDRASTAR, the SKB stochastic continuum (SC) groundwater modelling program, to compute the heads, Darcy velocities at each representative canister position, and the advective travel times and paths through the geosphere. The Base Case simulation takes its constant head boundary conditions from a modified version of the deterministic regional scale model of Hartley et al. The flow balance between the regional and site-scale models suggests that the nested modelling conserves mass only in a general sense, and that the upscaling is only approximately valid. The results for 100 realisation of 120 starting positions, a flow porosity of εf 10-4, and a flow-wetted surface of ar = 1.0 m2/(m3 rock) suggest the following statistics for the Base Case: The median travel time is 56 years. The median canister flux is 1.2 x 10-3 m/year. The median F-ratio is 5.6 x 105 year/m. The travel times, flow paths and exit locations were compatible with the observations on site, approximate scoping calculations and the results of related modelling studies. Variability within realisations indicates that the change in hydraulic gradient across the

  19. Site-scale groundwater flow modelling of Beberg

    Energy Technology Data Exchange (ETDEWEB)

    Gylling, B. [Kemakta Konsult AB, Stockholm (Sweden); Walker, D. [Duke Engineering and Services (United States); Hartley, L. [AEA Technology, Harwell (United Kingdom)

    1999-08-01

    The Swedish Nuclear Fuel and Waste Management Company (SKB) Safety Report for 1997 (SR 97) study is a comprehensive performance assessment illustrating the results for three hypothetical repositories in Sweden. In support of SR 97, this study examines the hydrogeologic modelling of the hypothetical site called Beberg, which adopts input parameters from the SKB study site near Finnsjoen, in central Sweden. This study uses a nested modelling approach, with a deterministic regional model providing boundary conditions to a site-scale stochastic continuum model. The model is run in Monte Carlo fashion to propagate the variability of the hydraulic conductivity to the advective travel paths from representative canister positions. A series of variant cases addresses uncertainties in the inference of parameters and the boundary conditions. The study uses HYDRASTAR, the SKB stochastic continuum (SC) groundwater modelling program, to compute the heads, Darcy velocities at each representative canister position, and the advective travel times and paths through the geosphere. The Base Case simulation takes its constant head boundary conditions from a modified version of the deterministic regional scale model of Hartley et al. The flow balance between the regional and site-scale models suggests that the nested modelling conserves mass only in a general sense, and that the upscaling is only approximately valid. The results for 100 realisation of 120 starting positions, a flow porosity of {epsilon}{sub f} 10{sup -4}, and a flow-wetted surface of a{sub r} = 1.0 m{sup 2}/(m{sup 3} rock) suggest the following statistics for the Base Case: The median travel time is 56 years. The median canister flux is 1.2 x 10{sup -3} m/year. The median F-ratio is 5.6 x 10{sup 5} year/m. The travel times, flow paths and exit locations were compatible with the observations on site, approximate scoping calculations and the results of related modelling studies. Variability within realisations indicates

  20. Metavanadate at the active site of the phosphatase VHZ.

    Science.gov (United States)

    Kuznetsov, Vyacheslav I; Alexandrova, Anastassia N; Hengge, Alvan C

    2012-09-01

    Vanadate is a potent modulator of a number of biological processes and has been shown by crystal structures and NMR spectroscopy to interact with numerous enzymes. Although these effects often occur under conditions where oligomeric forms dominate, the crystal structures and NMR data suggest that the inhibitory form is usually monomeric orthovanadate, a particularly good inhibitor of phosphatases because of its ability to form stable trigonal-bipyramidal complexes. We performed a computational analysis of a 1.14 Å structure of the phosphatase VHZ in complex with an unusual metavanadate species and compared it with two classical trigonal-bipyramidal vanadate-phosphatase complexes. The results support extensive delocalized bonding to the apical ligands in the classical structures. In contrast, in the VHZ metavanadate complex, the central, planar VO(3)(-) moiety has only one apical ligand, the nucleophilic Cys95, and a gap in electron density between V and S. A computational analysis showed that the V-S interaction is primarily ionic. A mechanism is proposed to explain the formation of metavanadate in the active site from a dimeric vanadate species that previous crystallographic evidence has shown to be able to bind to the active sites of phosphatases related to VHZ. Together, the results show that the interaction of vanadate with biological systems is not solely reliant upon the prior formation of a particular inhibitory form in solution. The catalytic properties of an enzyme may act upon the oligomeric forms primarily present in solution to generate species such as the metavanadate ion observed in the VHZ structure. PMID:22876963

  1. Human population and activities at Simpevarp. Site description

    International Nuclear Information System (INIS)

    The Swedish Nuclear Fuel and Waste Management Co (SKB) is in the process of selecting a safe and environmentally acceptable location for a deep repository of radioactive waste. Two alternative locations are under investigation. These are Forsmark, Oesthammars kommun (kommun = municipality) and Simpevarp/Laxemar, Oskarshamns kommun. SKB has expressed the importance of describing the humans and their activities in these areas and therefore has this synthesis concerning the human population in Forsmark been produced. The description is a statistical synthesis, mainly based upon statistical data from SCB (Statistics Sweden) that has been collected, processed and analysed. The statistical data has not been verified through site inspections and interviews. When using statistical data, it is advisable to note that the data becomes more unreliable if the areas are small, with small populations. The data in this description is essential for future evaluations of the impact on the environment and its human population (environmental impacts assessments). The data is also important when modelling the potential flows of radio nuclides and calculating the risk of exposure in future safety assessments. The actual area for the study is in this report called 'the Simpevarp area', an area of 127.0 km2 near Oskarshamn nuclear power plant. The land use in Simpevarp area differs notably from the land use in Kalmar laen. The forest area is far more dominating in Simpevarp area than in Kalmar laen and it represents as much as 89% compared to 63% of the total area. Only 4.4% of the area is arable land compared to 11.6% in Kalmar laen and only 0.3% is of other type (wetlands, bare rock, quarries, pites etc) compared to 15.6% in the county. The main observation is that Simpevarp area is a sparsely populated area located in a relatively lightly populated county. In 2002, the population density was 7.4 inhabitants/km2, three times lower than in Kalmar laen. The demography statistics show no

  2. Human population and activities at Simpevarp. Site description

    Energy Technology Data Exchange (ETDEWEB)

    Miliander, Sofia; Punakivi, Mari; Kylaekorpi, Lasse; Rydgren, Bernt [SwedPower AB, Stockholm (Sweden)

    2004-12-01

    The Swedish Nuclear Fuel and Waste Management Co (SKB) is in the process of selecting a safe and environmentally acceptable location for a deep repository of radioactive waste. Two alternative locations are under investigation. These are Forsmark, Oesthammars kommun (kommun = municipality) and Simpevarp/Laxemar, Oskarshamns kommun. SKB has expressed the importance of describing the humans and their activities in these areas and therefore has this synthesis concerning the human population in Forsmark been produced. The description is a statistical synthesis, mainly based upon statistical data from SCB (Statistics Sweden) that has been collected, processed and analysed. The statistical data has not been verified through site inspections and interviews. When using statistical data, it is advisable to note that the data becomes more unreliable if the areas are small, with small populations. The data in this description is essential for future evaluations of the impact on the environment and its human population (environmental impacts assessments). The data is also important when modelling the potential flows of radio nuclides and calculating the risk of exposure in future safety assessments. The actual area for the study is in this report called 'the Simpevarp area', an area of 127.0 km{sup 2} near Oskarshamn nuclear power plant. The land use in Simpevarp area differs notably from the land use in Kalmar laen. The forest area is far more dominating in Simpevarp area than in Kalmar laen and it represents as much as 89% compared to 63% of the total area. Only 4.4% of the area is arable land compared to 11.6% in Kalmar laen and only 0.3% is of other type (wetlands, bare rock, quarries, pites etc) compared to 15.6% in the county. The main observation is that Simpevarp area is a sparsely populated area located in a relatively lightly populated county. In 2002, the population density was 7.4 inhabitants/km{sup 2}, three times lower than in Kalmar laen. The

  3. Human population and activities at Simpevarp. Site description

    Energy Technology Data Exchange (ETDEWEB)

    Miliander, Sofia; Punakivi, Mari; Kylaekorpi, Lasse; Rydgren, Bernt [SwedPower AB, Stockholm (Sweden)

    2004-12-01

    The Swedish Nuclear Fuel and Waste Management Co (SKB) is in the process of selecting a safe and environmentally acceptable location for a deep repository of radioactive waste. Two alternative locations are under investigation. These are Forsmark, Oesthammars kommun (kommun = municipality) and Simpevarp/Laxemar, Oskarshamns kommun. SKB has expressed the importance of describing the humans and their activities in these areas and therefore has this synthesis concerning the human population in Forsmark been produced. The description is a statistical synthesis, mainly based upon statistical data from SCB (Statistics Sweden) that has been collected, processed and analysed. The statistical data has not been verified through site inspections and interviews. When using statistical data, it is advisable to note that the data becomes more unreliable if the areas are small, with small populations. The data in this description is essential for future evaluations of the impact on the environment and its human population (environmental impacts assessments). The data is also important when modelling the potential flows of radio nuclides and calculating the risk of exposure in future safety assessments. The actual area for the study is in this report called 'the Simpevarp area', an area of 127.0 km{sup 2} near Oskarshamn nuclear power plant. The land use in Simpevarp area differs notably from the land use in Kalmar laen. The forest area is far more dominating in Simpevarp area than in Kalmar laen and it represents as much as 89% compared to 63% of the total area. Only 4.4% of the area is arable land compared to 11.6% in Kalmar laen and only 0.3% is of other type (wetlands, bare rock, quarries, pites etc) compared to 15.6% in the county. The main observation is that Simpevarp area is a sparsely populated area located in a relatively lightly populated county. In 2002, the population density was 7.4 inhabitants/km{sup 2}, three times lower than in Kalmar laen. The

  4. Computation of Rate Constants for Diffusion of Small Ligands to and from Buried Protein Active Sites.

    Science.gov (United States)

    Wang, P-H; De Sancho, D; Best, R B; Blumberger, J

    2016-01-01

    The diffusion of ligands to actives sites of proteins is essential to enzyme catalysis and many cellular signaling processes. In this contribution we review our recently developed methodology for calculation of rate constants for diffusion and binding of small molecules to buried protein active sites. The diffusive dynamics of the ligand obtained from molecular dynamics simulation is coarse grained and described by a Markov state model. Diffusion and binding rate constants are then obtained either from the reactive flux formalism or by fitting the time-dependent population of the Markov state model to a phenomenological rate law. The method is illustrated by applications to diffusion of substrate and inhibitors in [NiFe] hydrogenase, CO-dehydrogenase, and myoglobin. We also discuss a recently developed sensitivity analysis that allows one to identify hot spots in proteins, where mutations are expected to have the strongest effects on ligand diffusion rates. PMID:27497172

  5. Three multimedia models used at hazardous and radioactive waste sites

    International Nuclear Information System (INIS)

    Multimedia models are used commonly in the initial phases of the remediation process where technical interest is focused on determining the relative importance of various exposure pathways. This report provides an approach for evaluating and critically reviewing the capabilities of multimedia models. This study focused on three specific models MEPAS Version 3.0, MMSOILS Version 2.2, and PRESTO-EPA-CPG Version 2.0. These models evaluate the transport and fate of contaminants from source to receptor through more than a single pathway. The presence of radioactive and mixed wastes at a site poses special problems. Hence, in this report, restrictions associated with the selection and application of multimedia models for sites contaminated with radioactive and mixed wastes are highlighted. This report begins with a brief introduction to the concept of multimedia modeling, followed by an overview of the three models. The remaining chapters present more technical discussions of the issues associated with each compartment and their direct application to the specific models. In these analyses, the following components are discussed: source term; air transport; ground water transport; overland flow, runoff, and surface water transport; food chain modeling; exposure assessment; dosimetry/risk assessment; uncertainty; default parameters. The report concludes with a description of evolving updates to the model; these descriptions were provided by the model developers

  6. Three multimedia models used at hazardous and radioactive waste sites

    Energy Technology Data Exchange (ETDEWEB)

    Moskowitz, P.D.; Pardi, R.; Fthenakis, V.M.; Holtzman, S.; Sun, L.C. [Brookhaven National Lab., Upton, NY (United States); Rambaugh, J.O.; Potter, S. [Geraghty and Miller, Inc., Plainview, NY (United States)

    1996-02-01

    Multimedia models are used commonly in the initial phases of the remediation process where technical interest is focused on determining the relative importance of various exposure pathways. This report provides an approach for evaluating and critically reviewing the capabilities of multimedia models. This study focused on three specific models MEPAS Version 3.0, MMSOILS Version 2.2, and PRESTO-EPA-CPG Version 2.0. These models evaluate the transport and fate of contaminants from source to receptor through more than a single pathway. The presence of radioactive and mixed wastes at a site poses special problems. Hence, in this report, restrictions associated with the selection and application of multimedia models for sites contaminated with radioactive and mixed wastes are highlighted. This report begins with a brief introduction to the concept of multimedia modeling, followed by an overview of the three models. The remaining chapters present more technical discussions of the issues associated with each compartment and their direct application to the specific models. In these analyses, the following components are discussed: source term; air transport; ground water transport; overland flow, runoff, and surface water transport; food chain modeling; exposure assessment; dosimetry/risk assessment; uncertainty; default parameters. The report concludes with a description of evolving updates to the model; these descriptions were provided by the model developers.

  7. The 2-site Hubbard and {t}-{J} models

    Science.gov (United States)

    Avella, A.; Mancini, F.; Saikawa, T.

    2003-12-01

    The fermionic and bosonic sectors of the 2-site Hubbard model have been exactly solved by means of the equation of motion and Green’s function formalism. The exact solution of the t- J model has been also reported to investigate the low-energy dynamics. We have successfully searched for the exact eigenoperators, and the corresponding eigenenergies, having in mind the possibility to use them as an operatorial basis on the lattice. Many local, single-particle, thermodynamical and response properties have been studied as functions of the external parameters and compared between the two models and with some numerical and exact results. It has been shown that the 2-site Hubbard model already contains the most relevant energy scales of the Hubbard model: the local Coulomb interaction U and the spin-exchange one J = frac{4t^2}U. As a consequence of this, for some relevant properties (kinetic energy, double occupancy, energy, specific heat and entropy) and as regards the metal-insulator transition issue, it has resulted possible to almost exactly mime the behavior of larger systems, sometimes using a higher temperature to get a comparable level spacing. The 2-site models have been also used as toy models to test the efficiency of the Green’s function formalism for composite operators. The capability to reproduce the exact solutions, obtained by the exact diagonalization technique, gives a firm ground to the approximate treatments based on this formalism.

  8. Using Automated On-Site Monitoring to Calibrate Empirical Models of Trihalomethanes Concentrations in Drinking Water

    OpenAIRE

    Thomas E. Watts III; Robyn A. Snow; Brown, Aaron W.; J. C. York; Greg Fantom; Paul S. Simone Jr.; Gary L. Emmert

    2015-01-01

    An automated, on-site trihalomethanes concentration data set from a conventional water treatment plant was used to optimize powdered activated carbon and pre-chlorination doses. The trihalomethanes concentration data set was used with commonly monitored water quality parameters to improve an empirical model of trihalomethanes formation. A calibrated model was used to predict trihalomethanes concentrations the following year. The agreement between the models and measurements was evaluated. The...

  9. Coordination geometries of Zn(II) and Cd(II) in phosphotriesterase: Influence of water molecules in the active site

    DEFF Research Database (Denmark)

    Krauss, M; Olsen, Lars; Antony, J;

    2002-01-01

    Models of the metal ion binding sites of native ZnZn and of cadmium-substituted ZnCd and CdCd phosphotriesterase, including full amino acid side chains, were geometry optimized with quantum mechanical methods, with effective fragment potentials (EFP) representing the protein environment surrounding...... the active site. One to three water molecules were included in the active site in addition to the bridging hydroxide. Comparison with recent X-ray diffraction results Benning, M. M.; Shim, H.; Raushel, F. M.; Holden, H. M. Biochemistry 2001, 40, 2712-22 is hindered by the presence of ethylene glycol...... molecules in the active site. We suggest that the ethylene glycol required for crystallization distorts the structure of the water network in the active site and that the theoretical structures provide a better description of the system in aqueous solution. Cd-113 NMR isotropic shielding calculations were...

  10. Hydrodynamic model of Fukushima-Daiichi NPP Industrial site flooding

    CERN Document Server

    Vaschenko, V N; Gerasimenko, T V; Vachev, B

    2014-01-01

    While the Fukushima-Daiichi was designed and constructed the maximal tsunami height estimate was about 3 m based on analysis of statistical data including Chile earthquake in 1960. The NPP project industrial site height was 10 m. The further deterministic estimates TPCO-JSCE confirmed the impossibility of the industrial site flooding by a tsunami and therefore confirmed ecological safety of the NPP. However, as a result of beyond design earthquake of 11 March 2011 the tsunami height at the shore near the Fukushima-Daiichi NPP reached 15 m. This led to flooding and severe emergencies having catastrophic environmental consequences. This paper proposes hydrodynamic model of tsunami emerging and traveling based on conservative assumptions. The possibility of a tsunami wave reaching 15 m height at the Fukushima-Daiichi NPP shore was confirmed for deduced hydrodynamic resistance coefficient of 1.8. According to the model developed a possibility of flooding is determined not only by the industrial site height, magni...

  11. Active Learning for Player Modeling

    DEFF Research Database (Denmark)

    Shaker, Noor; Abou-Zleikha, Mohamed; Shaker, Mohammad

    2015-01-01

    Learning models of player behavior has been the focus of several studies. This work is motivated by better understanding of player behavior, a knowledge that can ultimately be employed to provide player-adapted or personalized content. In this paper, we propose the use of active learning for player...... experience modeling. We use a dataset from hundreds of players playing Infinite Mario Bros. as a case study and we employ the random forest method to learn mod- els of player experience through the active learning approach. The results obtained suggest that only part of the dataset (up to half the size...

  12. 10 CFR 60.18 - Review of site characterization activities. 2

    Science.gov (United States)

    2010-01-01

    ... 10 Energy 2 2010-01-01 2010-01-01 false Review of site characterization activities. 2 60.18... IN GEOLOGIC REPOSITORIES Licenses Preapplication Review § 60.18 Review of site characterization activities. 2 2 In addition to the review of site characterization activities specified in this section,...

  13. Characterization of the active site properties of CYP4F12.

    Science.gov (United States)

    Eksterowicz, John; Rock, Dan A; Rock, Brooke M; Wienkers, Larry C; Foti, Robert S

    2014-10-01

    Cytochrome P450 4F12 is a drug-metabolizing enzyme that is primarily expressed in the liver, kidney, colon, small intestine, and heart. The properties of CYP4F12 that may impart an increased catalytic selectivity (decreased promiscuity) were explored through in vitro metabolite elucidation, kinetic isotope effect experiments, and computational modeling of the CYP4F12 active site. By using astemizole as a probe substrate for CYP4F12 and CYP3A4, it was observed that although CYP4F12 favored astemizole O-demethylation as the primary route of metabolism, CYP3A4 was capable of metabolizing astemizole at multiple sites on the molecule. Deuteration of astemizole at the site of O-demethylation resulted in an isotope effect of 7.1 as well as an 8.3-fold decrease in the rate of clearance for astemizole by CYP4F12. Conversely, although an isotope effect of 3.8 was observed for the formation of the O-desmethyl metabolite when deuterated astemizole was metabolized by CYP3A4, there was no decrease in the clearance of astemizole. Development of a homology model of CYP4F12 based on the crystal structure of cytochrome P450 BM3 predicted an active site volume for CYP4F12 that was approximately 76% of the active site volume of CYP3A4. As predicted, multiple favorable binding orientations were available for astemizole docked into the active site of CYP3A4, but only a single binding orientation with the site of O-demethylation oriented toward the heme was identified for CYP4F12. Overall, it appears that although CYP4F12 may be capable of binding similar ligands to other cytochrome P450 enzymes such as CYP3A4, the ability to achieve catalytically favorable orientations may be inherently more difficult because of the increased steric constraints of the CYP4F12 active site. PMID:25074871

  14. Karstification beneath dam sites: From conceptual models to realistic scenarios

    Science.gov (United States)

    Hiller, Thomas; Kaufmann, Georg; Romanov, Douchko

    2010-05-01

    Dam sites located above soluble rock such as limestone or gypsum can leak in relatively short times (tenths of years), when compared to the natural time scale of karstification (10.000-100.000 years). The reason for this leakage is the high hydraulic gradient imposed by the reservoir that drives aggressive water through the fracture and fissure system of the bedrock and this aggressive water dissolves the rock and increases permeability fairly fast. Thus, on the one hand water losses through enlarged fractures can become a problem for the reservoir. On the other hand, the void space itself can be a risk for the dam structure above. This may have unpredictable ecological and economical consequences. We present a three-dimensional conceptual model study of karstification in dam-site areas on limestone bedrock. We compare our three-dimensional model to a standard two-dimensional dam site model to verify the results of our code. We further carry out a sensitivity analysis on the physical and chemical parameters driving the karstification to derive an empirical formulation of the breakthrough time TB. In a next step we implement a statistical fracture network and topography to approach a more realistic scenario. Finally we show the results of a three dimensional model based on a real dam site.

  15. A site dependent top height growth model for hybrid aspen

    Institute of Scientific and Technical Information of China (English)

    Tord Johansson

    2013-01-01

    In this study height growth models for hybrid aspen were developed using three growth equations. The mean age of the hybrid aspen was 21 years (range 15−51 years) with a mean stand density of 946 stems ha-1 (87−2374) and a mean diameter at breast height (over bark) of 19.6 cm (8.5−40.8 cm). Site index was also examined in relation to soil type. Multiple samples were collected for three types of soil: light clay, medium clay and till. Site index curves were constructed using the col-lected data and compared with published reports. A number of dynamic equations were assessed for modeling top-height growth from total age. A Generalized Algebraic Difference Approach model derived by Cieszewski (2001) performed the best. This model explained 99% of the observed variation in tree height growth and exhibited no apparent bias across the range of predicted site indices. There were no significant differences between the soil types and site indices.

  16. Modeling in support of Hanford site waste management

    International Nuclear Information System (INIS)

    The waste management practices for both radioactive and hazardous wastes at the Hanford Site are designed to comply with all applicable state and federal regulations. Results from numerical simulation models are used to assess the risk to human health and the environment. The numerical models simulate flow and transport of contaminants through the vadose zone and the underlying unconfined aquifer. Numerical simulation results from several studies are summarized

  17. The 2-site Hubbard and t-J models

    OpenAIRE

    Avella, Adolfo; Mancini, Ferdinando; Saikawa, Taiichiro

    2001-01-01

    The fermionic and bosonic sectors of the 2-site Hubbard model have been exactly solved by means of the equation of motion and Green's function formalism. The exact solution of the t-J model has been also reported to investigate the low-energy dynamics. We have successfully searched for the exact eigenoperators, and the corresponding eigenenergies, having in mind the possibility to use them as an operatorial basis on the lattice. Many local, single-particle, thermodynamical and response proper...

  18. Hazardous Material Storage Facilities and Sites - WASTE_SOLID_ACTIVE_PERMITTED_IDEM_IN: Active Permitted Solid Waste Sites in Indiana (Indiana Department of Environmental Management, Point Shapefile)

    Data.gov (United States)

    NSGIC GIS Inventory (aka Ramona) — WASTE_SOLID_ACTIVE_PERMITTED_IDEM_IN is a point shapefile that contains active permitted solid waste site locations in Indiana, provided by personnel of Indiana...

  19. Using Automated On-Site Monitoring to Calibrate Empirical Models of Trihalomethanes Concentrations in Drinking Water

    Directory of Open Access Journals (Sweden)

    Thomas E. Watts III

    2015-10-01

    Full Text Available An automated, on-site trihalomethanes concentration data set from a conventional water treatment plant was used to optimize powdered activated carbon and pre-chlorination doses. The trihalomethanes concentration data set was used with commonly monitored water quality parameters to improve an empirical model of trihalomethanes formation. A calibrated model was used to predict trihalomethanes concentrations the following year. The agreement between the models and measurements was evaluated. The original model predicted trihalomethanes concentrations within ~10 μg·L−1 of the measurement. Calibration improved model prediction by a factor of three to five times better than the literature model.

  20. Active site conformational dynamics in human uridine phosphorylase 1.

    Directory of Open Access Journals (Sweden)

    Tarmo P Roosild

    Full Text Available Uridine phosphorylase (UPP is a central enzyme in the pyrimidine salvage pathway, catalyzing the reversible phosphorolysis of uridine to uracil and ribose-1-phosphate. Human UPP activity has been a focus of cancer research due to its role in activating fluoropyrimidine nucleoside chemotherapeutic agents such as 5-fluorouracil (5-FU and capecitabine. Additionally, specific molecular inhibitors of this enzyme have been found to raise endogenous uridine concentrations, which can produce a cytoprotective effect on normal tissues exposed to these drugs. Here we report the structure of hUPP1 bound to 5-FU at 2.3 A resolution. Analysis of this structure reveals new insights as to the conformational motions the enzyme undergoes in the course of substrate binding and catalysis. The dimeric enzyme is capable of a large hinge motion between its two domains, facilitating ligand exchange and explaining observed cooperativity between the two active sites in binding phosphate-bearing substrates. Further, a loop toward the back end of the uracil binding pocket is shown to flexibly adjust to the varying chemistry of different compounds through an "induced-fit" association mechanism that was not observed in earlier hUPP1 structures. The details surrounding these dynamic aspects of hUPP1 structure and function provide unexplored avenues to develop novel inhibitors of this protein with improved specificity and increased affinity. Given the recent emergence of new roles for uridine as a neuron protective compound in ischemia and degenerative diseases, such as Alzheimer's and Parkinson's, inhibitors of hUPP1 with greater efficacy, which are able to boost cellular uridine levels without adverse side-effects, may have a wide range of therapeutic applications.

  1. The role of consequence modeling in LNG facility siting.

    Science.gov (United States)

    Taylor, Dennis W

    2007-04-11

    Liquefied natural gas (LNG) project modeling focuses on two primary issues, facility siting and the physical layout of element spacing. Modeling often begins with an analysis of these issues, while ensuring code compliance and sound engineering practice. The most commonly performed analysis involves verifying compliance with the siting provisions of NFPA 59A, which primarily concern property-line spacing (offsite hazard impacts). If the facility is located in the US, compliance with 49 CFR 193 is also required. Other consequence modeling is often performed to determine the spacing of elements within the facility (onsite hazard impacts). Often, many issues concerning in-plant spacing are addressed with the guidance provided in Europe's LNG standard, EN-1473. Spacing of plant buildings in relation to process areas is also a concern as analyzed using the approach given in API RP 752. Studies may also include probabilistic analysis, depending on the perceived risk and cost of mitigation.

  2. Detection limit for activation measurements in ultralow background sites

    Science.gov (United States)

    Trache, Livius; Chesneanu, D.; Margineanu, R.; Pantelica, A.; Ghita, D. G.; Burducea, I.; Straticiuc, M.; Tang, X. D.

    2014-09-01

    We used 12C +13C fusion at the beam energies E = 6, 7 and 8 MeV to determine the sensitivity and the limits of activation method measurements in ultralow background sites. A 13C beam of 0.5 μA from the 3 MV Tandem accelerator of the Horia Hulubei National Institute of Physics and Nuclear Engineering - IFIN HH impinged on thick graphite targets. After about 24 hrs of irradiation targets were measured in two different laboratories: one with a heavy shielded Ge detector in the institute (at the surface) and one located underground in the microBequerel laboratory, in the salt mine of Slanic-Prahova, Romania. The 1369- and 2754 keV peaks from 24Na deactivation were clearly observed in the γ-ray spectra obtained for acquisitions lasting a few hours, or a few days. Determination of the detection limit in evaluating the cross sections for the target irradiated at Ec . m = 3 MeV indicates the fact that it is possible to measure gamma spectrum in underground laboratory down to Ec . m = 2 . 6 MeV. Cleaning the spectra with beta-gamma coincidences and increasing beam intensity 20 times will take as further down. The measurements are motivated by the study of the 12 C +12 C reaction at astrophysical energies.

  3. NMR crystallography of enzyme active sites: probing chemically detailed, three-dimensional structure in tryptophan synthase.

    Science.gov (United States)

    Mueller, Leonard J; Dunn, Michael F

    2013-09-17

    NMR crystallography--the synergistic combination of X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry--offers unprecedented insight into three-dimensional, chemically detailed structure. Initially, researchers used NMR crystallography to refine diffraction data from organic and inorganic solids. Now we are applying this technique to explore active sites in biomolecules, where it reveals chemically rich detail concerning the interactions between enzyme site residues and the reacting substrate. Researchers cannot achieve this level of detail from X-ray, NMR,or computational methodologies in isolation. For example, typical X-ray crystal structures (1.5-2.5 Å resolution) of enzyme-bound intermediates identify possible hydrogen-bonding interactions between site residues and substrate but do not directly identify the protonation states. Solid-state NMR can provide chemical shifts for selected atoms of enzyme-substrate complexes, but without a larger structural framework in which to interpret them only empirical correlations with local chemical structure are possible. Ab initio calculations and molecular mechanics can build models for enzymatic processes, but they rely on researcher-specified chemical details. Together, however, X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry can provide consistent and testable models for structure and function of enzyme active sites: X-ray crystallography provides a coarse framework upon which scientists can develop models of the active site using computational chemistry; they can then distinguish these models by comparing calculated NMR chemical shifts with the results of solid-state NMR spectroscopy experiments. Conceptually, each technique is a puzzle piece offering a generous view of the big picture. Only when correctly pieced together, however, can they reveal the big picture at the highest possible resolution. In this Account, we detail our first steps in the development of

  4. Application of data fusion modeling (DFM) to site characterization

    International Nuclear Information System (INIS)

    Subsurface characterization is faced with substantial uncertainties because the earth is very heterogeneous, and typical data sets are fragmented and disparate. DFM removes many of the data limitations of current methods to quantify and reduce uncertainty for a variety of data types and models. DFM is a methodology to compute hydrogeological state estimates and their uncertainties from three sources of information: measured data, physical laws, and statistical models for spatial heterogeneities. The benefits of DFM are savings in time and cost through the following: the ability to update models in real time to help guide site assessment, improved quantification of uncertainty for risk assessment, and improved remedial design by quantifying the uncertainty in safety margins. A Bayesian inverse modeling approach is implemented with a Gauss Newton method where spatial heterogeneities are viewed as Markov random fields. Information from data, physical laws, and Markov models is combined in a Square Root Information Smoother (SRIS). Estimates and uncertainties can be computed for heterogeneous hydraulic conductivity fields in multiple geological layers from the usually sparse hydraulic conductivity data and the often more plentiful head data. An application of DFM to the Old Burial Ground at the DOE Savannah River Site will be presented. DFM estimates and quantifies uncertainty in hydrogeological parameters using variably saturated flow numerical modeling to constrain the estimation. Then uncertainties are propagated through the transport modeling to quantify the uncertainty in tritium breakthrough curves at compliance points

  5. Geological evolution, palaeoclimate and historical development of the Forsmark and Laxemar-Simpevarp areas. Site descriptive modelling SDM-Site

    International Nuclear Information System (INIS)

    The Swedish Nuclear Fuel and Waste Management Company (SKB) is undertaking site characterization at two different locations, the Forsmark and Laxemar-Simpevarp areas, with the objective of siting a geological repository for spent nuclear fuel. The site investigations started in 2002 and were completed in 2007. The analysis and modelling of data from the site investigations, which have taken place during and after these investigations, provide a foundation for the development of an integrated, multidisciplinary site descriptive model (SDM) for each of the two sites. A site descriptive model constitutes a description of the site and its regional setting, covering the current state of the geosphere and the biosphere, as well as those natural processes that affect or have affected their long-term development. Hitherto, a number of reports presenting preliminary site descriptive models for Forsmark and Laxemar-Simpevarp have been published. In these reports, the evolutionary and historical aspects of the site were included in a separate chapter. The present report comprises a further elaboration of the evolutionary and historical information included in the preliminary SDM reports, but presented here in a separate, supplementary report to the final site description, SDM-Site. The report is common to the two investigated areas, and the overall objective is to describe the long-term geological evolution, the palaeoclimate, and the post-glacial development of ecosystems and of the human population at the two sites. The report largely consists of a synthesis of information derived from the scientific literature and other sources not related to the site investigations. However, considerable information from the site investigations that has contributed to our understanding of the past development at each site is also included. This unique synthesis of both published information in a regional perspective and new site-specific information breaks new ground in our understanding

  6. Geological evolution, palaeoclimate and historical development of the Forsmark and Laxemar-Simpevarp areas. Site descriptive modelling SDM-Site

    Energy Technology Data Exchange (ETDEWEB)

    Soederbaeck, Bjoern (ed.)

    2008-06-15

    The Swedish Nuclear Fuel and Waste Management Company (SKB) is undertaking site characterization at two different locations, the Forsmark and Laxemar-Simpevarp areas, with the objective of siting a geological repository for spent nuclear fuel. The site investigations started in 2002 and were completed in 2007. The analysis and modelling of data from the site investigations, which have taken place during and after these investigations, provide a foundation for the development of an integrated, multidisciplinary site descriptive model (SDM) for each of the two sites. A site descriptive model constitutes a description of the site and its regional setting, covering the current state of the geosphere and the biosphere, as well as those natural processes that affect or have affected their long-term development. Hitherto, a number of reports presenting preliminary site descriptive models for Forsmark and Laxemar-Simpevarp have been published. In these reports, the evolutionary and historical aspects of the site were included in a separate chapter. The present report comprises a further elaboration of the evolutionary and historical information included in the preliminary SDM reports, but presented here in a separate, supplementary report to the final site description, SDM-Site. The report is common to the two investigated areas, and the overall objective is to describe the long-term geological evolution, the palaeoclimate, and the post-glacial development of ecosystems and of the human population at the two sites. The report largely consists of a synthesis of information derived from the scientific literature and other sources not related to the site investigations. However, considerable information from the site investigations that has contributed to our understanding of the past development at each site is also included. This unique synthesis of both published information in a regional perspective and new site-specific information breaks new ground in our understanding

  7. HOW DO STUDENTS SELECT SOCIAL NETWORKING SITES? AN ANALYTIC HIERARCHY PROCESS (AHP MODEL

    Directory of Open Access Journals (Sweden)

    Chun Meng Tang

    2015-12-01

    Full Text Available Social networking sites are popular among university students, and students today are indeed spoiled for choice. New emerging social networking sites sprout up amid popular sites, while some existing ones die out. Given the choice of so many social networking sites, how do students decide which one they will sign up for and stay on as an active user? The answer to this question is of interest to social networking site designers and marketers. The market of social networking sites is highly competitive. To maintain the current user base and continue to attract new users, how should social networking sites design their sites? Marketers spend a fairly large percent of their marketing budget on social media marketing. To formulate an effective social media strategy, how much do marketers understand the users of social networking sites? Learning from website evaluation studies, this study intends to provide some answers to these questions by examining how university students decide between two popular social networking sites, Facebook and Twitter. We first developed an analytic hierarchy process (AHP model of four main selection criteria and 12 sub-criteria, and then administered a questionnaire to a group of university students attending a course at a Malaysian university. AHP analyses of the responses from 12 respondents provided an insight into the decision-making process involved in students’ selection of social networking sites. It seemed that of the four main criteria, privacy was the top concern, followed by functionality, usability, and content. The sub-criteria that were of key concern to the students were apps, revenue-generating opportunities, ease of use, and information security. Between Facebook and Twitter, the students thought that Facebook was the better choice. This information is useful for social networking site designers to design sites that are more relevant to their users’ needs, and for marketers to craft more effective

  8. Emphasis: an active management model

    International Nuclear Information System (INIS)

    The Institute of Nuclear Materials Management was founded and has grown on the basis of promoting professionalism in the nuclear industry. This paper is concerned with professional management of nuclear material. The paper introduces the reader to Emphasis, an active management model. The management model provides the framework to assist a manager in directing his available resources. Emphasis provides for establishing goals, identifying and selecting objectives, matching objectives to specific personnel, preparing and monitoring action plans, and evaluating results. The model stresses crisis prevention by systematically administering and controlling resources. A critical requirement for implementation of the model is the desire to manage, to be in charge of the situation. The nuclear industry does need managers - people who realize the sensitive nature of the industry, professionals who insist on improved performance

  9. Identification of Errors in the Hanford Site-Wide Groundwater Flow Model by Inverse Modeling of Alternative Conceptual Models

    Science.gov (United States)

    Cole, C. R.; Scheibe, T. D.; Vermeul, V. R.; Wurstner, S. K.; Thorne, P. D.; Freedman, V. L.; Murray, C. J.; Bergeron, M. P.

    2002-12-01

    A regional-scale, three-dimensional groundwater flow and transport modeling effort has been undertaken to quantify the environmental consequences of past waste disposal activities and support ongoing environmental management activities at the U.S. Department of Energy's Hanford Site. An important aspect of this effort is the identification and quantification of uncertainties associated with model predictions. It is recognized that such uncertainties arise not only from selection of inappropriate groundwater model parameters (parameter error), but also from the underlying conceptualization of the groundwater system (model error). Therefore, we have adopted an approach to uncertainty characterization that involves the evaluation of multiple alternative conceptual models (ACMs) within an inverse modeling framework. The initial step in implementation of the framework was the development of a multi-processor implementation of the UCODE inverse modeling system and application of the inverse framework to update parameter estimates from a prior deterministic model. A preliminary first-order uncertainty analysis was performed based on the model results. At the same time, site geologists developed an improved conceptual model of the 3D structure of the aquifer system. Inverse modeling of the updated conceptual model led to estimates of some parameters, especially specific yield, that were not plausible, indicating that there were problems with the conceptual model. As a result, additional ACMs were developed and subjected to inverse analysis, including an alternative with modified boundary conditions (leaky underlying bedrock), an alternative incorporating surface recharge modifications based on surface run-on from an adjacent topographic feature, and an alternative incorporating an improved description of the timing and volume of waste discharges arriving at the water table (upper model boundary). Model predictions of transient hydraulic heads under each ACM were compared

  10. Astrophysical site(s of r-process elements in galactic chemodynamical evolution model

    Directory of Open Access Journals (Sweden)

    Hirai Yutaka

    2016-01-01

    Full Text Available Astrophysical site(s of rapid neutron-capture process (r-process is (are not identified yet. Although core-collapse supernovae have been regarded as one of the possible candidates of the astrophysical site of r-process, nucleosynthesis studies suggest that serious difficulties in core-collapse supernovae to produce heavy elements with mass number of ≳110. Recent studies show that neutron star mergers (NSMs can synthesize these elements due to their neutron rich environment. Some chemical evolution studies of the Milky Way halo, however, hardly reproduce the observed star-to-star scatters of the abundance ratios of r-process elements (e.g., Eu in extremely metal-poor stars. This is because of their low rate (∼ 10−4 yr−1 for a Milky Way size galaxy and long merger time (≳ 100 Myr. This problem might be solved if the stars in the Galactic halo are consisted of the stars formed in dwarf galaxies where the star formation efficiencies were very low. In this study, we carry out numerical simulations of galactic chemo-dynamical evolution using an N-body/smoothed particle hydrodynamics code. We construct detailed chemo-dynamical evolution model for the Local Group dwarf spheroidal galaxies (dSphs assuming that the NSMs are the major source of r-process elements. Our models successfully reproduce the observed dispersion in [Eu/Fe] as a function of [Fe/H] if we set merger time of NSMs, ≲ 300 Myr with the Galactic NSM rate of ∼ 10−4 yr−1. In addition, our results are consistent with the observed metallicity distribution of dSphs. In the early phase (≲1 Gyr of galaxy evolution is constant due to low star formation efficiency of dSphs. This study supports the idea that NSMs are the major site of r-process nucleosynthesis.

  11. Controlling activation site density by low-energy far-field stimulation in cardiac tissue

    Science.gov (United States)

    Hörning, Marcel; Takagi, Seiji; Yoshikawa, Kenichi

    2012-06-01

    Tachycardia and fibrillation are potentially fatal arrhythmias associated with the formation of rotating spiral waves in the heart. Presently, the termination of these types of arrhythmia is achieved by use of antitachycardia pacing or cardioversion. However, these techniques have serious drawbacks, in that they either have limited application or produce undesirable side effects. Low-energy far-field stimulation has recently been proposed as a superior therapy. This proposed therapeutic method would exploit the phenomenon in which the application of low-energy far-field shocks induces a large number of activation sites (“virtual electrodes”) in tissue. It has been found that the formation of such sites can lead to the termination of undesired states in the heart and the restoration of normal beating. In this study we investigate a particular aspect of this method. Here we seek to determine how the activation site density depends on the applied electric field through in vitro experiments carried out on neonatal rat cardiac tissue cultures. The results indicate that the activation site density increases exponentially as a function of the intracellular conductivity and the level of cell isotropy. Additionally, we report numerical results obtained from bidomain simulations of the Beeler-Reuter model that are quantitatively consistent with our experimental results. Also, we derive an intuitive analytical framework that describes the activation site density and provides useful information for determining the ratio of longitudinal to transverse conductivity in a cardiac tissue culture. The results obtained here should be useful in the development of an actual therapeutic method based on low-energy far-field pacing. In addition, they provide a deeper understanding of the intrinsic properties of cardiac cells.

  12. Three dimensional visualization in support of Yucca Mountain Site characterization activities

    International Nuclear Information System (INIS)

    An understanding of the geologic and hydrologic environment for the proposed high-level nuclear waste repository at Yucca Mountain, NV is a critical component of site characterization activities. Conventional methods allow visualization of geologic data in only two or two and a half dimensions. Recent advances in computer workstation hardware and software now make it possible to create interactive three dimensional visualizations. Visualization software has been used to create preliminary two-, two-and-a-half-, and three-dimensional visualizations of Yucca Mountain structure and stratigraphy. The three dimensional models can also display lithologically dependent or independent parametric data. Yucca Mountain site characterization studies that will be supported by this capability include structural, lithologic, and hydrologic modeling, and repository design

  13. Site-scale groundwater flow modelling of Aberg

    Energy Technology Data Exchange (ETDEWEB)

    Walker, D. [Duke Engineering and Services (United States); Gylling, B. [Kemakta Konsult AB, Stockholm (Sweden)

    1998-12-01

    The Swedish Nuclear Fuel and Waste Management Company (SKB) SR 97 study is a comprehensive performance assessment illustrating the results for three hypothetical repositories in Sweden. In support of SR 97, this study examines the hydrogeologic modelling of the hypothetical site called Aberg, which adopts input parameters from the Aespoe Hard Rock Laboratory in southern Sweden. This study uses a nested modelling approach, with a deterministic regional model providing boundary conditions to a site-scale stochastic continuum model. The model is run in Monte Carlo fashion to propagate the variability of the hydraulic conductivity to the advective travel paths from representative canister locations. A series of variant cases addresses uncertainties in the inference of parameters and the boundary conditions. The study uses HYDRASTAR, the SKB stochastic continuum groundwater modelling program, to compute the heads, Darcy velocities at each representative canister position and the advective travel times and paths through the geosphere. The nested modelling approach and the scale dependency of hydraulic conductivity raise a number of questions regarding the regional to site-scale mass balance and the method`s self-consistency. The transfer of regional heads via constant head boundaries preserves the regional pattern recharge and discharge in the site-scale model, and the regional to site-scale mass balance is thought to be adequate. The upscaling method appears to be approximately self-consistent with respect to the median performance measures at various grid scales. A series of variant cases indicates that the study results are insensitive to alternative methods on transferring boundary conditions from the regional model to the site-scale model. The flow paths, travel times and simulated heads appear to be consistent with on-site observations and simple scoping calculations. The variabilities of the performance measures are quite high for the Base Case, but the

  14. Site-scale groundwater flow modelling of Aberg

    International Nuclear Information System (INIS)

    The Swedish Nuclear Fuel and Waste Management Company (SKB) SR 97 study is a comprehensive performance assessment illustrating the results for three hypothetical repositories in Sweden. In support of SR 97, this study examines the hydrogeologic modelling of the hypothetical site called Aberg, which adopts input parameters from the Aespoe Hard Rock Laboratory in southern Sweden. This study uses a nested modelling approach, with a deterministic regional model providing boundary conditions to a site-scale stochastic continuum model. The model is run in Monte Carlo fashion to propagate the variability of the hydraulic conductivity to the advective travel paths from representative canister locations. A series of variant cases addresses uncertainties in the inference of parameters and the boundary conditions. The study uses HYDRASTAR, the SKB stochastic continuum groundwater modelling program, to compute the heads, Darcy velocities at each representative canister position and the advective travel times and paths through the geosphere. The nested modelling approach and the scale dependency of hydraulic conductivity raise a number of questions regarding the regional to site-scale mass balance and the method's self-consistency. The transfer of regional heads via constant head boundaries preserves the regional pattern recharge and discharge in the site-scale model, and the regional to site-scale mass balance is thought to be adequate. The upscaling method appears to be approximately self-consistent with respect to the median performance measures at various grid scales. A series of variant cases indicates that the study results are insensitive to alternative methods on transferring boundary conditions from the regional model to the site-scale model. The flow paths, travel times and simulated heads appear to be consistent with on-site observations and simple scoping calculations. The variabilities of the performance measures are quite high for the Base Case, but the

  15. Site-Specific Seismic Site Response Model for the Waste Treatment Plant, Hanford, Washington

    International Nuclear Information System (INIS)

    The seismic design basis for the Waste Treatment Plant (WTP) at the Department of Energy's Hanford Site near Richland, Washington, was established in 1999 based on an extensive probabilistic seismic hazard analysis completed in 1996 by Geomatrix Consultants, Inc. In subsequent years, the Defense Nuclear Facilities Safety Board (DNFSB) staff questioned the some of the assumptions used in developing the seismic design basis, particularly the adequacy of the site geotechnical surveys. Existing site-specific shear wave velocity data were considered insufficient to reliably use California earthquake response data to directly predict ground motions at the Hanford Site. To address this concern, the Department of Energy's Office of River Protection (ORP) and Pacific Northwest National Laboratory (PNNL) developed and executed a plan for acquiring site-specific soil data down to approximately 500 feet, and for reanalyzing the effects of deeper layers of sediments interbedded with basalt. New geophysical data were acquired, analyzed, and interpreted with respect to existing geologic information gathered from other Hanford-related projects in the WTP area. Existing data from deep boreholes were assembled and interpreted to produce a model of the deeper rock layers consisting of inter-layered basalts and sedimentary interbeds. These data were analyzed statistically to determine the variability of seismic velocities. The earthquake ground motion response was simulated on a large number of models resulting from a weighted logic tree approach that addressed the geologic and geophysical uncertainties. Weights in the logic tree were chosen by a working group based on the strength or weakness of the available data for each combination of logic tree parameters. Finally, interim design ground motion spectra were developed to envelope the remaining uncertainties. The results of this study demonstrate that the site-specific soil structure (Hanford and Ringold formations) beneath the WTP

  16. Management of Ground and Groundwater Contamination on a Compact Site Constrained by Ongoing Activities

    International Nuclear Information System (INIS)

    the design of a new characterisation project has had to be constantly reworked to ensure fragile plants, site services, current operations and decommissioning projects are not impacted. 2. Assessment of Risk to the public and workforce. Risks need to be assessed for the short, medium and long term. The main pathways to receptors are through groundwater or excavations. Risks to the public are complicated through the proximity of the site to major receptors such as the sea and a near-by farm. As entry to the site is controlled, excavations into contaminated ground are only possible by members of the workforce whose activities are managed to minimise any risk. This is through a system of excavation permits and authorisations for disposal of excavated material which can add significant time and cost to construction projects on site. 3. Prioritisation of remediation. Large volumes of impacted ground and groundwater sit beneath fragile buildings with significant inventories. With current decommissioning schedules whole-scale remediation of ground and groundwater near or under key buildings cannot commence for at least another 40 plus years. Early remediation and/or containment of groundwater further away from the source terms and remediation of smaller accessible areas of contamination are being considered and will be assessed through a comprehensive optioneering process. Long term clean-up strategies run into the early part of the 22. Century, making any predictions as to the end-use of the site and therefore clean-up criteria for current projects difficult to determine. Management of information and data is key in establishing this strategy and information relevant to contaminated land has been collected in various forms over the 60 year history of the site. This data and information is currently being pulled together by the Land Quality team where it can be put into a form that can be easily assessed, visualised and modelled as well as being managed and stored for future

  17. Aespoe modelling task force - experiences of the site specific flow and transport modelling (in detailed and site scale)

    International Nuclear Information System (INIS)

    The Aespoe Task Force on modelling of groundwater flow and transport of solutes was initiated in 1992. The Task Force shall be a forum for the organisations supporting the Aespoe Hard Rock Laboratory Project to interact in the area of conceptual and numerical modelling of groundwater flow and solute transport in fractured rock. Much emphasis is put on building of confidence in the approaches and methods in use for modelling of groundwater flow and nuclide migration in order to demonstrate their use for performance and safety assessment. The modelling work within the Task Force is linked to the experiments performed at the Aespoe Laboratory. As the first Modelling Task, a large scale pumping and tracer experiment called LPT2 was chosen. This was the final part of the characterisation work for the Aespoe site before the construction of the laboratory in 1990. The construction of the Aespoe HRL access tunnel caused an even larger hydraulic disturbance on a much larger scale than that caused by the LPT2 pumping test. This was regarded as an interesting test case for the conceptual and numerical models of the Aespoe site developed during Task No 1, and was chosen as the third Modelling Task. The aim of Task 3 can be seen from two different perspectives. The Aespoe HRL project saw it as a test of their ability to define a conceptual and structural model of the site that can be utilised by independent modelling groups and be transformed to a predictive groundwater flow model. The modelling groups saw it as a means of understanding groundwater flow in a large fractured rock volume and of testing their computational tools. A general conclusion is that Task 3 has served these purposes well. Non-sorbing tracers tests, made as a part of the TRUE-experiments were chosen as the next predictive modelling task. A preliminary comparison between model predictions made by the Aespoe Task Force and the experimental results, shows that most modelling teams predicted breakthrough from

  18. Monoclonal antibody against the active site of caeruloplasmin and the ELISA system detecting active caeruloplasmin.

    Science.gov (United States)

    Hiyamuta, S; Ito, K

    1994-04-01

    Serum caeruloplasmin deficiency is a characteristic biochemical abnormality found in patients with Wilson's disease, but the mechanism of this disease is unknown. Although the phenylenediamine oxidase activity of serum caeruloplasmin is markedly low in patients with Wilson's disease, mRNA of caeruloplasmin exists to some extent. To investigate the deficiency of caeruloplasmin oxidase activity in Wilson's disease, we generated 14 monoclonal antibodies (MAbs) and selected ID1, which had the strongest reactivity, and ID2, which had neutralizing ability. We also established a system to measure active caeruloplasmin specifically using these MAbs. These MAbs and the system will be useful tools in analyzing the active site of caeruloplasmin in patients with Wilson's disease.

  19. Robotics and Automation Activities at the Savannah River Site: A Site Report for SUBWOG 39F

    International Nuclear Information System (INIS)

    The Savannah River Site has successfully used robots, teleoperators, and remote video to reduce exposure to ionizing radiation, improve worker safety, and improve the quality of operations. Previous reports have described the use of mobile teleoperators in coping with a high level liquid waste spill, the removal of highly contaminated equipment, and the inspection of nuclear reactor vessels. This report will cover recent applications at the Savannah River, as well as systems which SRS has delivered to other DOE site customers

  20. Site-scale groundwater flow modelling of Ceberg

    International Nuclear Information System (INIS)

    The Swedish Nuclear Fuel and Waste Management Company (SKB) SR 97 study is a comprehensive performance assessment illustrating the results for three hypothetical repositories in Sweden. In support of SR 97, this study examines the hydrogeologic modelling of the hypothetical site called Ceberg, which adopts input parameters from the SKB study site near Gideaa, in northern Sweden. This study uses a nested modelling approach, with a deterministic regional model providing boundary conditions to a site-scale stochastic continuum model. The model is run in Monte Carlo fashion to propagate the variability of the hydraulic conductivity to the advective travel paths from representative canister locations. A series of variant cases addresses uncertainties in the inference of parameters and the model of conductive fracture zones. The study uses HYDRASTAR, the SKB stochastic continuum (SC) groundwater modelling program, to compute the heads, Darcy velocities at each representative canister position, and the advective travel times and paths through the geosphere. The volumetric flow balance between the regional and site-scale models suggests that the nested modelling and associated upscaling of hydraulic conductivities preserve mass balance only in a general sense. In contrast, a comparison of the base and deterministic (Variant 4) cases indicates that the upscaling is self-consistent with respect to median travel time and median canister flux. These suggest that the upscaling of hydraulic conductivity is approximately self-consistent but the nested modelling could be improved. The Base Case yields the following results for a flow porosity of εf 10-4 and a flow-wetted surface area of ar = 0.1 m2/(m3 rock): The median travel time is 1720 years. The median canister flux is 3.27x10-5 m/year. The median F-ratio is 1.72x106 years/m. The base case and the deterministic variant suggest that the variability of the travel times within individual realisations is due to the position of

  1. Rate of hydrolysis in ATP synthase is fine-tuned by  -subunit motif controlling active site conformation

    KAUST Repository

    Beke-Somfai, T.

    2013-01-23

    Computer-designed artificial enzymes will require precise understanding of how conformation of active sites may control barrier heights of key transition states, including dependence on structure and dynamics at larger molecular scale. F(o)F(1) ATP synthase is interesting as a model system: a delicate molecular machine synthesizing or hydrolyzing ATP using a rotary motor. Isolated F(1) performs hydrolysis with a rate very sensitive to ATP concentration. Experimental and theoretical results show that, at low ATP concentrations, ATP is slowly hydrolyzed in the so-called tight binding site, whereas at higher concentrations, the binding of additional ATP molecules induces rotation of the central γ-subunit, thereby forcing the site to transform through subtle conformational changes into a loose binding site in which hydrolysis occurs faster. How the 1-Å-scale rearrangements are controlled is not yet fully understood. By a combination of theoretical approaches, we address how large macromolecular rearrangements may manipulate the active site and how the reaction rate changes with active site conformation. Simulations reveal that, in response to γ-subunit position, the active site conformation is fine-tuned mainly by small α-subunit changes. Quantum mechanics-based results confirm that the sub-Ångström gradual changes between tight and loose binding site structures dramatically alter the hydrolysis rate.

  2. SR-Site groundwater flow modelling methodology, setup and results

    International Nuclear Information System (INIS)

    As a part of the license application for a final repository for spent nuclear fuel at Forsmark, the Swedish Nuclear Fuel and Waste Management Company (SKB) has undertaken three groundwater flow modelling studies. These are performed within the SR-Site project and represent time periods with different climate conditions. The simulations carried out contribute to the overall evaluation of the repository design and long-term radiological safety. Three time periods are addressed; the Excavation and operational phases, the Initial period of temperate climate after closure, and the Remaining part of the reference glacial cycle. The present report is a synthesis of the background reports describing the modelling methodology, setup, and results. It is the primary reference for the conclusions drawn in a SR-Site specific context concerning groundwater flow during the three climate periods. These conclusions are not necessarily provided explicitly in the background reports, but are based on the results provided in these reports. The main results and comparisons presented in the present report are summarised in the SR-Site Main report

  3. SR-Site groundwater flow modelling methodology, setup and results

    Energy Technology Data Exchange (ETDEWEB)

    Selroos, Jan-Olof (Swedish Nuclear Fuel and Waste Management Co., Stockholm (Sweden)); Follin, Sven (SF GeoLogic AB, Taeby (Sweden))

    2010-12-15

    As a part of the license application for a final repository for spent nuclear fuel at Forsmark, the Swedish Nuclear Fuel and Waste Management Company (SKB) has undertaken three groundwater flow modelling studies. These are performed within the SR-Site project and represent time periods with different climate conditions. The simulations carried out contribute to the overall evaluation of the repository design and long-term radiological safety. Three time periods are addressed; the Excavation and operational phases, the Initial period of temperate climate after closure, and the Remaining part of the reference glacial cycle. The present report is a synthesis of the background reports describing the modelling methodology, setup, and results. It is the primary reference for the conclusions drawn in a SR-Site specific context concerning groundwater flow during the three climate periods. These conclusions are not necessarily provided explicitly in the background reports, but are based on the results provided in these reports. The main results and comparisons presented in the present report are summarised in the SR-Site Main report.

  4. The active sites of supported silver particle catalysts in formaldehyde oxidation.

    Science.gov (United States)

    Chen, Yaxin; Huang, Zhiwei; Zhou, Meijuan; Hu, Pingping; Du, Chengtian; Kong, Lingdong; Chen, Jianmin; Tang, Xingfu

    2016-08-01

    Surface silver atoms with upshifted d-orbitals are identified as the catalytically active sites in formaldehyde oxidation by correlating their activity with the number of surface silver atoms, and the degree of the d-orbital upshift governs the catalytic performance of the active sites. PMID:27406403

  5. Double site-bond percolation model for biomaterial implants

    CERN Document Server

    Mely, H

    2011-01-01

    We present a double site-bond percolation model to account, on the one hand, for the vascularization and/or resorption of biomaterial implant in bones and, on the other hand, for its mechanical continuity. The transformation of the implant into osseous material, and the dynamical formation/destruction of this osseous material is accounted for by creation and destruction of links and sites in two, entangled, networks. We identify the relevant parameters to describe the implant and its evolution, and separate their biological or chemical origin from their physical one. We classify the various phenomena in the two regimes, percolating or non-percolating, of the networks. We present first numerical results in two dimensions.

  6. A comparative structure-function analysis of active-site inhibitors of Vibrio cholerae cholix toxin.

    Science.gov (United States)

    Lugo, Miguel R; Merrill, A Rod

    2015-09-01

    Cholix toxin from Vibrio cholerae is a novel mono-ADP-ribosyltransferase (mART) toxin that shares structural and functional properties with Pseudomonas aeruginosa exotoxin A and Corynebacterium diphtheriae diphtheria toxin. Herein, we have used the high-resolution X-ray structure of full-length cholix toxin in the apo form, NAD(+) bound, and 10 structures of the cholix catalytic domain (C-domain) complexed with several strong inhibitors of toxin enzyme activity (NAP, PJ34, and the P-series) to study the binding mode of the ligands. A pharmacophore model based on the active pose of NAD(+) was compared with the active conformation of the inhibitors, which revealed a cationic feature in the side chain of the inhibitors that may determine the active pose. Moreover, a conformational search was conducted for the missing coordinates of one of the main active-site loops (R-loop). The resulting structural models were used to evaluate the interaction energies and for 3D-QSAR modeling. Implications for a rational drug design approach for mART toxins were derived.

  7. Understanding brittle deformation at the Olkiluoto site. Literature compilation for site characterization and geological modelling

    International Nuclear Information System (INIS)

    The present report arose from the belief that geological modelling at Olkiluoto, Finland, where an underground repository for spent nuclear fuel is at present under construction, could be significantly improved by an increased understanding of the phenomena being modelled, in conjunction with the more sophisticated data acquisition and processing methods which are now being introduced. Since the geological model is the necessary basis for the rock engineering and hydrological models, which in turn provide the foundation for identifying suitable rock volumes underground and for demonstrating longterm safety, its scientific basis is of critical importance. As a contribution to improving this scientific basis, the literature on brittle deformation in the Earth's crust has been reviewed, and key references chosen and arranged, with the particular geology of the Olkiluoto site in mind. The result is a compilation of scientific articles, reports and books on some of the key topics, which are of significance for an improved understanding of brittle deformation of hard, crystalline rocks, such as those typical for Olkiluoto. The report is subdivided into six Chapters, covering (1) background information, (2) important aspects of the fabric of intact rock, (3) fracture mechanics and brittle microtectonics, (4) fracture data acquisition and processing, for the statistical characterisation and modelling of fracture systems, (5) the characterisation of brittle deformation zones for deterministic modelling, and (6) the regional geological framework of the Olkiluoto site. The Chapters are subdivided into a number of Sections, and each Section into a number of Topics. The citations are mainly collected under each Topic, embedded in a short explanatory text or listed chronologically without comment. The systematic arrangement of Chapters, Sections and Topics is such that the Table of Contents can be used to focus quickly on the theme of interest without the necessity of looking

  8. Model summary report for the safety assessment SR-Site

    Energy Technology Data Exchange (ETDEWEB)

    Vahlund, Fredrik; Zetterstroem Evins, Lena (Swedish Nuclear Fuel and Waste Management Co., Stockholm (Sweden)); Lindgren, Maria (Kemakta Konsult AB, Stockholm (Sweden))

    2010-12-15

    This document is the model summary report for the safety assessment SR-Site. In the report, the quality assurance (QA) measures conducted for assessment codes are presented together with the chosen QA methodology. In the safety assessment project SR-Site, a large number of numerical models are used to analyse the system and to show compliance. In order to better understand how the different models interact and how information are transferred between the different models Assessment Model Flowcharts, AMFs, are used. From these, different modelling tasks can be identify and the computer codes used. As a large number of computer codes are used in the assessment the complexity of these differs to a large extent, some of the codes are commercial while others are developed especially for the assessment at hand. QA requirements must on the one hand take this diversity into account and on the other hand be well defined. In the methodology section of the report the following requirements are defined for all codes: - It must be demonstrated that the code is suitable for its purpose. - It must be demonstrated that the code has been properly used. - It must be demonstrated that the code development process has followed appropriate procedures and that the code produces accurate results. - It must be described how data are transferred between the different computational tasks. Although the requirements are identical for all codes in the assessment, the measures used to show that the requirements are fulfilled will be different for different types of codes (for instance due to the fact that for some software the source-code is not available for review). Subsequent to the methodology section, each assessment code is presented together with a discussion on how the requirements are met

  9. Model summary report for the safety assessment SR-Site

    International Nuclear Information System (INIS)

    This document is the model summary report for the safety assessment SR-Site. In the report, the quality assurance (QA) measures conducted for assessment codes are presented together with the chosen QA methodology. In the safety assessment project SR-Site, a large number of numerical models are used to analyse the system and to show compliance. In order to better understand how the different models interact and how information are transferred between the different models Assessment Model Flowcharts, AMFs, are used. From these, different modelling tasks can be identify and the computer codes used. As a large number of computer codes are used in the assessment the complexity of these differs to a large extent, some of the codes are commercial while others are developed especially for the assessment at hand. QA requirements must on the one hand take this diversity into account and on the other hand be well defined. In the methodology section of the report the following requirements are defined for all codes: - It must be demonstrated that the code is suitable for its purpose. - It must be demonstrated that the code has been properly used. - It must be demonstrated that the code development process has followed appropriate procedures and that the code produces accurate results. - It must be described how data are transferred between the different computational tasks. Although the requirements are identical for all codes in the assessment, the measures used to show that the requirements are fulfilled will be different for different types of codes (for instance due to the fact that for some software the source-code is not available for review). Subsequent to the methodology section, each assessment code is presented together with a discussion on how the requirements are met

  10. Interpretation and Modelling of Data from Site Investigations for a Geological Disposal facility located in the UK

    Science.gov (United States)

    Clark, H.; Bailey, L.; Parkes, A.

    2012-04-01

    The Radioactive Waste Management Directorate (RWMD) of the Nuclear Decommissioning Authority (NDA) has been given the responsibility for implementing geological disposal in the United Kingdom. The implementation process envisaged is that once a candidate site or sites for a geological disposal facility have been identified, NDA-RWMD will undertake surface-based investigations at the site or sites. The information acquired through these investigations would be used as an input to the development of the safety case, for engineering design of the disposal facility and to demonstrate confidence to the key stakeholders that the potential disposal facility site is adequately understood. NDA-RWMD proposes to develop and present the information derived from site characterisation activities in the form of a single integrated Site Descriptive Model, i.e. a description of the geometry, properties of the bedrock and water, and the associated interacting processes and mechanisms, which will be used to address the information requirements of all the end users (including the safety case). It is anticipated that, in a similar way to the approach adopted by international radioactive waste programmes led by SKB (Sweden) and Posiva (Finland), the integrated Site Descriptive Model will be divided into parts comprising clearly defined disciplines which may form either chapters or discipline-based models such as: • Geology; • Hydrogeology; • Hydrochemistry; • Geotechnical; • Radionuclide Transport Properties; • Thermal Properties; and • Biosphere. The integrated Site Descriptive Model will evolve as understanding of the particular site advances and will describe the current understanding of a specific site and, where relevant, the historical development of conditions at the site where this supports the conceptual understanding. The Site Descriptive Model will not include prediction of the future evolution of the conditions at the site: this will be an important component

  11. Water-rock interaction modelling and uncertainties of mixing modelling. SDM-Site Laxemar

    Energy Technology Data Exchange (ETDEWEB)

    Gimeno, Maria J.; Auque, Luis F.; Gomez, Javier B.; Acero, Patricia (Univ. of Zaragoza, Zaragoza (Spain))

    2009-01-15

    The overall objectives of hydrogeochemical description for Laxemar are to establish a detailed understanding of the hydrogeochemical conditions at the site and to develop models that fulfil the needs identified by the safety assessment groups during the site investigation phase. Issues of concern to safety assessment are radionuclide transport and technical barrier behaviour, both of which are dependent on the chemistry of groundwater and pore water and their evolution with time. The work has involved the development of descriptive and mathematical models for groundwaters in relation to rock domains, fracture domains and deformation zones. Past climate changes are the major driving force for hydrogeochemical changes and therefore of fundamental importance for understanding the palaeohydrogeological, palaeohydrogeochemical and present evolution of groundwater in the crystalline bedrock of the Fennoscandian Shield. Understanding current undisturbed hydrochemical conditions at the proposed repository site is important when predicting future changes in groundwater chemistry. The causes of copper corrosion and/or bentonite degradation are of particular interest as they may jeopardise the long-term integrity of the planned SKB repository system. Thus, the following variables are considered for the hydrogeochemical site descriptive modelling: pH, Eh, sulphur species, iron, manganese, carbonate, phosphate, nitrogen species, total dissolved solids (TDS), isotopes, colloids, fulvic and humic acids and microorganisms. In addition, dissolved gases (e.g. carbon dioxide, methane and hydrogen) are of interest because of their likely participation in microbial reactions. In this series of reports, the final hydrogeochemical evaluation work of the site investigation at the Laxemar site, is presented. The work was conducted by SKB's hydrogeochemical project group, ChemNet, which consists of independent consultants and Univ. researchers with expertise in geochemistry

  12. Water-rock interaction modelling and uncertainties of mixing modelling. SDM-Site Laxemar

    International Nuclear Information System (INIS)

    The overall objectives of hydrogeochemical description for Laxemar are to establish a detailed understanding of the hydrogeochemical conditions at the site and to develop models that fulfil the needs identified by the safety assessment groups during the site investigation phase. Issues of concern to safety assessment are radionuclide transport and technical barrier behaviour, both of which are dependent on the chemistry of groundwater and pore water and their evolution with time. The work has involved the development of descriptive and mathematical models for groundwaters in relation to rock domains, fracture domains and deformation zones. Past climate changes are the major driving force for hydrogeochemical changes and therefore of fundamental importance for understanding the palaeohydrogeological, palaeohydrogeochemical and present evolution of groundwater in the crystalline bedrock of the Fennoscandian Shield. Understanding current undisturbed hydrochemical conditions at the proposed repository site is important when predicting future changes in groundwater chemistry. The causes of copper corrosion and/or bentonite degradation are of particular interest as they may jeopardise the long-term integrity of the planned SKB repository system. Thus, the following variables are considered for the hydrogeochemical site descriptive modelling: pH, Eh, sulphur species, iron, manganese, carbonate, phosphate, nitrogen species, total dissolved solids (TDS), isotopes, colloids, fulvic and humic acids and microorganisms. In addition, dissolved gases (e.g. carbon dioxide, methane and hydrogen) are of interest because of their likely participation in microbial reactions. In this series of reports, the final hydrogeochemical evaluation work of the site investigation at the Laxemar site, is presented. The work was conducted by SKB's hydrogeochemical project group, ChemNet, which consists of independent consultants and Univ. researchers with expertise in geochemistry, hydrochemistry

  13. Identification of residues involved in nucleotidyltransferase activity of JHP933 from helicobacter pyloriby site-directed mutagenesis

    Directory of Open Access Journals (Sweden)

    Ye Xianren

    2016-01-01

    Full Text Available Helicobacter pylori is a well-known bacterial pathogen involved in the development of peptic ulcer, gastric adenocarcinoma and other forms of gastric cancer. Evidence has suggested that certain strain-specific genes in the plasticity region may play key roles in the pathogenesis of H. pylori-associated gastroduodenal diseases. Therefore there is considerable interest in the strain-specific genes located in the plasticity regions of H. pylori. JHP933 is encoded by the gene in the plasticity region of H. pylori strain J99. Recently, the crystal structure of JHP933 has confirmed it as a nucleotidyltransferase (NTase superfamily protein and a putative active site has been proposed. However, no evidence from direct functional assay has been presented to confirm the active site and little is known about the functional mechanism of JHP933. Here, through superimposition with Cid1/NTP complex structures, we modelled the complex structures of JHP933 with different NTPs. Based on the models and using rational site-directed mutagenesis combined with enzymatic activity assays, we confirm the active site and identify several residues important for the nucleotidyl transferring function of JHP933. Furthermore, mutations of these active site residues result in the abolishment of the nucleotidyltransferase activity of JHP933. This work provides preliminary insight into the molecular mechanism underlying the pathophysiological role in H. pylori infection of JHP933 as a novel NTase superfamily protein.

  14. Insights Into the Effects of Internal Variability, External Variability, and Active Sites on Heterogeneous Ice Nucleation

    Science.gov (United States)

    Beydoun, H.; Sullivan, R. C.; Polen, M.

    2015-12-01

    Heterogeneous ice nucleation (HIN) remains one of the outstanding problems in cloud physics and atmospheric science. Experimental challenges in properly simulating HIN processes with relevant atmospheric conditions have largely contributed to the absence of a consistent and comprehensive parameterization. Here we formulate a new ice active surface site-based stochastic model of HIN with the unique feature of invoking a continuum assumption on the ice nucleation activity (contact angle) of an aerosol particle's surface. The result is a particle specific property g that defines a distribution of local surface ice nucleation rates. Upon integration this yields a full freezing probability function for an ice nucleating particle. Current cold plate droplet freezing measurements provide a great resource for studying the freezing ability of many atmospheric aerosol systems. A method based on statistical significance and critical area analysis is presented that can resolve the two-dimensional nature of the ice nucleation ability of aerosol particles: variability in active sites and freezing rates along an individual particle's surface, as well as variability between two particles of the same type in an aerosol population. When applied to published experimental data, the method demonstrates its ability to comprehensively interpret droplet freezing spectra of variable particle mass and surface area concentrations. By fitting the high concentration freezing curves to a statistically significant active site density function, the lower concentration freezing curves are successfully fitted via a process of random sampling from the statistically significant distribution. Using the new scheme, comprehensive parameterizations that can track the frozen fraction of cloud droplets in larger atmospheric models are derived.

  15. Identification of Active Edge Sites for Electrochemical H2 Evolution from MoS2 Nanocatalysts

    DEFF Research Database (Denmark)

    Jaramillo, Thomas; Jørgensen, Kristina Pilt; Bonde, Jacob;

    2007-01-01

    The identification of the active sites in heterogeneous catalysis requires a combination of surface sensitive methods and reactivity studies. We determined the active site for hydrogen evolution, a reaction catalyzed by precious metals, on nanoparticulate molybdenum disulfide (MoS2) by atomically...... resolving the surface of this catalyst before measuring electrochemical activity in solution. By preparing MoS2 nanoparticles of different sizes, we systematically varied the distribution of surface sites on MoS2 nanoparticles on Au(111), which we quantified with scanning tunneling microscopy....... Electrocatalytic activity measurements for hydrogen evolution correlate linearly with the number of edge sites on the MoS2 catalyst....

  16. Identification of promiscuous ene-reductase activity by mining structural databases using active site constellations.

    Science.gov (United States)

    Steinkellner, Georg; Gruber, Christian C; Pavkov-Keller, Tea; Binter, Alexandra; Steiner, Kerstin; Winkler, Christoph; Lyskowski, Andrzej; Schwamberger, Orsolya; Oberer, Monika; Schwab, Helmut; Faber, Kurt; Macheroux, Peter; Gruber, Karl

    2014-01-01

    The exploitation of catalytic promiscuity and the application of de novo design have recently opened the access to novel, non-natural enzymatic activities. Here we describe a structural bioinformatic method for predicting catalytic activities of enzymes based on three-dimensional constellations of functional groups in active sites ('catalophores'). As a proof-of-concept we identify two enzymes with predicted promiscuous ene-reductase activity (reduction of activated C-C double bonds) and compare them with known ene-reductases, that is, members of the Old Yellow Enzyme family. Despite completely different amino acid sequences, overall structures and protein folds, high-resolution crystal structures reveal equivalent binding modes of typical Old Yellow Enzyme substrates and ligands. Biochemical and biocatalytic data show that the two enzymes indeed possess ene-reductase activity and reveal an inverted stereopreference compared with Old Yellow Enzymes for some substrates. This method could thus be a tool for the identification of viable starting points for the development and engineering of novel biocatalysts. PMID:24954722

  17. A Graph Based Framework to Model Virus Integration Sites.

    Science.gov (United States)

    Fronza, Raffaele; Vasciaveo, Alessandro; Benso, Alfredo; Schmidt, Manfred

    2016-01-01

    With next generation sequencing thousands of virus and viral vector integration genome targets are now under investigation to uncover specific integration preferences and to define clusters of integration, termed common integration sites (CIS), that may allow to assess gene therapy safety or to detect disease related genomic features such as oncogenes. Here, we addressed the challenge to: 1) define the notion of CIS on graph models, 2) demonstrate that the structure of CIS enters in the category of scale-free networks and 3) show that our network approach analyzes CIS dynamically in an integrated systems biology framework using the Retroviral Transposon Tagged Cancer Gene Database (RTCGD) as a testing dataset. PMID:27257470

  18. Testing the methodology for site descriptive modelling. Application for the Laxemar area

    Energy Technology Data Exchange (ETDEWEB)

    Andersson, Johan [JA Streamflow AB, Aelvsjoe (Sweden); Berglund, Johan [SwedPower AB, Stockholm (Sweden); Follin, Sven [SF Geologic AB, Stockholm (Sweden); Hakami, Eva [Itasca Geomekanik AB, Stockholm (Sweden); Halvarson, Jan [Swedish Nuclear Fuel and Waste Management Co, Stockholm (Sweden); Hermanson, Jan [Golder Associates AB, Stockholm (Sweden); Laaksoharju, Marcus [Geopoint (Sweden); Rhen, Ingvar [Sweco VBB/VIAK, Stockholm (Sweden); Wahlgren, C.H. [Sveriges Geologiska Undersoekning, Uppsala (Sweden)

    2002-08-01

    and after this compared to check for potential inconsistencies. The processed data are used for three-dimensional modelling. The geological modelling provides the geometrical framework for the modelling in other disciplines and results in descriptions of geometry and properties of deformation zones of sizes down to 'local major zones' Q-10 km) and geometry and properties of rock domains. Two descriptions have been derived; the Base Geological Model and the Alternative Geological Model. Given the limited amount of data, regions of the model domain still have quite uncertain descriptions. The geometry is represented using a 3D CAD software (RVS), which is also used as an active interpretation tool for the geometric modelling. The base for the hydrogeological modelling is the Geological Model with its identified volumetric objects. Essential hydrogeological evaluation tools include: assessment of single hole hydraulic tests, interpretation of interference tests and numerical modelling of groundwater flow tests and other observations. The resulting hydrogeological description comprises hydraulic properties for defined geometrical units and boundary conditions for the present day conditions for the rock volume defined by the Base Geological Model. The major tasks for the hydrogeochemical evaluation include: (i) characterisation of undisturbed groundwater chemistry including the origin, depth/lateral distribution and the turnover time; (ii) focusing on data of importance for the safety evaluation such as pH, Eh, chloride, sulphide, colloids and microbes; (iii) identification of possible dissolved oxygen at repository depth. The hydrogeochemical description concerns distribution of the major water types, the water type mixing proportions and lists the major type of chemical reactions occurring at the site. Even if much of the modelling can be done in parallel with other disciplines, consistency checks with hydrogeology can and have been made. These comparisons

  19. Proposal of a web site engagement scale and research model. Analysis of the influence of intra web site comparative behaviour

    OpenAIRE

    Hyder Espiñeira, Antonio

    2011-01-01

    A Web site engagement scale is suggested that serves as the basis of a two part-model. The first part studies the influence of the online comparative behaviour of consumers on Web site engagement using data obtained from respondents that selected a holiday package on an online travel agency capable of remotely tracing and recording their intra-Web page and intra-Web site behaviour. The second part of the model studies the influence of Web site engagement on consequences highly relevant for on...

  20. Proportion cured models applied to 23 cancer sites in Norway.

    Science.gov (United States)

    Cvancarova, Milada; Aagnes, Bjarte; Fosså, Sophie D; Lambert, Paul C; Møller, Bjørn; Bray, Freddie

    2013-04-01

    Statistical cure is reached when a group of patients has the same mortality as cancer-free individuals. Cure models predict the cured proportion and the median survival of fatal cases. Cure models have seldom been applied and tested systematically across all major cancer sites. Incidence and follow-up data on 23 cancer sites recorded at the Cancer Registry of Norway 1963-2007 were obtained. Mixture cure models were fitted to obtain trends and up-to-date estimates (based on period approach) assuming cured and uncured groups exist. The model converged for cancers of the mouth and pharynx, oesophagus, stomach, colon, rectum, liver, gallbladder, pancreas, lung and trachea, ovary, kidney, bladder, CNS, non-Hodgkin lymphoma (only for males) and leukemia. The proportion of cured patients increased 1963-2002 for both sexes, with the largest changes (in percent) seen for leukemia (46.4 and 46.7) and CNS (35.9, 42.0), males given first. Median survival time for the uncured cases increased for colon and rectal cancer, and there was a three- fold increase in median survival time for patients with fatal ovarian cancers. Cancers of bladder and CNS had the highest up-to-date proportion cured (in percent), 67.4 and 64.0, respectively, pancreas and liver were amongst the lowest (5.7 and 9.9, respectively). Cure models are useful when monitoring progress in cancer care, but must be applied and interpreted with caution. The absolute estimates of the cure proportion are speculative and should not be calculated where cure is not medically anticipated. PMID:22927104

  1. Mapping of the Allosteric Site in Cholesterol Hydroxylase CYP46A1 for Efavirenz, a Drug That Stimulates Enzyme Activity.

    Science.gov (United States)

    Anderson, Kyle W; Mast, Natalia; Hudgens, Jeffrey W; Lin, Joseph B; Turko, Illarion V; Pikuleva, Irina A

    2016-05-27

    Cytochrome P450 46A1 (CYP46A1) is a microsomal enzyme and cholesterol 24-hydroxylase that controls cholesterol elimination from the brain. This P450 is also a potential target for Alzheimer disease because it can be activated pharmacologically by some marketed drugs, as exemplified by efavirenz, the anti-HIV medication. Previously, we suggested that pharmaceuticals activate CYP46A1 allosterically through binding to a site on the cytosolic protein surface, which is different from the enzyme active site facing the membrane. Here we identified this allosteric site for efavirenz on CYP46A1 by using a combination of hydrogen-deuterium exchange coupled to MS, computational modeling, site-directed mutagenesis, and analysis of the CYP46A1 crystal structure. We also mapped the binding region for the CYP46A1 redox partner oxidoreductase and found that the allosteric and redox partner binding sites share a common border. On the basis of the data obtained, we propose the mechanism of CYP46A1 allostery and the pathway for the signal transmission from the P450 allosteric site to the active site. PMID:27056331

  2. O2 activation by binuclear Cu sites: Noncoupled versus exchange coupled reaction mechanisms

    Science.gov (United States)

    Chen, Peng; Solomon, Edward I.

    2004-09-01

    Binuclear Cu proteins play vital roles in O2 binding and activation in biology and can be classified into coupled and noncoupled binuclear sites based on the magnetic interaction between the two Cu centers. Coupled binuclear Cu proteins include hemocyanin, tyrosinase, and catechol oxidase. These proteins have two Cu centers strongly magnetically coupled through direct bridging ligands that provide a mechanism for the 2-electron reduction of O2 to a µ-2:2 side-on peroxide bridged species. This side-on bridged peroxo-CuII2 species is activated for electrophilic attack on the phenolic ring of substrates. Noncoupled binuclear Cu proteins include peptidylglycine -hydroxylating monooxygenase and dopamine -monooxygenase. These proteins have binuclear Cu active sites that are distant, that exhibit no exchange interaction, and that activate O2 at a single Cu center to generate a reactive CuII/O2 species for H-atom abstraction from the C-H bond of substrates. O2 intermediates in the coupled binuclear Cu enzymes can be trapped and studied spectroscopically. Possible intermediates in noncoupled binuclear Cu proteins can be defined through correlation to mononuclear CuII/O2 model complexes. The different intermediates in these two classes of binuclear Cu proteins exhibit different reactivities that correlate with their different electronic structures and exchange coupling interactions between the binuclear Cu centers. These studies provide insight into the role of exchange coupling between the Cu centers in their reaction mechanisms.

  3. Preliminary siting activities for new waste handling facilities at the Idaho National Engineering Laboratory

    International Nuclear Information System (INIS)

    The Idaho Waste Processing Facility, the Mixed and Low-Level Waste Treatment Facility, and the Mixed and Low-Level Waste Disposal Facility are new waste treatment, storage, and disposal facilities that have been proposed at the Idaho National Engineering Laboratory (INEL). A prime consideration in planning for such facilities is the selection of a site. Since spring of 1992, waste management personnel at the INEL have been involved in activities directed to this end. These activities have resulted in the (a) identification of generic siting criteria, considered applicable to either treatment or disposal facilities for the purpose of preliminary site evaluations and comparisons, (b) selection of six candidate locations for siting,and (c) site-specific characterization of candidate sites relative to selected siting criteria. This report describes the information gathered in the above three categories for the six candidate sites. However, a single, preferred site has not yet been identified. Such a determination requires an overall, composite ranking of the candidate sites, which accounts for the fact that the sites under consideration have different advantages and disadvantages, that no single site is superior to all the others in all the siting criteria, and that the criteria should be assigned different weighing factors depending on whether a site is to host a treatment or a disposal facility. Stakeholder input should now be solicited to help guide the final selection. This input will include (a) siting issues not already identified in the siting, work to date, and (b) relative importances of the individual siting criteria. Final site selection will not be completed until stakeholder input (from the State of Idaho, regulatory agencies, the public, etc.) in the above areas has been obtained and a strategy has been developed to make a composite ranking of all candidate sites that accounts for all the siting criteria

  4. Preliminary siting activities for new waste handling facilities at the Idaho National Engineering Laboratory

    Energy Technology Data Exchange (ETDEWEB)

    Taylor, D.D.; Hoskinson, R.L.; Kingsford, C.O.; Ball, L.W.

    1994-09-01

    The Idaho Waste Processing Facility, the Mixed and Low-Level Waste Treatment Facility, and the Mixed and Low-Level Waste Disposal Facility are new waste treatment, storage, and disposal facilities that have been proposed at the Idaho National Engineering Laboratory (INEL). A prime consideration in planning for such facilities is the selection of a site. Since spring of 1992, waste management personnel at the INEL have been involved in activities directed to this end. These activities have resulted in the (a) identification of generic siting criteria, considered applicable to either treatment or disposal facilities for the purpose of preliminary site evaluations and comparisons, (b) selection of six candidate locations for siting,and (c) site-specific characterization of candidate sites relative to selected siting criteria. This report describes the information gathered in the above three categories for the six candidate sites. However, a single, preferred site has not yet been identified. Such a determination requires an overall, composite ranking of the candidate sites, which accounts for the fact that the sites under consideration have different advantages and disadvantages, that no single site is superior to all the others in all the siting criteria, and that the criteria should be assigned different weighing factors depending on whether a site is to host a treatment or a disposal facility. Stakeholder input should now be solicited to help guide the final selection. This input will include (a) siting issues not already identified in the siting, work to date, and (b) relative importances of the individual siting criteria. Final site selection will not be completed until stakeholder input (from the State of Idaho, regulatory agencies, the public, etc.) in the above areas has been obtained and a strategy has been developed to make a composite ranking of all candidate sites that accounts for all the siting criteria.

  5. 78 FR 33908 - Commercial Wind Lease Issuance and Site Assessment Activities on the Atlantic Outer Continental...

    Science.gov (United States)

    2013-06-05

    ... renewable energy leases and subsequent site characterization activities (geophysical, geotechnical, archaeological, and biological surveys needed to develop specific project proposals on those leases) in an... from leasing, site characterization, and site assessment in and around the Call Area (76 FR 51391)....

  6. Complement receptor 2-mediated targeting of complement inhibitors to sites of complement activation.

    Science.gov (United States)

    Song, Hongbin; He, Chun; Knaak, Christian; Guthridge, Joel M; Holers, V Michael; Tomlinson, Stephen

    2003-06-01

    In a strategy to specifically target complement inhibitors to sites of complement activation and disease, recombinant fusion proteins consisting of a complement inhibitor linked to a C3 binding region of complement receptor (CR) 2 were prepared and characterized. Natural ligands for CR2 are C3 breakdown products deposited at sites of complement activation. Fusion proteins were prepared consisting of a human CR2 fragment linked to either the N terminus or C terminus of soluble forms of the membrane complement inhibitors decay accelerating factor (DAF) or CD59. The targeted complement inhibitors bound to C3-opsonized cells, and all were significantly more effective (up to 20-fold) than corresponding untargeted inhibitors at protecting target cells from complement. CR2 fusion proteins also inhibited CR3-dependent adhesion of U937 cells to C3 opsonized erythrocytes, indicating a second potential anti-inflammatory mechanism of CR2 fusion proteins, since CR3 is involved in endothelial adhesion and diapedesis of leukocytes at inflammatory sites. Finally, the in vivo validity of the targeting strategy was confirmed by the demonstration that CR2-DAF, but not soluble DAF, targets to the kidney in mouse models of lupus nephritis that are associated with renal complement deposition. PMID:12813023

  7. Complement receptor 2-mediated targeting of complement inhibitors to sites of complement activation.

    Science.gov (United States)

    Song, Hongbin; He, Chun; Knaak, Christian; Guthridge, Joel M; Holers, V Michael; Tomlinson, Stephen

    2003-06-01

    In a strategy to specifically target complement inhibitors to sites of complement activation and disease, recombinant fusion proteins consisting of a complement inhibitor linked to a C3 binding region of complement receptor (CR) 2 were prepared and characterized. Natural ligands for CR2 are C3 breakdown products deposited at sites of complement activation. Fusion proteins were prepared consisting of a human CR2 fragment linked to either the N terminus or C terminus of soluble forms of the membrane complement inhibitors decay accelerating factor (DAF) or CD59. The targeted complement inhibitors bound to C3-opsonized cells, and all were significantly more effective (up to 20-fold) than corresponding untargeted inhibitors at protecting target cells from complement. CR2 fusion proteins also inhibited CR3-dependent adhesion of U937 cells to C3 opsonized erythrocytes, indicating a second potential anti-inflammatory mechanism of CR2 fusion proteins, since CR3 is involved in endothelial adhesion and diapedesis of leukocytes at inflammatory sites. Finally, the in vivo validity of the targeting strategy was confirmed by the demonstration that CR2-DAF, but not soluble DAF, targets to the kidney in mouse models of lupus nephritis that are associated with renal complement deposition.

  8. Geochemical modelling of the groundwater at the Olkiluoto site

    International Nuclear Information System (INIS)

    A preliminary model for probable processes responsible for the evolution of the groundwater at the nuclear waste investigation site Olkiluoto (in Finland) is presented. The hydrological data was collected from boreholes drilled down to 1000-m depth into crystalline bedrock. Based on chemical, isotopic, petrographic and hydrological data as well as ion plots and speciation calculations with PHREEQE the thermodynamic controls on the water composition and trends constraining these processes are evaluated. In order to determine the reactions which can explain the changes along the flow path during the evolution of groundwater system and to determine to which extent these reactions take place, mass-balance calculations with the NETPATH program were used. Mass transfer calculations with the EQ6 program were used to test the feasibility of the model derived, to predict reaction paths and composition of equilibrium solutions for the redox reactions. (57 refs., 43 figs., 10 tabs.)

  9. Optical Turbulence Characterization at LAMOST Site: Observations and Models

    CERN Document Server

    Liu, L -Y; Yao, Y -Q; Vernin, J; Chadid, M; Wang, H -S; Yin, J; Wang, Y -P

    2015-01-01

    Atmospheric optical turbulence seriously limits the performance of high angular resolution instruments. An 8-night campaign of measurements was carried out at the LAMOST site in 2011, to characterize the optical turbulence. Two instruments were set up during the campaign: a Differential Image Motion Monitor (DIMM) used to measure the total atmospheric seeing, and a Single Star Scidar (SSS) to measure the vertical profiles of the turbulence C_n^2(h) and the horizontal wind velocity V(h). The optical turbulence parameters are also calculated with the Weather Research and Forecasting (WRF) model coupled with the Trinquet-Vernin model, which describes optical effects of atmospheric turbulence by using the local meteorological parameters. This paper presents assessment of the optical parameters involved in high angular resolution astronomy. Its includes seeing, isoplanatic angle, coherence time, coherence etendue, vertical profiles of optical turbulence intensity _n^2(h)$ and horizontal wind speed V(h). The median...

  10. Prioritizing conservation activities using reserve site selection methods and population viability analysis.

    Science.gov (United States)

    Newbold, Stephen C; Siikamäki, Juha

    2009-10-01

    In recent years a large literature on reserve site selection (RSS) has developed at the interface between ecology, operations research, and environmental economics. Reserve site selection models use numerical optimization techniques to select sites for a network of nature reserves for protecting biodiversity. In this paper, we develop a population viability analysis (PVA) model for salmon and incorporate it into an RSS framework for prioritizing conservation activities in upstream watersheds. We use spawner return data for three closely related salmon stocks in the upper Columbia River basin and estimates of the economic costs of watershed protection from NOAA to illustrate the framework. We compare the relative cost-effectiveness of five alternative watershed prioritization methods, based on various combinations of biological and economic information. Prioritization based on biological benefit-economic cost comparisons and accounting for spatial interdependencies among watersheds substantially outperforms other more heuristic methods. When using this best-performing prioritization method, spending 10% of the cost of protecting all upstream watersheds yields 79% of the biological benefits (increase in stock persistence) from protecting all watersheds, compared to between 20% and 64% for the alternative methods. We also find that prioritization based on either costs or benefits alone can lead to severe reductions in cost-effectiveness. PMID:19831069

  11. Methodology for geometric modelling. Presentation and administration of site descriptive models

    International Nuclear Information System (INIS)

    This report presents a methodology to construct, visualise and present geoscientific descriptive models based on data from the site investigations, which the SKB currently performs, to build an underground nuclear waste disposal facility in Sweden. It is designed for interaction with SICADA (SKB:s site characterisation database) and RVS (SKB:s Rock Visualisation System). However, the concepts of the methodology are general and can be used with other tools capable of handling 3D geometries and parameters. The descriptive model is intended to be an instrument where site investigation data from all disciplines are put together to form a comprehensive visual interpretation of the studied rock mass. The methodology has four main components: 1. Construction of a geometrical model of the interpreted main structures at the site. 2. Description of the geoscientific characteristics of the structures. 3. Description and geometrical implementation of the geometric uncertainties in the interpreted model structures. 4. Quality system for the handling of the geometrical model, its associated database and some aspects of the technical auditing. The geometrical model forms a basis for understanding the main elements and structures of the investigated site. Once the interpreted geometries are in place in the model, the system allows for adding descriptive and quantitative data to each modelled object through a system of intuitive menus. The associated database allows each geometrical object a complete quantitative description of all geoscientific disciplines, variabilities, uncertainties in interpretation and full version history. The complete geometrical model and its associated database of object descriptions are to be recorded in a central quality system. Official, new and old versions of the model are administered centrally in order to have complete quality assurance of each step in the interpretation process. The descriptive model is a cornerstone in the understanding of the

  12. Active-Site Hydration and Water Diffusion in Cytochrome P450cam: A Highly Dynamic Process

    Energy Technology Data Exchange (ETDEWEB)

    Miao, Yinglong [ORNL; Baudry, Jerome Y [ORNL

    2011-01-01

    Long-timescale molecular dynamics simulations (300 ns) are performed on both the apo- (i.e., camphor-free) and camphor-bound cytochrome P450cam (CYP101). Water diffusion into and out of the protein active site is observed without biased sampling methods. During the course of the molecular dynamics simulation, an average of 6.4 water molecules is observed in the camphor-binding site of the apo form, compared to zero water molecules in the binding site of the substrate-bound form, in agreement with the number of water molecules observed in crystal structures of the same species. However, as many as 12 water molecules can be present at a given time in the camphor-binding region of the active site in the case of apo-P450cam, revealing a highly dynamic process for hydration of the protein active site, with water molecules exchanging rapidly with the bulk solvent. Water molecules are also found to exchange locations frequently inside the active site, preferentially clustering in regions surrounding the water molecules observed in the crystal structure. Potential-of-mean-force calculations identify thermodynamically favored trans-protein pathways for the diffusion of water molecules between the protein active site and the bulk solvent. Binding of camphor in the active site modifies the free-energy landscape of P450cam channels toward favoring the diffusion of water molecules out of the protein active site.

  13. Blogs and Social Network Sites as Activity Systems: Exploring Adult Informal Learning Process through Activity Theory Framework

    Science.gov (United States)

    Heo, Gyeong Mi; Lee, Romee

    2013-01-01

    This paper uses an Activity Theory framework to explore adult user activities and informal learning processes as reflected in their blogs and social network sites (SNS). Using the assumption that a web-based space is an activity system in which learning occurs, typical features of the components were investigated and each activity system then…

  14. Description of surface hydrology and near-surface hydrogeology at Forsmark. Site descriptive modelling SDM. Site Forsmark

    Energy Technology Data Exchange (ETDEWEB)

    Johansson, Per-Olof (Artesia Grundvattenkonsult AB, Taeby (Sweden))

    2008-12-15

    This report describes the modelling of the surface hydrology and near-surface hydrogeology that was performed for the final site descriptive model of Forsmark produced in the site investigation stage, SDM-Site Forsmark. The comprehensive investigation and monitoring programme forms a strong basis for the developed conceptual and descriptive model of the hydrological and near-surface hydrological system of the site investigation area. However, there are some remaining uncertainties regarding the interaction of deep and near-surface groundwater and surface water of importance for the understanding of the system: The groundwaters in till below Lake Eckarfjaerden, Lake Gaellbotraesket, Lake Fiskarfjaerden and Lake Bolundsfjaerden have high salinities. The hydrological and hydrochemical interpretations indicate that these waters are relict waters of mainly marine origin. From the perspective of the overall water balance, the water below the central parts of the lakes can be considered as stagnant. However, according to the hydrochemical interpretation, these waters also contain weak signatures of deep saline water. Rough chloride budget calculations for the Gaellbotraesket depression also raise the question of a possible upward flow of deep groundwater. No absolute conclusion can be drawn from the existing data analyses regarding the key question of whether there is a small ongoing upward flow of deep saline water. However, Lake Bolundsfjaerden is an exception where the clear downward flow gradient from the till to the bedrock excludes the possibility of an active deep saline source. The available data indicate that there are no discharge areas for flow systems involving deep bedrock groundwater in the northern part of the tectonic lens, where the repository is planned to be located (the so-called 'target area'). However, it can not be excluded that such discharge areas exist. Data indicate that the prevailing downward vertical flow gradients from the QD to

  15. Geological Model of the Olkiluoto Site. Version 2.0

    International Nuclear Information System (INIS)

    The rocks of Olkiluoto can be divided into two major classes: 1) supracrustal high-grade metamorphic rocks including various migmatitic gneisses, tonalitic-granodioriticgranitic gneisses, mica gneisses, quartz gneisses and mafic gneisses, and 2) igneous rocks including pegmatitic granites and diabase dykes. The migmatitic gneisses can further be divided into three subgroups in terms of the type of migmatite structure: veined gneisses, stromatic gneisses and diatexitic gneisses. On the basis of refolding and crosscutting relationships, the metamorphic supracrustal rocks have been subjected to polyphased ductile deformation, consisting of five stages, the D2 being locally the most intensive phase, producing thrust-related folding, strong migmatisation and pervasive foliation. In 3D modelling of the lithological units, an assumption has been made, on the basis of measurements in the outcrops, investigation trenches and drill cores, that the pervasive, composite foliation produced as a result of polyphase ductile deformation has a rather constant attitude in the ONKALO area. Consequently, the strike and dip of the foliation has been used as a tool, through which the lithologies have been correlated between the drillholes and from the surface to the drillholes. In addition, the largest ductile deformation zones and tectonic units are described in 3D model. The bedrock at the Olkiluoto site has been subjected to extensive hydrothermal alteration, which has taken place at reasonably low temperature conditions, the estimated temperature interval being from slightly over 300 deg C to less than 100 deg C. Two types of alteration can be observed: firstly, pervasive alteration and secondly fracturecontrolled alteration. Clay mineralisation and sulphidisation are the most prominent alteration events in the site area. Sulphides are located in the uppermost part of the model volume following roughly the foliation and lithological trend. Kaolinite is also mainly located in the

  16. Geological Model of the Olkiluoto Site. Version 2.0

    Energy Technology Data Exchange (ETDEWEB)

    Aaltonen, I. (ed.) (and others)

    2010-10-15

    The rocks of Olkiluoto can be divided into two major classes: 1) supracrustal high-grade metamorphic rocks including various migmatitic gneisses, tonalitic-granodioriticgranitic gneisses, mica gneisses, quartz gneisses and mafic gneisses, and 2) igneous rocks including pegmatitic granites and diabase dykes. The migmatitic gneisses can further be divided into three subgroups in terms of the type of migmatite structure: veined gneisses, stromatic gneisses and diatexitic gneisses. On the basis of refolding and crosscutting relationships, the metamorphic supracrustal rocks have been subjected to polyphased ductile deformation, consisting of five stages, the D2 being locally the most intensive phase, producing thrust-related folding, strong migmatisation and pervasive foliation. In 3D modelling of the lithological units, an assumption has been made, on the basis of measurements in the outcrops, investigation trenches and drill cores, that the pervasive, composite foliation produced as a result of polyphase ductile deformation has a rather constant attitude in the ONKALO area. Consequently, the strike and dip of the foliation has been used as a tool, through which the lithologies have been correlated between the drillholes and from the surface to the drillholes. In addition, the largest ductile deformation zones and tectonic units are described in 3D model. The bedrock at the Olkiluoto site has been subjected to extensive hydrothermal alteration, which has taken place at reasonably low temperature conditions, the estimated temperature interval being from slightly over 300 deg C to less than 100 deg C. Two types of alteration can be observed: firstly, pervasive alteration and secondly fracturecontrolled alteration. Clay mineralisation and sulphidisation are the most prominent alteration events in the site area. Sulphides are located in the uppermost part of the model volume following roughly the foliation and lithological trend. Kaolinite is also mainly located in the

  17. Early Site Permit Demonstration Program: Recommendations for communication activities and public participation in the Early Site Permit Demonstration Program

    International Nuclear Information System (INIS)

    On October 24, 1992, President Bush signed into law the National Energy Policy Act of 1992. The bill is a sweeping, comprehensive overhaul of the Nation's energy laws, the first in more than a decade. Among other provisions, the National Energy Policy Act reforms the licensing process for new nuclear power plants by adopting a new approach developed by the US Nuclear Regulatory Commission (NRC) in 1989, and upheld in court in 1992. The NRC 10 CFR Part 52 rule is a three-step process that guarantees public participation at each step. The steps are: early site permit approval; standard design certifications; and, combined construction/operating licenses for nuclear power reactors. Licensing reform increases an organization's ability to respond to future baseload electricity generation needs with less financial risk for ratepayers and the organization. Costly delays can be avoided because design, safety and siting issues will be resolved before a company starts to build a plant. Specifically, early site permit approval allows for site suitability and acceptability issues to be addressed prior to an organization's commitment to build a plant. Responsibility for site-specific activities, including communications and public participation, rests with those organizations selected to try out early site approval. This plan has been prepared to assist those companies (referred to as sponsoring organizations) in planning their communications and public involvement programs. It provides research findings, information and recommendations to be used by organizations as a resource and starting point in developing their own plans

  18. Early Site Permit Demonstration Program: Recommendations for communication activities and public participation in the Early Site Permit Demonstration Program

    Energy Technology Data Exchange (ETDEWEB)

    1993-01-27

    On October 24, 1992, President Bush signed into law the National Energy Policy Act of 1992. The bill is a sweeping, comprehensive overhaul of the Nation`s energy laws, the first in more than a decade. Among other provisions, the National Energy Policy Act reforms the licensing process for new nuclear power plants by adopting a new approach developed by the US Nuclear Regulatory Commission (NRC) in 1989, and upheld in court in 1992. The NRC 10 CFR Part 52 rule is a three-step process that guarantees public participation at each step. The steps are: early site permit approval; standard design certifications; and, combined construction/operating licenses for nuclear power reactors. Licensing reform increases an organization`s ability to respond to future baseload electricity generation needs with less financial risk for ratepayers and the organization. Costly delays can be avoided because design, safety and siting issues will be resolved before a company starts to build a plant. Specifically, early site permit approval allows for site suitability and acceptability issues to be addressed prior to an organization`s commitment to build a plant. Responsibility for site-specific activities, including communications and public participation, rests with those organizations selected to try out early site approval. This plan has been prepared to assist those companies (referred to as sponsoring organizations) in planning their communications and public involvement programs. It provides research findings, information and recommendations to be used by organizations as a resource and starting point in developing their own plans.

  19. Geological model of the Olkiluoto site. Version 1.0

    International Nuclear Information System (INIS)

    The rocks of Olkiluoto can be divided into two major classes: (1) supracrustal high-grade metamorphic rocks including various migmatitic gneisses, tonalitic-granodioriticgranitic gneisses, mica gneisses, quartz gneisses and mafic gneisses, and (2) igneous rocks including pegmatitic granites and diabase dykes. The migmatitic gneisses can further be divided into three subgroups in terms of the type of migmatite structure: veined gneisses, stromatic gneisses and diatexitic gneisses. On the basis of refolding and crosscutting relationships, the metamorphic supracrustal rocks have been subjected to polyphased ductile deformation, consisting of five stages, the D2 being locally the most intensive phase, producing thrust-related folding, strong migmatisation and pervasive foliation. In 3D modelling of the lithological units, an assumption has been made, on the basis of measurements in the outcrops, investigation trenches and drill cores, that the pervasive, composite foliation produced as a result of polyphase ductile deformation has a rather constant attitude in the ONKALO area. Consequently, the strike and dip of the foliation has been used as a tool, through which the lithologies have been correlated between the drillholes and from the surface to the drillholes. The bedrock at the Olkiluoto site has been subjected to extensive hydrothermal alteration, which has taken place at reasonably low temperature conditions, the estimated temperature interval being from slightly over 300 deg C to less than 100 deg C. Two types of alteration can be observed: (1) pervasive (disseminated) alteration and (2) fracture-controlled (veinlet) alteration. Kaolinisation and sulphidisation are the most prominent alteration events in the site area. Sulphides are located in the uppermost part of the model volume following roughly the lithological trend (slightly dipping to the SE). Kaolinite is also located in the uppermost part, but the orientation is opposite to the main lithological trend

  20. 76 FR 30696 - Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites

    Science.gov (United States)

    2011-05-26

    ... Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites AGENCY: Department of... eligible active uranium and thorium processing site licensees for reimbursement under Title X of the Energy... requires DOE to reimburse eligible uranium and thorium licensees for certain costs of...

  1. 76 FR 24871 - Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites

    Science.gov (United States)

    2011-05-03

    ... Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites AGENCY: Department of... from eligible active uranium and thorium processing site licensees for reimbursement under Title X of...). Title X requires DOE to reimburse eligible uranium and thorium licensees for certain costs...

  2. Identification of ice nucleation active sites on feldspar dust particles.

    Science.gov (United States)

    Zolles, Tobias; Burkart, Julia; Häusler, Thomas; Pummer, Bernhard; Hitzenberger, Regina; Grothe, Hinrich

    2015-03-19

    Mineral dusts originating from Earth's crust are known to be important atmospheric ice nuclei. In agreement with earlier studies, feldspar was found as the most active of the tested natural mineral dusts. Here we investigated in closer detail the reasons for its activity and the difference in the activity of the different feldspars. Conclusions are drawn from scanning electron microscopy, X-ray powder diffraction, infrared spectroscopy, and oil-immersion freezing experiments. K-feldspar showed by far the highest ice nucleation activity. Finally, we give a potential explanation of this effect, finding alkali-metal ions having different hydration shells and thus an influence on the ice nucleation activity of feldspar surfaces. PMID:25584435

  3. Active site densities, oxygen activation and adsorbed reactive oxygen in alcohol activation on npAu catalysts.

    Science.gov (United States)

    Wang, Lu-Cun; Friend, C M; Fushimi, Rebecca; Madix, Robert J

    2016-07-01

    The activation of molecular O2 as well as the reactivity of adsorbed oxygen species is of central importance in aerobic selective oxidation chemistry on Au-based catalysts. Herein, we address the issue of O2 activation on unsupported nanoporous gold (npAu) catalysts by applying a transient pressure technique, a temporal analysis of products (TAP) reactor, to measure the saturation coverage of atomic oxygen, its collisional dissociation probability, the activation barrier for O2 dissociation, and the facility with which adsorbed O species activate methanol, the initial step in the catalytic cycle of esterification. The results from these experiments indicate that molecular O2 dissociation is associated with surface silver, that the density of reactive sites is quite low, that adsorbed oxygen atoms do not spill over from the sites of activation onto the surrounding surface, and that methanol reacts quite facilely with the adsorbed oxygen atoms. In addition, the O species from O2 dissociation exhibits reactivity for the selective oxidation of methanol but not for CO. The TAP experiments also revealed that the surface of the npAu catalyst is saturated with adsorbed O under steady state reaction conditions, at least for the pulse reaction. PMID:27376884

  4. Description of regolith at Laxemar-Simpevarp. Site descriptive modelling SDM-Site Laxemar

    Energy Technology Data Exchange (ETDEWEB)

    Sohlenius, Gustav; Hedenstroem, Anna (Geological Survey of Sweden (SGU), Uppsala (Sweden))

    2008-11-15

    This report compiles all known available information regarding the regolith in the Laxemar-Simpevarp regional model area. Regolith refers to the loose deposits overlying the bedrock. In the Laxemar-Simpevarp area, all known regolith was deposited during the Quaternary period and is consequently often referred to as Quaternary deposits (QD). In the terrestrial areas the uppermost part of the regolith, which has been affected by climate and vegetation, is referred to as soil. The geographical and stratigraphical distributions of the regolith have been used to construct a model showing the distribution of regolith depths in the whole model area. The stratigraphical units shown in the regolith depth and stratigraphy model have been characterised with respect to physical and chemical properties. Most of the data used for that characterisation have been obtained from the site investigation but some data were taken from the literature. All QD in the Laxemar area have most probably been deposited during or after the latest deglaciation. The ice sheet in the area moved from the north-west during the latest ice age. The Baltic Sea completely covered the investigated area after the latest deglaciation c 12,000 BC. Land uplift was fastest during the first few thousand years following the deglaciation and has subsequently decreased to the present value of 1 mm/year. Older QD have been eroded in areas exposed to waves and currents and the material has later been redeposited. Fine-grained sediments have been deposited on the floor of bays and in other sheltered positions. Peat has accumulated in many of the wetlands situated in topographically low positions. The groundwater table in many of the former wetlands has been artificially lowered to obtain land for forestry and agriculture, which has caused the peat to partly or completely oxidise. As land uplift proceeds, some new areas are being subjected to erosion at the same time as other new areas are becoming lakes and sheltered

  5. An Explosion Aftershock Model with Application to On-Site Inspection

    Science.gov (United States)

    Ford, Sean R.; Labak, Peter

    2016-01-01

    An estimate of aftershock activity due to a theoretical underground nuclear explosion is produced using an aftershock rate model. The model is developed with data from the Nevada National Security Site, formerly known as the Nevada Test Site, and the Semipalatinsk Test Site, which we take to represent soft-rock and hard-rock testing environments, respectively. Estimates of expected magnitude and number of aftershocks are calculated using the models for different testing and inspection scenarios. These estimates can help inform the Seismic Aftershock Monitoring System (SAMS) deployment in a potential Comprehensive Test Ban Treaty On-Site Inspection (OSI), by giving the OSI team a probabilistic assessment of potential aftershocks in the Inspection Area (IA). The aftershock assessment, combined with an estimate of the background seismicity in the IA and an empirically derived map of threshold magnitude for the SAMS network, could aid the OSI team in reporting. We apply the hard-rock model to a M5 event and combine it with the very sensitive detection threshold for OSI sensors to show that tens of events per day are expected up to a month after an explosion measured several kilometers away.

  6. Conceptual Model of Iodine Behavior in the Subsurface at the Hanford Site

    Energy Technology Data Exchange (ETDEWEB)

    Truex, Michael J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Lee, Brady D. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Johnson, Christian D. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Qafoku, Nikolla P. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Last, George V. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Lee, Michelle H. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Kaplan, Daniel I. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2015-09-01

    The fate and transport of 129I in the environment and potential remediation technologies are currently being studied as part of environmental remediation activities at the Hanford Site. A conceptual model describing the nature and extent of subsurface contamination, factors that control plume behavior, and factors relevant to potential remediation processes is needed to support environmental remedy decisions. Because 129I is an uncommon contaminant, relevant remediation experience and scientific literature are limited. Thus, the conceptual model also needs to both describe known contaminant and biogeochemical process information and to identify aspects about which additional information needed to effectively support remedy decisions. this document summarizes the conceptual model of iodine behavior relevant to iodine in the subsurface environment at the Hanford site.

  7. A descriptive ecosystem model - a strategy for model development during site investigations

    Energy Technology Data Exchange (ETDEWEB)

    Loefgren, Anders [Stockholm Univ. (Sweden). Dept. of Botany; Lindborg, Tobias [Swedish Nuclear Fuel and Waste Management Co., Stockholm (Sweden)

    2003-09-01

    This report describes a strategy for the development of a site descriptive model for the surface ecosystem on the potential deep repository sites. The surface ecosystem embraces many disciplines, and these have to be identified, described and integrated in order to construct a descriptive ecosystem model that describes and quantifies biotic and abiotic patterns and processes of importance for the ecosystem on the site. The descriptive model includes both present day conditions and historical information. The descriptive ecosystem model will be used to supply input data for the safety assessment and to serve as the baseline model for devising a monitoring program to detect short-term disturbances caused first by the site investigations and later by the construction of the deep repository. Furthermore, it will serve as a reference for future comparisons to determine more long-term effects or changes caused by the deep repository. The report adopts a non-site-specific approach focusing on the following aims: 1. To present and define the properties that will constitute the descriptive ecosystem model. 2. To present a methodology for determining those properties. 3. To describe and develop the framework for the descriptive ecosystem model by integrating the different properties. 4. To present vital data from other site descriptive models such as those for geology or hydrogeology that interacts with and affects the descriptive ecosystem model. The properties are described under four different sections: general physical properties of the landscape, the terrestrial system, the limnic system and the marine system. These headings are further subdivided into entities that integrate properties in relation to processes.

  8. A descriptive ecosystem model - a strategy for model development during site investigations

    International Nuclear Information System (INIS)

    This report describes a strategy for the development of a site descriptive model for the surface ecosystem on the potential deep repository sites. The surface ecosystem embraces many disciplines, and these have to be identified, described and integrated in order to construct a descriptive ecosystem model that describes and quantifies biotic and abiotic patterns and processes of importance for the ecosystem on the site. The descriptive model includes both present day conditions and historical information. The descriptive ecosystem model will be used to supply input data for the safety assessment and to serve as the baseline model for devising a monitoring program to detect short-term disturbances caused first by the site investigations and later by the construction of the deep repository. Furthermore, it will serve as a reference for future comparisons to determine more long-term effects or changes caused by the deep repository. The report adopts a non-site-specific approach focusing on the following aims: 1. To present and define the properties that will constitute the descriptive ecosystem model. 2. To present a methodology for determining those properties. 3. To describe and develop the framework for the descriptive ecosystem model by integrating the different properties. 4. To present vital data from other site descriptive models such as those for geology or hydrogeology that interacts with and affects the descriptive ecosystem model. The properties are described under four different sections: general physical properties of the landscape, the terrestrial system, the limnic system and the marine system. These headings are further subdivided into entities that integrate properties in relation to processes

  9. SR-Site Pre-modelling: Sensitivity studies of hydrogeological model variants for the Laxemar site using CONNECTFLOW

    Energy Technology Data Exchange (ETDEWEB)

    Joyce, Steven; Hoek, Jaap; Hartley, Lee (Serco (United Kingdom)); Marsic, Niko (Kemakta Konsult AB, Stockholm (Sweden))

    2010-12-15

    This study investigated a number of potential model variants of the SR-Can hydrogeological models of the temperate period and the sensitivity of the performance measures to the chosen parameters. This will help to guide the choice of potential variants for the SR-Site project and provide an input to design premises for the underground construction of the repository. It was found that variation of tunnel backfill properties in the tunnels had a significant effect on performance measures, but in the central area, ramps and shafts it had a lesser effect for those property values chosen. Variation of tunnel EDZ properties only had minor effects on performance measures. The presence of a crown space in the deposition tunnels had a significant effect on the tunnel performance measures and a lesser effect on the rock and EDZ performance measures. The presence of a deposition hole EDZ and spalling also had an effect on the performance measures.

  10. Assessment of former uranium sites and their ongoing remediation activities

    International Nuclear Information System (INIS)

    Carried out analysis on tailing's buildings operation shows that period for engineer barrier service, taking into account any catastrophic natural impacts, is too little in comparison with life-time of long-live radionuclides. Priorities should be defined by danger degree and isolation costs (protection optimization), therefore uncommon, non-traditional methods, developed taking into account natural factors for long-live waste (radionuclides) isolation are necessary. That's why, it is necessary to carry out specialized research and development, design and exploratory and other works on monitoring of social-ecological condition of these sites, as well as on demographic public diseases, living in these regions.

  11. Development and Verification of CFD Models for Modeling Wind Conditions on Forested Wind Turbine Sites

    DEFF Research Database (Denmark)

    Andersen, Morten Q.; Mortensen, Kasper; Nielsen, Daniel E.;

    2009-01-01

    This paper describes a proposed CFD model to simulate the wind conditions on a forested site. The model introduces porous subdomains representing the forests in the terrain. Obtained simulation values are compared to field measurements in- and outside a forest. Initial results are very promising...

  12. Nanoscale electrochemical patterning reveals the active sites for catechol oxidation at graphite surfaces.

    Science.gov (United States)

    Patel, Anisha N; McKelvey, Kim; Unwin, Patrick R

    2012-12-19

    Graphite-based electrodes (graphite, graphene, and nanotubes) are used widely in electrochemistry, and there is a long-standing view that graphite step edges are needed to catalyze many reactions, with the basal surface considered to be inert. In the present work, this model was tested directly for the first time using scanning electrochemical cell microscopy reactive patterning and shown to be incorrect. For the electro-oxidation of dopamine as a model process, the reaction rate was measured at high spatial resolution across a surface of highly oriented pyrolytic graphite. Oxidation products left behind in a pattern defined by the scanned electrochemical cell served as surface-site markers, allowing the electrochemical activity to be correlated directly with the graphite structure on the nanoscale. This process produced tens of thousands of electrochemical measurements at different locations across the basal surface, unambiguously revealing it to be highly electrochemically active, with step edges providing no enhanced activity. This new model of graphite electrodes has significant implications for the design of carbon-based biosensors, and the results are additionally important for understanding electrochemical processes on related sp(2)-hybridized materials such as pristine graphene and nanotubes.

  13. Synthesis and characterization of 18F-labeled active site inhibited factor VII (ASIS)

    DEFF Research Database (Denmark)

    Erlandsson, Maria; Nielsen, Carsten Haagen; Jeppesen, Troels Elmer;

    2015-01-01

    Activated factor VII blocked in the active site with Phe-Phe-Arg-chloromethyl ketone (active site inhibited factor VII (ASIS)) is a 50-kDa protein that binds with high affinity to its receptor, tissue factor (TF). TF is a transmembrane glycoprotein that plays an important role in, for example......, thrombosis, metastasis, tumor growth, and tumor angiogenesis. The aim of this study was to develop an 18F-labeled ASIS derivative to assess TF expression in tumors. Active site inhibited factor VII was labeled using N-succinimidyl-4-[18F]fluorobenzoate, and the [18F]ASIS was purified on a PD-10 desalting...

  14. Residents’ Environmental Conservation Behaviors at Tourist Sites: Broadening the Norm Activation Framework by Adopting Environment Attachment

    Directory of Open Access Journals (Sweden)

    Yuling Zhang

    2016-06-01

    Full Text Available Understanding the factors that affect residents’ environmental conservation behaviors help in managing the environment of tourist sites. This research provides an integrative understanding of how residents near tourist sites form their environmental conservation behaviors by merging the norm-activation model and cognitive-affective model into one theoretical framework. Results of the structural analysis from a sample of 642 residents showed that this study’s proposed composite model includes a satisfactory level of predictive power for environmental conservation behaviors. The findings identify the following two dimensions of awareness of environmental consequences as having a key role in predicting environmental conservation behaviors: (1 awareness of positive consequences of environmental protection; and (2 awareness of disaster consequences. Results also show that environment attachment and personal norms about environmentalism played a mediating role between awareness of environmental consequences and environmental conservation behaviors, and that personal norms about environmentalism were the most powerful factor in predicting behaviors. Several practical implications were derived from the research findings that can contribute to environment management policy both within and outside the field of tourism, mostly notably: (1 how the effective promotion of these factors can encourage environmental conservation behaviors for residents; and (2 how governments can develop and implement environmental management measures to improve locals’ awareness of positive consequences of environmental protection.

  15. Geochemical modelling of the Broubster natural analogue site, Caithness, Scotland

    International Nuclear Information System (INIS)

    The work described here forms part of an on going programme of research into natural radionuclide migration, and is primarily aimed at improving confidence in predictive models used for radiological assessment. Anomalously high concentrations of uranium, thorium and the rare earth elements (REE) are associated with peat-rich soils near Broubster, northern Scotland. The source of the anomaly has been traced to a hydrocarbon-containing mineralised zone within a uraniferous, calcareous Devonian sedimentary sequence. From there, the elements have been transported approximately 100 metres downslope and fixed within waterlogged peat deposits. The degree of concentration and fractional accompanying actinide transport is extreme. This report describes the results of a theoretical modelling exercise and complementary experimental study carried out to determine the chemical speciation of actinides at the Broubster site. Efforts made to identify mobilisation and retention mechanisms for uranium and thorium have led to the development of a simple model for actinide behaviour in the peat soils. Chemical transport of uranium has been simulated using the directly coupled CHEMTARD program. (author)

  16. HOW DO STUDENTS SELECT SOCIAL NETWORKING SITES? AN ANALYTIC HIERARCHY PROCESS (AHP) MODEL

    OpenAIRE

    Chun Meng Tang; Miang Hong Ngerng

    2015-01-01

    Social networking sites are popular among university students, and students today are indeed spoiled for choice. New emerging social networking sites sprout up amid popular sites, while some existing ones die out. Given the choice of so many social networking sites, how do students decide which one they will sign up for and stay on as an active user? The answer to this question is of interest to social networking site designers and marketers. The market of social networking sites is highly co...

  17. WAG 2 remedial investigation and site investigation site-specific work plan/health and safety checklist for the sediment transport modeling task

    International Nuclear Information System (INIS)

    This site-specific Work Plan/Health and Safety Checklist (WP/HSC) is a supplement to the general health and safety plan (HASP) for Waste Area Grouping (WAG) 2 remedial investigation and site investigation (WAG 2 RI ampersand SI) activities [Health and Safety Plan for the Remedial Investigation and Site Investigation of Waste Area Grouping 2 at the Oak Ridge National Laboratory, Oak Ridge, Tennessee (ORNL/ER-169)] and provides specific details and requirements for the WAG 2 RI ampersand SI Sediment Transport Modeling Task. This WP/HSC identifies specific site operations, site hazards, and any recommendations by Oak Ridge National Laboratory (ORNL) health and safety organizations [i.e., Industrial Hygiene (IH), Health Physics (HP), and/or Industrial Safety] that would contribute to the safe completion of the WAG 2 RI ampersand SI. Together, the general HASP for the WAG 2 RI ampersand SI (ORNL/ER-169) and the completed site-specific WP/HSC meet the health and safety planning requirements specified by 29 CFR 1910.120 and the ORNL Hazardous Waste Operations and Emergency Response (HAZWOPER) Program Manual. In addition to the health and safety information provided in the general HASP for the WAG 2 RI ampersand SI, details concerning the site-specific task are elaborated in this site-specific WP/HSC, and both documents, as well as all pertinent procedures referenced therein, will be reviewed by all field personnel prior to beginning operations

  18. Lipolytic activity from bacteria prospected in polluted portuary sites

    Directory of Open Access Journals (Sweden)

    Kaori Levy Fonseca

    2014-06-01

    The aim of this study was to isolate and identify the TBT resistant marine bacteria capable to produce extracellular lipases and then test the lipolytic activity of their extracts. For this purpose, TBT resistant bacteria (able to grow at 3 mM TBT from 7 Portuguese harbors were collected (Póvoa de Varzim (V; 41.376120,-8.766945, Leixões (L; 41.195238,- 8.684177, Aveiro (A; 40.645899,-8.727098, Figueira da Foz (F; 40.146848,-8.849176, Peniche (P; 39.355422,-9.375479, Setúbal (St; 38.521228,-8.887277 e Sines (S; 37.950219,-8.864599, isolated and then REP-PCR characterized. Their extracellular lipase activity was assayed by the method of Rhodamine B in solid culture medium. Rhodamine is a dye which together with fatty acids released by the hydrolysis of triacylglycerols, forms a fluorescent complex when exposed to ultraviolet light. The use of this test was due to its sensitivity in detecting lipase activity even in organisms with low production of extracellular lipases. Lipolytic extracts activities were estimated using p-nitrophenyl palmitate method for optimization of activity conditions. This highly sensitive spectrophotometric method estimates the amount of p-nitrophenol (p-NP released during the hydrolysis of the substrate p-nitrophenyl palmitate (p-NPP. Isolates producing extracellular lipases were then identified by MALDI-TOF-M

  19. Description of regolith at Laxemar-Simpevarp. Site descriptive modelling SDM-Site Laxemar

    International Nuclear Information System (INIS)

    This report compiles all known available information regarding the regolith in the Laxemar-Simpevarp regional model area. Regolith refers to the loose deposits overlying the bedrock. In the Laxemar-Simpevarp area, all known regolith was deposited during the Quaternary period and is consequently often referred to as Quaternary deposits (QD). In the terrestrial areas the uppermost part of the regolith, which has been affected by climate and vegetation, is referred to as soil. The geographical and stratigraphical distributions of the regolith have been used to construct a model showing the distribution of regolith depths in the whole model area. The stratigraphical units shown in the regolith depth and stratigraphy model have been characterised with respect to physical and chemical properties. Most of the data used for that characterisation have been obtained from the site investigation but some data were taken from the literature. All QD in the Laxemar area have most probably been deposited during or after the latest deglaciation. The ice sheet in the area moved from the north-west during the latest ice age. The Baltic Sea completely covered the investigated area after the latest deglaciation c 12,000 BC. Land uplift was fastest during the first few thousand years following the deglaciation and has subsequently decreased to the present value of 1 mm/year. Older QD have been eroded in areas exposed to waves and currents and the material has later been redeposited. Fine-grained sediments have been deposited on the floor of bays and in other sheltered positions. Peat has accumulated in many of the wetlands situated in topographically low positions. The groundwater table in many of the former wetlands has been artificially lowered to obtain land for forestry and agriculture, which has caused the peat to partly or completely oxidise. As land uplift proceeds, some new areas are being subjected to erosion at the same time as other new areas are becoming lakes and sheltered

  20. Description of regolith at Laxemar-Simpevarp. Site descriptive modelling SDM-Site Laxemar

    Energy Technology Data Exchange (ETDEWEB)

    Sohlenius, Gustav; Hedenstroem, Anna (Geological Survey of Sweden (SGU), Uppsala (Sweden))

    2008-11-15

    This report compiles all known available information regarding the regolith in the Laxemar-Simpevarp regional model area. Regolith refers to the loose deposits overlying the bedrock. In the Laxemar-Simpevarp area, all known regolith was deposited during the Quaternary period and is consequently often referred to as Quaternary deposits (QD). In the terrestrial areas the uppermost part of the regolith, which has been affected by climate and vegetation, is referred to as soil. The geographical and stratigraphical distributions of the regolith have been used to construct a model showing the distribution of regolith depths in the whole model area. The stratigraphical units shown in the regolith depth and stratigraphy model have been characterised with respect to physical and chemical properties. Most of the data used for that characterisation have been obtained from the site investigation but some data were taken from the literature. All QD in the Laxemar area have most probably been deposited during or after the latest deglaciation. The ice sheet in the area moved from the north-west during the latest ice age. The Baltic Sea completely covered the investigated area after the latest deglaciation c 12,000 BC. Land uplift was fastest during the first few thousand years following the deglaciation and has subsequently decreased to the present value of 1 mm/year. Older QD have been eroded in areas exposed to waves and currents and the material has later been redeposited. Fine-grained sediments have been deposited on the floor of bays and in other sheltered positions. Peat has accumulated in many of the wetlands situated in topographically low positions. The groundwater table in many of the former wetlands has been artificially lowered to obtain land for forestry and agriculture, which has caused the peat to partly or completely oxidise. As land uplift proceeds, some new areas are being subjected to erosion at the same time as other new areas are becoming lakes and sheltered

  1. Characterization of an Active Thermal Erosion Site, Caribou Creek, Alaska

    Science.gov (United States)

    Busey, R.; Bolton, W. R.; Cherry, J. E.; Hinzman, L. D.

    2013-12-01

    The goal of this project is to estimate volume loss of soil over time from this site, provide parameterizations on erodibility of ice rich permafrost and serve as a baseline for future landscape evolution simulations. Located in the zone of discontinuous permafrost, the interior region of Alaska (USA) is home to a large quantity of warm, unstable permafrost that is both high in ice content and has soil temperatures near the freezing point. Much of this permafrost maintains a frozen state despite the general warming air temperature trend in the region due to the presence of a thick insulating organic mat and a dense root network in the upper sub-surface of the soil column. At a rapidly evolving thermo-erosion site, located within the Caribou-Poker Creeks Research Watershed (part of the Bonanza Creek LTER) near Chatanika, Alaska (N65.140, W147.570), the protective organic layer and associated plants were disturbed by an adjacent traditional use trail and the shifting of a groundwater spring. These triggers have led to rapid geomorphological change on the landscape as the soil thaws and sediment is transported into the creek at the valley bottom. Since 2006 (approximately the time of initiation), the thermal erosion has grown to 170 meters length, 3 meters max depth, and 15 meters maximum width. This research combines several data sets: DGPS survey, imagery from an extremely low altitude pole-based remote sensing (3 to 5 meters above ground level), and imagery from an Unmanned Aerial System (UAS) at about 60m altitude.

  2. LHC phenomenology of the three-site Higgsless model

    Energy Technology Data Exchange (ETDEWEB)

    Speckner, Christian

    2009-07-01

    In the last years, extra dimensional models have been proposed which can evade these constraints by delocalizing the Standard Model fermions within the extra dimension, thus allowing to tune the couplings to the new resonances in order to avoid these constraints. This way, such models are a viable method of breaking the electroweak symmetry and retaining perturbative TeV scale unitarity without introducing a fundamental Higgs field. However, extra dimensional models (excluding trivial cases) are intrinsically nonrenormalizable and valid only below a cutoff scale, with most of the new resonances lying in fact above the cutoff. Conceptionally, a honest extension of the Standard Model should only contain the structure below this cutoff, incorporating the extra dimensional mechanism of breaking the symmetry and delaying unitarity violation without making assumptions on the high energy physics above the cutoff scale. The Three-Site Higgsless Model is a minimal implementation of this idea. While it can be motivated by extra dimensional Higgsless models of electroweak symmetry breaking, it in fact contains only one set of extra resonances which lies below the cutoff, delaying unitarity violation to {approx}2-3 TeV. The non-Standard Model part of the spectrum consists of a set of heavy partners for all Standard Model particles with the exception of photon and gluon. The analysis of the experimental constraints reveals that, while the model is consistent with the precision observables, the couplings between the new heavy gauge bosons and the Standard Model fermions have to be exceedingly small ({approx}1% of the isospin gauge coupling) while the new fermions are constrained to be rather heavy with masses above 1.8 TeV. In this thesis, we explored the LHC phenomenology of this scenario. To this end, we calculated the couplings and widths of all the new particles and implemented the model into the Monte-Carlo event generator and WHIZARD / O'Mega. With this implementation

  3. LHC phenomenology of the three-site Higgsless model

    International Nuclear Information System (INIS)

    In the last years, extra dimensional models have been proposed which can evade these constraints by delocalizing the Standard Model fermions within the extra dimension, thus allowing to tune the couplings to the new resonances in order to avoid these constraints. This way, such models are a viable method of breaking the electroweak symmetry and retaining perturbative TeV scale unitarity without introducing a fundamental Higgs field. However, extra dimensional models (excluding trivial cases) are intrinsically nonrenormalizable and valid only below a cutoff scale, with most of the new resonances lying in fact above the cutoff. Conceptionally, a honest extension of the Standard Model should only contain the structure below this cutoff, incorporating the extra dimensional mechanism of breaking the symmetry and delaying unitarity violation without making assumptions on the high energy physics above the cutoff scale. The Three-Site Higgsless Model is a minimal implementation of this idea. While it can be motivated by extra dimensional Higgsless models of electroweak symmetry breaking, it in fact contains only one set of extra resonances which lies below the cutoff, delaying unitarity violation to ∼2-3 TeV. The non-Standard Model part of the spectrum consists of a set of heavy partners for all Standard Model particles with the exception of photon and gluon. The analysis of the experimental constraints reveals that, while the model is consistent with the precision observables, the couplings between the new heavy gauge bosons and the Standard Model fermions have to be exceedingly small (∼1% of the isospin gauge coupling) while the new fermions are constrained to be rather heavy with masses above 1.8 TeV. In this thesis, we explored the LHC phenomenology of this scenario. To this end, we calculated the couplings and widths of all the new particles and implemented the model into the Monte-Carlo event generator and WHIZARD / O'Mega. With this implementation, we simulated

  4. Molecular Basis for Enzymatic Sulfite Oxidation -- HOW THREE CONSERVED ACTIVE SITE RESIDUES SHAPE ENZYME ACTIVITY

    Energy Technology Data Exchange (ETDEWEB)

    Bailey, Susan; Rapson, Trevor; Johnson-Winters, Kayunta; Astashkin, Andrei; Enemark, John; Kappler, Ulrike

    2008-11-10

    Sulfite dehydrogenases (SDHs) catalyze the oxidation and detoxification of sulfite to sulfate, a reaction critical to all forms of life. Sulfite-oxidizing enzymes contain three conserved active site amino acids (Arg-55, His-57, and Tyr-236) that are crucial for catalytic competency. Here we have studied the kinetic and structural effects of two novel and one previously reported substitution (R55M, H57A, Y236F) in these residues on SDH catalysis. Both Arg-55 and His-57 were found to have key roles in substrate binding. An R55M substitution increased Km(sulfite)(app) by 2-3 orders of magnitude, whereas His-57 was required for maintaining a high substrate affinity at low pH when the imidazole ring is fully protonated. This effect may be mediated by interactions of His-57 with Arg-55 that stabilize the position of the Arg-55 side chain or, alternatively, may reflect changes in the protonation state of sulfite. Unlike what is seen for SDHWT and SDHY236F, the catalytic turnover rates of SDHR55M and SDHH57A are relatively insensitive to pH (~;;60 and 200 s-1, respectively). On the structural level, striking kinetic effects appeared to correlate with disorder (in SDHH57A and SDHY236F) or absence of Arg-55 (SDHR55M), suggesting that Arg-55 and the hydrogen bonding interactions it engages in are crucial for substrate binding and catalysis. The structure of SDHR55M has sulfate bound at the active site, a fact that coincides with a significant increase in the inhibitory effect of sulfate in SDHR55M. Thus, Arg-55 also appears to be involved in enabling discrimination between the substrate and product in SDH.

  5. Active Site Metal Occupancy and Cyclic Di-GMP Phosphodiesterase Activity of Thermotoga maritima HD-GYP.

    Science.gov (United States)

    Miner, Kyle D; Kurtz, Donald M

    2016-02-16

    HD-GYPs make up a subclass of the metal-dependent HD phosphohydrolase superfamily and catalyze conversion of cyclic di(3',5')-guanosine monophosphate (c-di-GMP) to 5'-phosphoguanylyl-(3'→5')-guanosine (pGpG) and GMP. Until now, the only reported crystal structure of an HD-GYP that also exhibits c-di-GMP phosphodiesterase activity contains a His/carboxylate ligated triiron active site. However, other structural and phylogenetic correlations indicate that some HD-GYPs contain dimetal active sites. Here we provide evidence that an HD-GYP c-di-GMP phosphodiesterase, TM0186, from Thermotoga maritima can accommodate both di- and trimetal active sites. We show that an as-isolated iron-containing TM0186 has an oxo/carboxylato-bridged diferric site, and that the reduced (diferrous) form is necessary and sufficient to catalyze conversion of c-di-GMP to pGpG, but that conversion of pGpG to GMP requires more than two metals per active site. Similar c-di-GMP phosphodiesterase activities were obtained with divalent iron or manganese. On the basis of activity correlations with several putative metal ligand residue variants and molecular dynamics simulations, we propose that TM0186 can accommodate both di- and trimetal active sites. Our results also suggest that a Glu residue conserved in a subset of HD-GYPs is required for formation of the trimetal site and can also serve as a labile ligand to the dimetal site. Given the anaerobic growth requirement of T. maritima, we suggest that this HD-GYP can function in vivo with either divalent iron or manganese occupying di- and trimetal sites.

  6. Surface binding sites in carbohydrate active enzymes: An emerging picture of structural and functional diversity

    DEFF Research Database (Denmark)

    Svensson, Birte; Cockburn, Darrell

    2013-01-01

    Carbohydrate active enzymes, particularly those that are active on polysaccharides, are often found associated with carbohydrate binding modules (CBMs), which can play several roles in supporting enzyme function, such as localizing the enzyme to the substrate. However, the presence of CBMs...... is not universal and is in fact rare among some families of enzymes. In some cases an alternative to possessing a CBM is for the enzyme to bind to the substrate at a site on the catalytic domain, but away from the active site. Such a site is termed a surface (or secondary) binding site (SBS). SBSs have been...... identified in enzymes from a wide variety of families, though almost half are found in the α-amylase family GH13. The roles attributed to SBSs are not limited to targeting the enzyme to the substrate, but also include a variety of others such as guiding the substrate into the active site, altering enzyme...

  7. Testing the methodology for site descriptive modelling. Application for the Laxemar area

    Energy Technology Data Exchange (ETDEWEB)

    Andersson, Johan [JA Streamflow AB, Aelvsjoe (Sweden); Berglund, Johan [SwedPower AB, Stockholm (Sweden); Follin, Sven [SF Geologic AB, Stockholm (Sweden); Hakami, Eva [Itasca Geomekanik AB, Stockholm (Sweden); Halvarson, Jan [Swedish Nuclear Fuel and Waste Management Co, Stockholm (Sweden); Hermanson, Jan [Golder Associates AB, Stockholm (Sweden); Laaksoharju, Marcus [Geopoint (Sweden); Rhen, Ingvar [Sweco VBB/VIAK, Stockholm (Sweden); Wahlgren, C.H. [Sveriges Geologiska Undersoekning, Uppsala (Sweden)

    2002-08-01

    and after this compared to check for potential inconsistencies. The processed data are used for three-dimensional modelling. The geological modelling provides the geometrical framework for the modelling in other disciplines and results in descriptions of geometry and properties of deformation zones of sizes down to 'local major zones' Q-10 km) and geometry and properties of rock domains. Two descriptions have been derived; the Base Geological Model and the Alternative Geological Model. Given the limited amount of data, regions of the model domain still have quite uncertain descriptions. The geometry is represented using a 3D CAD software (RVS), which is also used as an active interpretation tool for the geometric modelling. The base for the hydrogeological modelling is the Geological Model with its identified volumetric objects. Essential hydrogeological evaluation tools include: assessment of single hole hydraulic tests, interpretation of interference tests and numerical modelling of groundwater flow tests and other observations. The resulting hydrogeological description comprises hydraulic properties for defined geometrical units and boundary conditions for the present day conditions for the rock volume defined by the Base Geological Model. The major tasks for the hydrogeochemical evaluation include: (i) characterisation of undisturbed groundwater chemistry including the origin, depth/lateral distribution and the turnover time; (ii) focusing on data of importance for the safety evaluation such as pH, Eh, chloride, sulphide, colloids and microbes; (iii) identification of possible dissolved oxygen at repository depth. The hydrogeochemical description concerns distribution of the major water types, the water type mixing proportions and lists the major type of chemical reactions occurring at the site. Even if much of the modelling can be done in parallel with other disciplines, consistency checks with hydrogeology can and have been made. These comparisons

  8. The landscape degradation in the mining sites with suspended activity

    Directory of Open Access Journals (Sweden)

    Anca IONCE

    2009-08-01

    Full Text Available The extracting industry, through its extraction activities, of shipping the ores, of breaking the ores, of preparing the practical substances, of stowing the useless rock, of transporting the practical substances, etc. might modify the area’s relief and the quality of ground, of thesurface waters and of the air. Suceava County has an old tradition of mining, where the results of this activity are visible, especially the visual point of view, and where not taking certain measures of ecological remediation will emphasize the disappointing image of the landscape within the areas of mining activity performing.The predominant mountainous landscape, in which mining activities have been held, is being affected also by the abandoned industrial and administrative buildings, in an advanced degradation state.The hydrographic system, very rich in mining areas, has its water quality affected by the acid rock drainage- phenomenon which appeared in many mining waste deposits.

  9. Endolysosomes Are the Principal Intracellular Sites of Acid Hydrolase Activity.

    Science.gov (United States)

    Bright, Nicholas A; Davis, Luther J; Luzio, J Paul

    2016-09-12

    The endocytic delivery of macromolecules from the mammalian cell surface for degradation by lysosomal acid hydrolases requires traffic through early endosomes to late endosomes followed by transient (kissing) or complete fusions between late endosomes and lysosomes. Transient or complete fusion results in the formation of endolysosomes, which are hybrid organelles from which lysosomes are re-formed. We have used synthetic membrane-permeable cathepsin substrates, which liberate fluorescent reporters upon proteolytic cleavage, as well as acid phosphatase cytochemistry to identify which endocytic compartments are acid hydrolase active. We found that endolysosomes are the principal organelles in which acid hydrolase substrates are cleaved. Endolysosomes also accumulated acidotropic probes and could be distinguished from terminal storage lysosomes, which were acid hydrolase inactive and did not accumulate acidotropic probes. Using live-cell microscopy, we have demonstrated that fusion events, which form endolysosomes, precede the onset of acid hydrolase activity. By means of sucrose and invertase uptake experiments, we have also shown that acid-hydrolase-active endolysosomes and acid-hydrolase-inactive, terminal storage lysosomes exist in dynamic equilibrium. We conclude that the terminal endocytic compartment is composed of acid-hydrolase-active, acidic endolysosomes and acid hydrolase-inactive, non-acidic, terminal storage lysosomes, which are linked and function in a lysosome regeneration cycle. PMID:27498570

  10. Active site proton delivery and the lyase activity of human CYP17A1

    Energy Technology Data Exchange (ETDEWEB)

    Khatri, Yogan; Gregory, Michael C.; Grinkova, Yelena V.; Denisov, Ilia G.; Sligar, Stephen G., E-mail: s-sligar@illinois.edu

    2014-01-03

    equivalents and protons are funneled into non-productive pathways. This is similar to previous work with other P450 catalyzed hydroxylation. However, catalysis of carbon–carbon bond scission by the T306A mutant was largely unimpeded by disruption of the CYP17A1 acid-alcohol pair. The unique response of CYP17A1 lyase activity to mutation of Thr306 is consistent with a reactive intermediate formed independently of proton delivery in the active site, and supports involvement of a nucleophilic peroxo-anion rather than the traditional Compound I in catalysis.

  11. SITE-94. Discrete-feature modelling of the Aespoe site: 4. Source data and detailed analysis procedures

    Energy Technology Data Exchange (ETDEWEB)

    Geier, J.E. [Golder Associates AB, Uppsala (Sweden)

    1996-12-01

    Specific procedures and source data are described for the construction and application of discrete-feature hydrological models for the vicinity of Aespoe. Documentation is given for all major phases of the work, including: Statistical analyses to develop and validate discrete-fracture network models, Preliminary evaluation, construction, and calibration of the site-scale model based on the SITE-94 structural model of Aespoe, Simulation of multiple realizations of the integrated model, and variations, to predict groundwater flow, and Evaluation of near-field and far-field parameters for performance assessment calculations. Procedures are documented in terms of the computer batch files and executable scripts that were used to perform the main steps in these analyses, to provide for traceability of results that are used in the SITE-94 performance assessment calculations. 43 refs.

  12. Observed and modeled carbon and energy fluxes for agricultural sites under North American Carbon Program site-level interim synthesis

    Science.gov (United States)

    Lokupitiya, E. Y.; Denning, A.

    2010-12-01

    Croplands are unique, man-made ecosystems with dynamics mostly dependent on human decisions. Crops uptake a significant amount of Carbon dioxide (CO2) during their short growing seasons. Reliability of the available models to predict the carbon exchanges by croplands is important in estimating the cropland contribution towards overall land-atmosphere carbon exchange and global carbon cycle. The energy exchanges from croplands include both sensible and latent heat fluxes. This study focuses on analyzing the performance of 19 land surface models across five agricultural sites under the site-level interim synthesis of North American Carbon Program (NACP). Model simulations were performed using a common simulation protocol and input data, including gap-filled meteorological data corresponding to each site. The net carbon fluxes (i.e. net ecosystem exchange; NEE) and energy fluxes (sensible and latent heat) predicted by 12 models with sub-hourly/hourly temporal resolution and 7 models with daily temporal resolution were compared against the site-specific gap-filled observed flux tower data. Comparisons were made by site and crop type (i.e. maize, soybean, and wheat), mainly focusing on the coefficient of determination, correlation, root mean square error, and standard deviation. Analyses also compared the diurnal, seasonal, and inter-annual variability of the modeled fluxes against the observed data and the mean modeled data.

  13. Hydrochemistry in surface water and shallow groundwater. Site descriptive modelling SDM-Site Forsmark

    International Nuclear Information System (INIS)

    With a mathematical/statistical approach, a large number of visualisations and models reflect the hydrochemistry in the Forsmark area, with the intention to give an understanding of important processes and factors that affect the hydrochemistry in the surface systems. In order to widen the perspective, all data from the Forsmark 2.2 stage including observations from different levels of the bedrock, as well as hydrological measurements and characterisations of the Quaternary deposits, have been included in the analyses. The purpose of this report is to give a general understanding of the site and to explain observed overall patterns as well as anomalies, and, ultimately, to present a conceptual model that explains the present hydrochemistry in the surface system in the light of the past. The report may also function as a basis for further evaluation and testing of scenarios, and may be regarded as an intermediate step between raw data compilations from the vast SICADA database and specialised expert models. The flat topography and the recent withdrawal of the Baltic Sea due to the isostatic land-uplift are two important factors determining the hydrochemistry in the Forsmark area. Marine remnants in the Quaternary deposits, as well as modern sea water intrusions, are therefore strongly influencing the hydrochemistry, especially in areas at low altitude close to the coast. Large-scale marine gradients in the surface system are consistent with the conceptual model that describes the hydrochemical evolution in a paleo-hydrologic perspective. The Forsmark area is covered by glacial remnants, mostly in the form of a till layer, which was deposited during the Weichselian glaciation and deglaciation. When the ice cover retreated about 11,000 years ago, these deposits were exposed on the sea floor. This till layer is characterized by a rich content of calcite, originating from the sedimentary bedrock of Gaevlebukten about 100 km north of Forsmark. The dissolution of this

  14. Hydrochemistry in surface water and shallow groundwater. Site descriptive modelling SDM-Site Forsmark

    Energy Technology Data Exchange (ETDEWEB)

    Troejbom, Mats (Mopelikan, Norrtaelje (SE)); Soederbaeck, Bjoern (Swedish Nuclear Fuel and Waste Management Co., Stockholm (SE)); Johansson, Per-Olof (Artesia Grundvattenkonsult AB, Taeby (SE))

    2007-10-15

    With a mathematical/statistical approach, a large number of visualisations and models reflect the hydrochemistry in the Forsmark area, with the intention to give an understanding of important processes and factors that affect the hydrochemistry in the surface systems. In order to widen the perspective, all data from the Forsmark 2.2 stage including observations from different levels of the bedrock, as well as hydrological measurements and characterisations of the Quaternary deposits, have been included in the analyses. The purpose of this report is to give a general understanding of the site and to explain observed overall patterns as well as anomalies, and, ultimately, to present a conceptual model that explains the present hydrochemistry in the surface system in the light of the past. The report may also function as a basis for further evaluation and testing of scenarios, and may be regarded as an intermediate step between raw data compilations from the vast SICADA database and specialised expert models. The flat topography and the recent withdrawal of the Baltic Sea due to the isostatic land-uplift are two important factors determining the hydrochemistry in the Forsmark area. Marine remnants in the Quaternary deposits, as well as modern sea water intrusions, are therefore strongly influencing the hydrochemistry, especially in areas at low altitude close to the coast. Large-scale marine gradients in the surface system are consistent with the conceptual model that describes the hydrochemical evolution in a paleo-hydrologic perspective. The Forsmark area is covered by glacial remnants, mostly in the form of a till layer, which was deposited during the Weichselian glaciation and deglaciation. When the ice cover retreated about 11,000 years ago, these deposits were exposed on the sea floor. This till layer is characterized by a rich content of calcite, originating from the sedimentary bedrock of Gaevlebukten about 100 km north of Forsmark. The dissolution of this

  15. Three-Dimensional Groundwater Models of the 300 Area at the Hanford Site, Washington State

    Energy Technology Data Exchange (ETDEWEB)

    Williams, Mark D.; Rockhold, Mark L.; Thorne, Paul D.; Chen, Yousu

    2008-09-01

    Researchers at Pacific Northwest National Laboratory developed field-scale groundwater flow and transport simulations of the 300 Area to support the 300-FF-5 Operable Unit Phase III Feasibility Study. The 300 Area is located in the southeast portion of the U.S. Department of Energy’s Hanford Site in Washington State. Historical operations involving uranium fuel fabrication and research activities at the 300 Area have contaminated engineered liquid-waste disposal facilities, the underlying vadose zone, and the uppermost aquifer with uranium. The main objectives of this research were to develop numerical groundwater flow and transport models to help refine the site conceptual model, and to assist assessment of proposed alternative remediation technologies focused on the 300 Area uranium plume.

  16. PCR-based site-specific mutagenesis of peptide antibiotics FALL-39 and its biologic activities

    Institute of Scientific and Technical Information of China (English)

    Yun-xia YANG; Yun FENG; Bo-yao WANG; Qi WU

    2004-01-01

    AIM: To construct PGEX-1λT-FALL-39 expression vector and its mutant vector, and study the relationship of function and structure. METHODS: A cDNA encoding mature FALL-39 was cloned from SPCA- 1 cell mRNA and the prokaryotic expression vector PGEX- 1λT-FALL-39 was constructed. Two kinds of polymerase chain reaction (PCR) for the site-direction mutagenesis were used to construct FALL-39 mutant expression vector, FALL-39-Lys-32 and FALL-39-Lys-24. Minimal effective concentration, minimal inhibitory concentration, and minimal bactericidal concentration were used to assay the antibacterial activities of these peptides. Effects of different solution on the antibacterial activity of FALL-39 and FALL-39-Lys-32 were observed by CFU determination. The hemolytic effects of these peptides were also examined on human red blood cells. RESULTS: Two site-specific mutants FALL-39-Lys-32 and FALL-39-Lys24 were obtained by PCR-induced mutagenesis. In comparison with two-step PCR which required two pairs of primers, one step PCR which required one pair of primers is a simple and efficient method for the PCR based site-specific mutagenesis. Using the prokaryotic expression system, the E coli-based products of recombinant FALL39 and its mutant peptides were also obtained. The antibacterial assay showed that FALL-39-Lys-32 and FALL-39-Lys24 were more potential in the antibacterial activity against E coli ML35p and Pseltdomonas aeruginosa ATCC27853 than that of FALL-39, and no increase in hemolysis was observed at the antibacterial concentrations. The antibacterial activity of FALL-39-Lys-32 against E coli was more potent than that of FALL-39 in NaCl-containing LB medium, while its activity was almost the same as FALL-39 in SO2-4 containing Medium E. CONCLUSION: PCR-based mutagensis is a useful model system for studying the structure and function relationship of antimicrobial peptides. Keeping α-helical conformation of FALL-39 and increasing net positive charge can increase the

  17. Estimating unbiased phenological trends by adapting site-occupancy models.

    Science.gov (United States)

    Roth, Tobias; Strebel, Nicolas; Amrhein, Valentin

    2014-08-01

    As a response to climate warming, many animals and plants have been found to shift phenologies, such as appearance in spring or timing of reproduction. However, traditional measures for shifts in phenology that are based on observational data likely are biased due to a large influence of population size, observational effort, starting date of a survey, or other causes that may affect the probability of detecting a species. Understanding phenological responses of species to climate change, however, requires a robust measure that could be compared among studies and study years. Here, we developed a new method for estimating arrival and departure dates based on site-occupancy models. Using simulated data, we show that our method provided virtually unbiased estimates of phenological events even if detection probability or the number of sites occupied by the species is changing over time. To illustrate the flexibility of our method, we analyzed spring arrival of two long-distance migrant songbirds and the length of the flight period of two butterfly species, using data from a long-term biodiversity monitoring program in Switzerland. In contrast to many birds that migrate short distances, the two long-distance migrant songbirds tended to postpone average spring arrival by -0.5 days per year between 1995 and 2012. Furthermore, the flight period of the short-distance-flying butterfly species apparently became even shorter over the study period, while the flight period of the longer-distance-flying butterfly species remained relatively stable. Our method could be applied to temporally and spatially extensive data from a wide range of monitoring programs and citizen science projects, to help unravel how species and communities respond to global warming. PMID:25230466

  18. Hanford Site ground-water model: Geographic information system linkages and model enhancements, FY 1993

    International Nuclear Information System (INIS)

    Models of the unconfined aquifer are important tools that are used to (1) identify and quantify existing, emerging, or potential ground-water quality problems, (2) predict changes in ground-water flow and contaminant transport as waste-water discharge operations change, and (3) assess the potential for contaminants to migrate from the US Department of Energy's Hanford Site through the ground water. Formerly, most of the numerical models developed at the Hanford Site were two-dimensional. However, contaminant concentrations cannot be accurately predicted with a two-dimensional model, which assumes a constant vertical distribution of contaminants in the aquifer. Development of two- and three-dimensional models of ground-water flow based on the Coupled Fluid, Energy, and Solute Transport (CFEST) code began in the mid- 1980s. The CFEST code was selected because of its ability to simulate both ground-water flow and contaminant transport. Physical processes that can be modeled by CFEST include aquifer geometry, heterogeneity, boundary conditions, and initial conditions. The CFEST ground-water modeling library has been integrated with the commercially available geographic information system (GIS) ARC/INFO. The display and analysis capabilities of a GIS are well suited to the size and diversity of databases being generated at the Hanford Site. The ability to visually inspect large databases through a graphical analysis tool provides a stable foundation for site assessments and ground-water modeling studies. Any ground-water flow model being used by an ongoing project should be continually updated and refined to reflect the most current knowledge of the system. The two-dimensional ground-water flow model being used in support of the Ground-Water Surveillance Project has recently been updated and enhanced. One major enhancement was the extension of the model area to include North Richland

  19. Identifying high dose activities in industrial site radiography

    International Nuclear Information System (INIS)

    Although the radiation doses received by industrial radiographers in the UK have progressively fallen over the last few years, with most now receiving less than 1 mSv/y, a few still receive, relative to the rest, much higher doses. As a percentage of all radiographers the number stays surprisingly constant from year to year. This paper describes a survey to identify the work causing these doses and suggest possible solutions. The UK Central Index of Dose Information was interrogated to identify the industrial radiography companies having staff (not necessarily the same person) with doses of greater than 5mSv/y in the last three years for which information was available. This was 15 in total. The people on the staff receiving these doses were identified and a questionnaire sent to the companies concerned requesting information about their work. A general questionnaire about the operation of the company was also included. With the agreement of the company these questionnaires were followed up by a visit to the company to interviews a number of the management and the radiographers if available. Both groups were generally very open about their problems and every discussion had a positive outcome. Several areas of work/reasons for the doses have been identified. These are: pipeline radiography, ultra sound radiographers working on nuclear reactors, complex plant work often with several teams in the area, inability to retreat from the wind out equipment due to height or access problems, site pressure to not follow the best practices and a lack of appreciation when a dose was being received or, alternatively, carelessness. Some o these problem areas are very difficult to resolve. However ways in which the Health and Safety can help influence the doses have been identified together with practical suggestions radiographers could adopt. These will be reported. (author)

  20. School Pharmacist/School Environmental Hygienic Activities at School Site.

    Science.gov (United States)

    Muramatsu, Akiyoshi

    2016-01-01

    The "School Health and Safety Act" was enforced in April 2009 in Japan, and "school environmental health standards" were established by the Minister of Education, Culture, Sports, Science and Technology. In Article 24 of the Enforcement Regulations, the duties of the school pharmacist have been clarified; school pharmacists have charged with promoting health activities in schools and carrying out complete and regular checks based on the "school environmental health standards" in order to protect the health of students and staff. In supported of this, the school pharmacist group of Japan Pharmaceutical Association has created and distributed digital video discs (DVDs) on "check methods of school environmental health standards" as support material. We use the DVD to ensure the basic issues that school pharmacists deal with, such as objectives, criteria, and methods for each item to be checked, advice, and post-measures. We conduct various workshops and classes, and set up Q&A committees so that inquiries from members are answered with the help of such activities. In addition, school pharmacists try to improve the knowledge of the school staff on environmental hygiene during their in-service training. They also conduct "drug abuse prevention classes" at school and seek to improve knowledge and recognition of drugs, including "dangerous drugs". PMID:27252053

  1. Alternative DFN model based on initial site investigations at Simpevarp

    Energy Technology Data Exchange (ETDEWEB)

    Darcel, C. [Itasca Consultants, Ecully (France); Davy, S.A.P.; Bour, O.; Dreuzy, J.R. de [Geosciences, Rennes (France)

    2004-12-01

    In this report, we provide a first-order analysis of the fracture network at the Simpevarp site. The first order model is the fracture distribution function, noted, fdf, which provides the number of fractures having a given orientation and length, and belonging to a given volume of observation. The first-order distribution model does not describe higher-order correlation between fracture parameters, such as a possible dependency of fracture length distribution with orientations. We also check that most of the information is contained in this 1st-order distribution model, and that dividing the fracture networks into different sets do not bring a better statistical description. The fracture distribution function contains 3 main distributions: the probability distribution of fracture orientations, the dependency on the size of the sampling domain that may exhibit non-trivial scaling in case of fractal correlations, and the fracture-length density distribution, which appears to be well fitted by a power law. The main scaling parameters are the fractal dimension and the power-law exponent of the fracture length distribution. The former was found to be about equal to the embedding dimension, meaning that fractal correlations are weak and can be neglected in the DFN model. The latter depends on geology, that is either lithology or grain size, with values that ranges from 3.2 for granite-like outcrops to 4 for diorite or monzodiorite outcrops, as well as for the large-scale lineament maps. When analyzing the consistency of the different datasets (boreholes, outcrops, lineament maps), we found that two different DFNs can be described: the first one is derived from the fdf of the outcrop with fine-grained size lithology, and is valid across all scales investigated in this study, from the highly-fractured cores to large-scale maps; the second one is derived from the fdf of the outcrops with coarse-grained size lithology, and is found consistent with cores that present the

  2. Can Bayesian Belief Networks help tackling conceptual model uncertainties in contaminated site risk assessment?

    DEFF Research Database (Denmark)

    Troldborg, Mads; Thomsen, Nanna Isbak; McKnight, Ursula S.;

    models that are effective for integrating quantitative and qualitative information, and thus can strengthen decisions when empirical data are lacking. The developed BBN combines data from desk studies and initial site investigations with expert opinion to assess which of the conceptual models are more......A key component in risk assessment of contaminated sites is the formulation of a conceptual site model. The conceptual model is a simplified representation of reality and forms the basis for the mathematical modelling of contaminant fate and transport at the site. A conceptual model should...... therefore identify the most important site-specific features and processes that may affect the contaminant transport behaviour at the site. The development of a conceptual model will always be associated with uncertainties due to lack of data and understanding of the site conditions, and often many...

  3. DRINK: a biogeochemical source term model for low level radioactive waste disposal sites.

    Science.gov (United States)

    Humphreys, P; McGarry, R; Hoffmann, A; Binks, P

    1997-07-01

    Interactions between element chemistry and the ambient geochemistry play a significant role in the control of radionuclide migration in the geosphere. These same interactions influence radionuclide release from near surface, low level radioactive waste, disposal sites once physical containment has degraded. In situations where LLW contains significant amounts of metal and organic materials such as cellulose, microbial degradation in conjunction with corrosion can significantly perturb the ambient geochemistry. These processes typically produce a transition from oxidising to reducing conditions and can influence radionuclide migration through changes in both the dominant radionuclide species and mineral phases. The DRINK (DRIgg Near field Kinetic) code is a biogeochemical transport code designed to simulate the long term evolution of the UK low level radioactive waste disposal site at Drigg. Drigg is the UK's principal solid low level radioactive waste disposal site and has been receiving waste since 1959. The interaction between microbial activity, the ambient geochemistry and radionuclide chemistry is central to the DRINK approach with the development of the ambient pH, redox potential and bulk geochemistry being directly influenced by microbial activity. This paper describes the microbial aspects of the code, site data underpinning the microbial model, the microbiology/chemistry interface and provides an example of the code in action. PMID:9340003

  4. Isolated metal active site concentration and stability control catalytic CO2 reduction selectivity.

    Science.gov (United States)

    Matsubu, John C; Yang, Vanessa N; Christopher, Phillip

    2015-03-01

    CO2 reduction by H2 on heterogeneous catalysts is an important class of reactions that has been studied for decades. However, atomic scale details of structure-function relationships are still poorly understood. Particularly, it has been suggested that metal particle size plays a unique role in controlling the stability of CO2 hydrogenation catalysts and the distribution of active sites, which dictates reactivity and selectivity. These studies often have not considered the possible role of isolated metal active sites in the observed dependences. Here, we utilize probe molecule diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) with known site-specific extinction coefficients to quantify the fraction of Rh sites residing as atomically dispersed isolated sites (Rhiso), as well as Rh sites on the surface of Rh nanoparticles (RhNP) for a series of TiO2 supported Rh catalysts. Strong correlations were observed between the catalytic reverse water gas shift turn over frequency (TOF) and the fraction of Rhiso sites and between catalytic methanation TOF and the fraction of RhNP sites. Furthermore, it was observed that reaction condition-induced disintegration of Rh nanoparticles, forming Rhiso active sites, controls the changing reactivity with time on stream. This work demonstrates that isolated atoms and nanoparticles of the same metal on the same support can exhibit uniquely different catalytic selectivity in competing parallel reaction pathways and that disintegration of nanoparticles under reaction conditions can play a significant role in controlling stability. PMID:25671686

  5. Active site coupling in PDE:PKA complexes promotes resetting of mammalian cAMP signaling.

    Science.gov (United States)

    Krishnamurthy, Srinath; Moorthy, Balakrishnan Shenbaga; Xin Xiang, Lim; Xin Shan, Lim; Bharatham, Kavitha; Tulsian, Nikhil Kumar; Mihalek, Ivana; Anand, Ganesh S

    2014-09-16

    Cyclic 3'5' adenosine monophosphate (cAMP)-dependent-protein kinase (PKA) signaling is a fundamental regulatory pathway for mediating cellular responses to hormonal stimuli. The pathway is activated by high-affinity association of cAMP with the regulatory subunit of PKA and signal termination is achieved upon cAMP dissociation from PKA. Although steps in the activation phase are well understood, little is known on how signal termination/resetting occurs. Due to the high affinity of cAMP to PKA (KD ∼ low nM), bound cAMP does not readily dissociate from PKA, thus begging the question of how tightly bound cAMP is released from PKA to reset its signaling state to respond to subsequent stimuli. It has been recently shown that phosphodiesterases (PDEs) can catalyze dissociation of bound cAMP and thereby play an active role in cAMP signal desensitization/termination. This is achieved through direct interactions with the regulatory subunit of PKA, thereby facilitating cAMP dissociation and hydrolysis. In this study, we have mapped direct interactions between a specific cyclic nucleotide phosphodiesterase (PDE8A) and a PKA regulatory subunit (RIα isoform) in mammalian cAMP signaling, by a combination of amide hydrogen/deuterium exchange mass spectrometry, peptide array, and computational docking. The interaction interface of the PDE8A:RIα complex, probed by peptide array and hydrogen/deuterium exchange mass spectrometry, brings together regions spanning the phosphodiesterase active site and cAMP-binding sites of RIα. Computational docking combined with amide hydrogen/deuterium exchange mass spectrometry provided a model for parallel dissociation of bound cAMP from the two tandem cAMP-binding domains of RIα. Active site coupling suggests a role for substrate channeling in the PDE-dependent dissociation and hydrolysis of cAMP bound to PKA. This is the first instance, to our knowledge, of PDEs directly interacting with a cAMP-receptor protein in a mammalian system, and

  6. 77 FR 74218 - Commercial Wind Leasing and Site Assessment Activities on the Atlantic Outer Continental Shelf...

    Science.gov (United States)

    2012-12-13

    ... published a Notice of Availability (NOA) in the Federal Register (72 FR 62,672) of the Programmatic EIS for... Federal Register (77 FR 5560) of the Final EA for Commercial Wind Lease Issuance and Site Assessment... Bureau of Ocean Energy Management Commercial Wind Leasing and Site Assessment Activities on the...

  7. 75 FR 71677 - Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites

    Science.gov (United States)

    2010-11-24

    ... Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites AGENCY: Department of... uranium and thorium processing site licensees for reimbursement under Title X of the Energy Policy Act of... requires DOE to reimburse eligible uranium and thorium licensees for certain costs of...

  8. 77 FR 3460 - Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites

    Science.gov (United States)

    2012-01-24

    ... Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites AGENCY: Department of... uranium and thorium processing site licensees for reimbursement under Title X of the Energy Policy Act of... requires DOE to reimburse eligible uranium and thorium licensees for certain costs of...

  9. The balance of flexibility and rigidity in the active site residues of hen egg white lysozyme

    Institute of Scientific and Technical Information of China (English)

    Qi Jian-Xun; Jiang Fan

    2011-01-01

    The crystallographic temperature factors (B factor) of individual atoms contain important information about the thermal motion of the atoms in a macromolecule. Previously the theory of flexibility of active site has been established based on the observation that the enzyme activity is sensitive to low concentration denaturing agents. It has been found that the loss of enzyme activity occurs well before the disruption of the three-dimensional structural scaffold of the enzyme. To test the theory of conformational flexibility of enzyme active site, crystal structures were perturbed by soaking in low concentration guanidine hydrochloride solutions. It was found that many lysozyme crystals tested could still diffract until the concentration of guanidine hydrochloride reached 3 M. It was also found that the B factors averaged over individually collected data sets were more accurate. Thus it suggested that accurate measurement of crystal temperature factors could be achieved for medium-high or even medium resolution crystals by averaging over multiple data sets. Furthermore, we found that the correctly predicted active sites included not only the more flexible residues, but also some more rigid residues. Both the flexible and the rigid residues in the active site played an important role in forming the active site residue network, covering the majority of the substrate binding residues. Therefore, this experimental prediction method may be useful for characterizing the binding site and the function of a protein, such as drug targeting.

  10. Modeling of active beam units with Modelica

    DEFF Research Database (Denmark)

    Maccarini, Alessandro; Hultmark, Göran; Vorre, Anders;

    2015-01-01

    This paper proposes an active beam model suitable for building energy simulations with the programming language Modelica. The model encapsulates empirical equations derived by a novel active beam terminal unit that operates with low-temperature heating and high-temperature cooling systems....... Measurements from a full-scale experiment are used to compare the thermal behavior of the active beam with the one predicted by simulations. The simulation results show that the model corresponds closely with the actual operation. The model predicts the outlet water temperature of the active beam...... with a maximum mean absolute error of 0.18 °C. In term of maximum mean absolute percentage error, simulation results differ by 0.9%. The methodology presented is general enough to be applied for modeling other active beam units. Modeling of active beam units with Modelica. Available from: https...

  11. A Carbon Flux Super Site. New Insights and Innovative Atmosphere-Terrestrial Carbon Exchange Measurements and Modeling

    Energy Technology Data Exchange (ETDEWEB)

    Leclerc, Monique Y. [The University of Georgia Research Foundation, Athens, GA (United States)

    2014-11-17

    This final report presents the main activities and results of the project “A Carbon Flux Super Site: New Insights and Innovative Atmosphere-Terrestrial Carbon Exchange Measurements and Modeling” from 10/1/2006 to 9/30/2014. It describes the new AmeriFlux tower site (Aiken) at Savanna River Site (SC) and instrumentation, long term eddy-covariance, sodar, microbarograph, soil and other measurements at the site, and intensive field campaigns of tracer experiment at the Carbon Flux Super Site, SC, in 2009 and at ARM-CF site, Lamont, OK, and experiments in Plains, GA. The main results on tracer experiment and modeling, on low-level jet characteristics and their impact on fluxes, on gravity waves and their influence on eddy fluxes, and other results are briefly described in the report.

  12. 1993 annual report of hazardous waste activities for the Oak Ridge K-25 site

    Energy Technology Data Exchange (ETDEWEB)

    1994-02-01

    This report is a detailed listing of all of the Hazardous Waste activities occurring at Martin Marietta`s K-25 site. Contained herein are hazardous waste notification forms, waste stream reports, generator fee forms and various TSDR reports.

  13. Conceptual Site Model for Newark Bay—Hydrodynamics and Sediment Transport

    Directory of Open Access Journals (Sweden)

    Parmeshwar L. Shrestha

    2014-02-01

    Full Text Available A conceptual site model (CSM has been developed for the Newark Bay Study Area (NBSA as part of the Remedial Investigation/Feasibility Study (RI/FS for this New Jersey site. The CSM is an evolving document that describes the influence of physical, chemical and biological processes on contaminant fate and transport. The CSM is initiated at the start of a project, updated during site activities, and used to inform sampling and remediation planning. This paper describes the hydrodynamic and sediment transport components of the CSM for the NBSA. Hydrodynamic processes are influenced by freshwater inflows, astronomical forcing through two tidal straits, meteorological conditions, and anthropogenic activities such as navigational dredging. Sediment dynamics are driven by hydrodynamics, waves, sediment loading from freshwater sources and the tidal straits, sediment size gradation, sediment bed properties, and particle-to-particle interactions. Cohesive sediment transport is governed by advection, dispersion, aggregation, settling, consolidation, and erosion. Noncohesive sediment transport is governed by advection, dispersion, settling, armoring, and transport in suspension and along the bed. The CSM will inform the development and application of a numerical model that accounts for all key variables to adequately describe the NBSA’s historical, current, and future physical conditions.

  14. Hydrochemistry in surface water and shallow groundwater. Site descriptive modelling SDM-Site Laxemar

    Energy Technology Data Exchange (ETDEWEB)

    Troejbom, Mats (Mopelikan, Norrtaelje (Sweden)); Soederbaeck, Bjoern; Kalinowski, Birgitta (Swedish Nuclear Fuel and Waste Management Co., Stockholm (Sweden))

    2008-10-15

    Based on a mathematical/statistical approach, a large number of visualisations and models reflect the hydrochemistry of the Laxemar-Simpevarp area, with the intention of providing an understanding of important processes and factors that affect the hydrochemistry of the surface systems. In order to widen the perspective, all data from Laxemar stage 2.3, including observations from different levels of the bedrock, as well as hydrological measurements and characterisations of the Quaternary deposits, have been included in the analyses. The purpose of this report is to provide a general understanding of the site and to explain observed overall patterns and anomalies, and ultimately to present a conceptual model that explains the present hydrochemistry of the surface system in the light of the past. The report may also serve as a basis for further evaluation and testing of scenarios, and may be regarded as an intermediate step between raw data compilations from the vast Sicada database and specialised expert models. The topography in the Laxemar-Simpevarp area is characterised by elevated areas covered by thin or no Quaternary deposits, intersected by deep fissure valleys filled with thick sediments. This topography, in combination with the withdrawal of the Baltic Sea due to isostatic land uplift, are two important factors determining the hydrochemistry of the Laxemar-Simpevarp area. Furthermore, marine remnants in the Quaternary deposits influence the hydrochemistry in areas at low elevation close to the coast, whereas higher-lying areas are mostly influenced by atmospheric deposition and weathering processes. The vegetation cover has also great impact on the hydrochemistry of the surface system. Degradation of biogenic carbon generates large numbers of H+ ions, which drive weathering processes in the Quaternary deposits as well as in the upper parts of the bedrock. The present situation in the surface system is a consequence of the palaeohydrological past. In higher

  15. Hydrochemistry in surface water and shallow groundwater. Site descriptive modelling SDM-Site Laxemar

    International Nuclear Information System (INIS)

    Based on a mathematical/statistical approach, a large number of visualisations and models reflect the hydrochemistry of the Laxemar-Simpevarp area, with the intention of providing an understanding of important processes and factors that affect the hydrochemistry of the surface systems. In order to widen the perspective, all data from Laxemar stage 2.3, including observations from different levels of the bedrock, as well as hydrological measurements and characterisations of the Quaternary deposits, have been included in the analyses. The purpose of this report is to provide a general understanding of the site and to explain observed overall patterns and anomalies, and ultimately to present a conceptual model that explains the present hydrochemistry of the surface system in the light of the past. The report may also serve as a basis for further evaluation and testing of scenarios, and may be regarded as an intermediate step between raw data compilations from the vast Sicada database and specialised expert models. The topography in the Laxemar-Simpevarp area is characterised by elevated areas covered by thin or no Quaternary deposits, intersected by deep fissure valleys filled with thick sediments. This topography, in combination with the withdrawal of the Baltic Sea due to isostatic land uplift, are two important factors determining the hydrochemistry of the Laxemar-Simpevarp area. Furthermore, marine remnants in the Quaternary deposits influence the hydrochemistry in areas at low elevation close to the coast, whereas higher-lying areas are mostly influenced by atmospheric deposition and weathering processes. The vegetation cover has also great impact on the hydrochemistry of the surface system. Degradation of biogenic carbon generates large numbers of H+ ions, which drive weathering processes in the Quaternary deposits as well as in the upper parts of the bedrock. The present situation in the surface system is a consequence of the palaeohydrological past. In higher

  16. Poisoning Experiments Aimed at Discriminating Active and Less-Active Sites of Silica-Supported Tantalum Hydride for Alkane Metathesis

    KAUST Repository

    Saggio, Guillaume

    2010-10-04

    Only 50% of the silica-supported tantalum hydride sites are active in the metathesis of propane. Indeed, more than 45% of the tantalum hydride can be eliminated by a selective oxygen poisoning of inactive sites with no significant decrease in the global turnover. Conversely, cyclopentane induces no such selective poisoning. Hence, the active tantalum hydride sites that show greater resistance to oxygen poisoning correspond to the νTa-H bands of higher wavenumbers, particularly that at 1860cm-1. These active tantalum hydride sites should correspond to tris- or monohydride species relatively far from silica surface oxygen atoms. © 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. A local spin evaluation into the active site models of [2Fe2S] ferrodoxin [Fe2S2(SR)4]2- (R=-H, -CH3)

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    To test the feasibility of local spin theory of Davidson and Clark for ferrodoxin clusters, the models [Fe2S2(SR)4]2- (R=-H, -CH3) are chosen for evaluation. This purpose is realized by calculating the local spin expectation values , , and mA and discussing the connection between these expected values and the Heisenberg spin model (HSM) and the Noodleman broken-symmetry approach. In practical calculation, the spin-unrestricted Hartree-Fock (UHF) and spin-polarized density functional theory (DFT) are used and the calculational qualities of these two methods are also discussed. In addition, the theoretical magnetic coupling constants JAB of these models are calculated by various computational schemes for comparison with both theoretical and experimental results previously reported.

  18. Approaches and algorithms for groundwater flow modeling in support of site investigations and safety assessment of the Forsmark site, Sweden

    Science.gov (United States)

    Hartley, Lee; Joyce, Steven

    2013-09-01

    The Swedish Nuclear Fuel and Waste Management Company (SKB) has in 2011 finalized a safety assessment project, SR-Site, with the objective to assess the long term safety of a final repository for spent nuclear fuel at Forsmark in Northern Uppland of Sweden. Prior to the safety assessment, comprehensive site investigations were conducted at the Forsmark site to build understanding and characterize the site. An essential part of the site investigations were to describe hydrological properties and characteristics of the site and use this to assess the groundwater pathway. The geological structural context of the crystalline bedrock at Forsmark implied a fracture network concept was the natural description for interpreting site data and assessing the groundwater pathway. Of primary importance to the description of the fracture system was the assignment of down-borehole flow-logging measurements to individual fractures identified by imaging techniques, providing the basis to relate hydrogeological characteristics such as anisotropy and heterogeneity to the geological structural framework. Also, the key input quantities to the assessment of long-term safety can be closely related to the derived fracture flow-rate distributions. Key success factors for this project were to develop and test strategies for modeling methodologies, as described in this paper, from an early stage, hand-in-hand with the planning and phased acquisition of site data as well as successive safety assessments.

  19. Use of a coastal biogeochemical model to select environmental monitoring sites

    Science.gov (United States)

    Wild-Allen, Karen; Thompson, Peter A.; Volkman, John K.; Parslow, John

    2011-10-01

    A method for the spatial selection of sites for a coastal environmental monitoring system is described. The study was completed in southeastern Tasmania, Australia, but the method can be applied in all regions with validated biogeochemical models. A 3-dimensional coupled hydrodynamic, sediment and biogeochemical model with high spatial and temporal resolution was validated against observations collected throughout 2002 and found to capture the essential features of the biogeochemical dynamics of the system. The model was used to predict the possible quantitative environmental impact of a projected increase in fish farming activity in the region. Integrated impacts of fish farm waste on labile nitrogen, phosphorus, chlorophyll and dissolved oxygen concentrations in the water column were spatially ranked to identify the most likely places to detect environmental change due to fish farming activities. Priority sites were found to be grouped in the Huon Estuary and northern part of the D'Entrecasteaux Channel consistent with the residual northward current in the region. The final monitoring program synthesized model and field understanding to ensure adequate spatial and temporal sampling of the region.

  20. Coordination environment of the active-site metal ion of liver alcohol dehydrogenase.

    OpenAIRE

    Makinen, M W; Yim, M B

    1981-01-01

    The coordination environment of the catalytically active metal ion of horse liver alcohol dehydrogenase (alcohol:NAD+ oxidoreductase, EC 1.1.1.1) has been investigated by electron paramagnetic resonance (EPR) methods with use of the active-site-specific Co2+-reconstituted enzyme. The EPR absorption spectrum of the metal-substituted enzyme is characteristic of a rhombically distorted environment. The spectrum of the enzyme--NAD+ complex shows approximate axial symmetry of the metal ion site, i...

  1. Denaturation studies of active-site labeled papain using electron paramagnetic resonance and fluorescence spectroscopy.

    OpenAIRE

    Ping, Z A; Butterfiel, D A

    1991-01-01

    A spin-labeled p-chloromercuribenzoate (SL-PMB) and a fluorescence probe, 6-acryloyl-2-dimethylaminonaphthalene (Acrylodan), both of which bind to the single SH group located in the active site of papain, were used to investigate the interaction of papain (EC 3.4.22.2) with two protein denaturants. It was found that the active site of papain was highly stable in urea solution, but underwent a large conformational change in guanidine hydrochloride solution. Electron paramagnetic resonance and ...

  2. Complement receptor 2–mediated targeting of complement inhibitors to sites of complement activation

    OpenAIRE

    Song, Hongbin; He, Chun; Knaak, Christian; GUTHRIDGE, JOEL M.; Holers, V. Michael; Tomlinson, Stephen

    2003-01-01

    In a strategy to specifically target complement inhibitors to sites of complement activation and disease, recombinant fusion proteins consisting of a complement inhibitor linked to a C3 binding region of complement receptor (CR) 2 were prepared and characterized. Natural ligands for CR2 are C3 breakdown products deposited at sites of complement activation. Fusion proteins were prepared consisting of a human CR2 fragment linked to either the N terminus or C terminus of soluble forms of the mem...

  3. The thermal stability of the framework, hydroxyl groups, and active sites of faujasites

    Energy Technology Data Exchange (ETDEWEB)

    Mishin, I.V.; Kalinin, V.P.; Nissenbaum, V.D. [Zelinskii Institute of Organic Chemistry, Moscow (Russian Federation); Beyer, H.K. [Hungarian Academy of Sciences, Budapest (Hungary); Karge, H.G. [Fritz Haber Institute of the Max Planck Soceity, Berlin (Germany)

    1994-07-01

    The effect of the framework composition on the crystallinity and {open_quotes}density{close_quotes} of hydroxyl groups and the concentration of active sites is reported for hydrogen forms of Y zeolites preheated at 400 - 1000{degrees}C. The increase in the Si/Al ratios results in improved resistance of the framework atoms and hydroxyl groups to high temperatures and in enhanced thermal stability of the sites that are active in the cracking of isooctane and disproportionation of ethylbenzene.

  4. Active site dynamics of toluene hydroxylation by cytochrome P-450

    International Nuclear Information System (INIS)

    Rat liver cytochrome P-450 hydroxylates toluene to benzyl alcohol plus o-, m-, and p-cresol. Deuterated toluenes were incubated under saturating conditions with liver microsomes from phenobarbital-pretreated rats, and product yields and ratios were measured. Stepwise deuteration of the methyl leads to stepwise decreases in the alcohol/cresol ratio without changing the cresol isomer ratios. Extensive deuterium retention in the benzyl alcohols from PhCH2D and PhCHD2 suggests there is a large intrinsic isotope effect for benzylic hydroxylation. After replacement of the third benzylic H by D, the drop in the alcohol/cresol ratio was particularly acute, suggsting that metabolic switching from D to H within the methyl group was easier than switching from the methyl to the ring. Comparison of the alcohol/cresol ratio for PhCH3 vs PhCD3 indicated a net isotope effect of 6.9 for benzylic hydroxylation. From product yield data for PhCH3 and PhCD3, DV for benzyl alcohol formation is only 1.92, whereas DV for total product formation is 0.67 (i.e., inverse). From competitive incubations of PhCH3/PhCD3 mixtures D(V/K) isotope effects on benzyl alcohol formation and total product formation (3.6 and 1.23, respectively) are greatly reduced, implying strong commitment to catalysis. In contrast, D(V/K) for the alcohol/cresol ratio is 6.3, indicating that the majority of the intrinsic isotope effect is expressed through metabolic switching. Overall, these data are consistent with reversible formation of a complex between toluene and the active oxygen form of cytochrome P-450, which rearranges internally and reacts to form products faster than it dissociates back to release substrate

  5. Modeling Students' Units Coordinating Activity

    OpenAIRE

    Boyce, Steven James

    2014-01-01

    Primarily via constructivist teaching experiment methodology, units coordination (Steffe, 1992) has emerged as a useful construct for modeling students' psychological constructions pertaining to several mathematical domains, including counting sequences, whole number multiplicative conceptions, and fractions schemes. I describe how consideration of units coordination as a Piagetian (1970b) structure is useful for modeling units coordination across contexts. In this study, I extend teaching ...

  6. Active sites for NO reduction over Fe-ZSM-5 catalysts.

    Science.gov (United States)

    Schwidder, M; Santhosh Kumar, M; Brückner, A; Grünert, W

    2005-02-14

    A study of Fe-ZSM-5 catalysts with variable amounts of isolated, oligomeric and heavily aggregated Fe3+ oxo sites (as evidenced by UV-Vis and EPR spectroscopic data) and their catalytic properties in the selective catalytic reduction of NO by isobutane or by NH3 is presented, which allows development of a unified concept of the active Fe sites in these reactions, according to which isolated Fe sites catalyse both SCR reactions while oligomeric sites, though also involved in the selective reduction path, limit the catalyst performance by causing the total oxidation of the reductant. PMID:15685345

  7. Benzene Hydroxylation over FeZSM-5 Catalysts: Which Fe-sites Are Active?

    OpenAIRE

    Yuranov, I.; Bulushev, D. A.; Renken, A.; Kiwi-Minsker, L.

    2004-01-01

    FeZSM-5 with a wide range of Fe content (0.015–2.1 wt%) were studied in the benzene hydroxylation to phenol with nitrous oxide (C6H6:N2O = 1:5) at low temperatures (98%) was obtained within 3 h without any deactivation of the catalyst. Three types of Fe(II) sites were formed in the zeolites extraframework due to activation and are attributed to: (1) Fe(II) sites in mononuclear species, (2) oligonuclear species with at least two oxygen-bridged Fe(II) sites, and (3) Fe(II) sites within Fe2O3 na...

  8. XAFS Study of the Photo-Active Site of Mo/MCM-41

    International Nuclear Information System (INIS)

    An Mo/MCM-41 catalyst was prepared and used for study of propene and 1-butene photo-metathesis reactions. XAFS analysis revealed that hydrogen reduction leads to a decreased role for the Mo=O site. The Mo-O site plays an important role for the olefin photo-metathesis reaction on the H2 reduced Mo/MCM-41. From EXAFS analysis, the active site of photo-metathesis reaction is the Mo=O part for oxidized Mo/MCM-41, whereas it is the Mo-O site for reduced Mo/MCM-41

  9. XAFS Study of the Photo-Active Site of Mo/MCM-41

    Science.gov (United States)

    Miyamoto, Daisuke; Ichikuni, Nobuyuki; Shimazu, Shogo

    2007-02-01

    An Mo/MCM-41 catalyst was prepared and used for study of propene and 1-butene photo-metathesis reactions. XAFS analysis revealed that hydrogen reduction leads to a decreased role for the Mo=O site. The Mo-O site plays an important role for the olefin photo-metathesis reaction on the H2 reduced Mo/MCM-41. From EXAFS analysis, the active site of photo-metathesis reaction is the Mo=O part for oxidized Mo/MCM-41, whereas it is the Mo-O site for reduced Mo/MCM-41.

  10. Modeling Workflow Using UML Activity Diagram

    Institute of Scientific and Technical Information of China (English)

    Wei Yinxing(韦银星); Zhang Shensheng

    2004-01-01

    An enterprise can improve its adaptability in the changing market by means of workflow technologies. In the build time, the main function of Workflow Management System (WFMS) is to model business process. Workflow model is an abstract representation of the real-world business process. The Unified Modeling Language (UML) activity diagram is an important visual process modeling language proposed by the Object Management Group (OMG). The novelty of this paper is representing workflow model by means of UML activity diagram. A translation from UML activity diagram to π-calculus is established. Using π-calculus, the deadlock property of workflow is analyzed.

  11. Hydrogeologic Framework Model for the Saturated Zone Site Scale flow and Transport Model

    International Nuclear Information System (INIS)

    The purpose of this report is to document the 19-unit, hydrogeologic framework model (19-layer version, output of this report) (HFM-19) with regard to input data, modeling methods, assumptions, uncertainties, limitations, and validation of the model results in accordance with AP-SIII.10Q, Models. The HFM-19 is developed as a conceptual model of the geometric extent of the hydrogeologic units at Yucca Mountain and is intended specifically for use in the development of the ''Saturated Zone Site-Scale Flow Model'' (BSC 2004 [DIRS 170037]). Primary inputs to this model report include the GFM 3.1 (DTN: MO9901MWDGFM31.000 [DIRS 103769]), borehole lithologic logs, geologic maps, geologic cross sections, water level data, topographic information, and geophysical data as discussed in Section 4.1. Figure 1-1 shows the information flow among all of the saturated zone (SZ) reports and the relationship of this conceptual model in that flow. The HFM-19 is a three-dimensional (3-D) representation of the hydrogeologic units surrounding the location of the Yucca Mountain geologic repository for spent nuclear fuel and high-level radioactive waste. The HFM-19 represents the hydrogeologic setting for the Yucca Mountain area that covers about 1,350 km2 and includes a saturated thickness of about 2.75 km. The boundaries of the conceptual model were primarily chosen to be coincident with grid cells in the Death Valley regional groundwater flow model (DTN: GS960808312144.003 [DIRS 105121]) such that the base of the site-scale SZ flow model is consistent with the base of the regional model (2,750 meters below a smoothed version of the potentiometric surface), encompasses the exploratory boreholes, and provides a framework over the area of interest for groundwater flow and radionuclide transport modeling. In depth, the model domain extends from land surface to the base of the regional groundwater flow model (D'Agnese et al. 1997 [DIRS 100131], p 2). For the site-scale SZ flow model, the HFM

  12. Hydrogeologic Framework Model for the Saturated Zone Site Scale flow and Transport Model

    Energy Technology Data Exchange (ETDEWEB)

    T. Miller

    2004-11-15

    The purpose of this report is to document the 19-unit, hydrogeologic framework model (19-layer version, output of this report) (HFM-19) with regard to input data, modeling methods, assumptions, uncertainties, limitations, and validation of the model results in accordance with AP-SIII.10Q, Models. The HFM-19 is developed as a conceptual model of the geometric extent of the hydrogeologic units at Yucca Mountain and is intended specifically for use in the development of the ''Saturated Zone Site-Scale Flow Model'' (BSC 2004 [DIRS 170037]). Primary inputs to this model report include the GFM 3.1 (DTN: MO9901MWDGFM31.000 [DIRS 103769]), borehole lithologic logs, geologic maps, geologic cross sections, water level data, topographic information, and geophysical data as discussed in Section 4.1. Figure 1-1 shows the information flow among all of the saturated zone (SZ) reports and the relationship of this conceptual model in that flow. The HFM-19 is a three-dimensional (3-D) representation of the hydrogeologic units surrounding the location of the Yucca Mountain geologic repository for spent nuclear fuel and high-level radioactive waste. The HFM-19 represents the hydrogeologic setting for the Yucca Mountain area that covers about 1,350 km2 and includes a saturated thickness of about 2.75 km. The boundaries of the conceptual model were primarily chosen to be coincident with grid cells in the Death Valley regional groundwater flow model (DTN: GS960808312144.003 [DIRS 105121]) such that the base of the site-scale SZ flow model is consistent with the base of the regional model (2,750 meters below a smoothed version of the potentiometric surface), encompasses the exploratory boreholes, and provides a framework over the area of interest for groundwater flow and radionuclide transport modeling. In depth, the model domain extends from land surface to the base of the regional groundwater flow model (D'Agnese et al. 1997 [DIRS 100131], p 2). For the site

  13. The limnic ecosystems at Forsmark and Laxemar-Simpevarp. Site descriptive modelling SDM-Site

    Energy Technology Data Exchange (ETDEWEB)

    Norden, Sara; Soederbaeck, Bjoern (Swedish Nuclear Fuel and Waste Management Co., Stockholm (Sweden)); Andersson, Eva (SWECO, Stockholm (Sweden))

    2008-11-15

    the lakes are dominated by species resistant to low oxygen concentrations, mainly due to poor oxygen conditions during the winter. The streams in Forsmark are all very small, and long stretches of the streams are dry during summer. The downstream parts of some of the streams may function as passages for migrating fish, and extensive spawning migration between the sea and a downstream lake has been observed. Human activities in the area have affected the limnic ecosystem, and large parts of the streams in the Forsmark area consist of man-made ditches. Moreover, one of the lakes has been lowered and one has been divided into two basins. The ecosystem carbon models for the Forsmark area show that the lakes that contain a microbial mat have larger primary production than respiration, and thus show a positive net ecosystem production (NEP). In lakes that lack a microbial mat, respiration is similar in magnitude as primary production and net ecosystem production is close to zero. Carbon mass balance models for the Forsmark lakes indicate, in accordance with the ecosystem models, that the larger lakes (with a microbial mat) in the area have a positive NEP. However, in contrast to the ecosystem models, the mass balance models indicate that the smaller lakes in the area have negative NEP, regardless of the occurrence of a microbial mat. A low proportion (7-10%) of the carbon incorporated into primary producers in the lake is transported upwards in the food web, and instead most carbon is consumed by bacteria in the form of DOC and POC. The mass balances for a number of elements in Forsmark lakes show that the proportions of different fluxes to and from the lakes are dependent on lake size and position in the catchment, but also on the specific properties of the different elements. The Laxemar-Simpevarp lakes are small and all but one are characterized as brown-water lakes. The lakes have moderate phosphorus concentrations, whereas the concentrations of nitrogen and dissolved

  14. Human uroporphyrinogen III synthase: NMR-based mapping of the active site.

    Science.gov (United States)

    Cunha, Luis; Kuti, Miklos; Bishop, David F; Mezei, Mihaly; Zeng, Lei; Zhou, Ming-Ming; Desnick, Robert J

    2008-05-01

    Uroporphyrinogen III synthase (URO-synthase) catalyzes the cyclization and D-ring isomerization of hydroxymethylbilane (HMB) to uroporphyrinogen (URO'gen) III, the cyclic tetrapyrrole and physiologic precursor of heme, chlorophyl, and corrin. The deficient activity of human URO-synthase results in the autosomal recessive cutaneous disorder, congenital erythropoietic porphyria. Mapping of the structural determinants that specify catalysis and, potentially, protein-protein interactions is lacking. To map the active site and assess the enzyme's possible interaction in a complex with hydroxymethylbilane-synthase (HMB-synthase) and/or uroporphyrinogen-decarboxylase (URO-decarboxylase) by NMR, an efficient expression and purification procedure was developed for these cytosolic enzymes of heme biosynthesis that enabled preparation of special isotopically-labeled protein samples for NMR characterization. Using an 800 MHz instrument, assignment of the URO-synthase backbone (13)C(alpha) (100%), (1)H(alpha) (99.6%), and nonproline (1)H(N) and (15)N resonances (94%) was achieved as well as 85% of the side-chain (13)C and (1)H resonances. NMR analyses of URO-synthase titrated with competitive inhibitors N(D)-methyl-1-formylbilane (NMF-bilane) or URO'gen III, revealed resonance perturbations of specific residues lining the cleft between the two major domains of URO synthase that mapped the enzyme's active site. In silico docking of the URO-synthase crystal structure with NMF-bilane and URO'gen III was consistent with the perturbation results and provided a 3D model of the enzyme-inhibitor complex. The absence of chemical shift changes in the (15)N spectrum of URO-synthase mixed with the homogeneous HMB-synthase holoenzyme or URO-decarboxylase precluded occurrence of a stable cytosolic enzyme complex. PMID:18004775

  15. Effect of positional dependence and alignment strategy on modeling transcription factor binding sites

    OpenAIRE

    Quader Saad; Huang Chun-Hsi

    2012-01-01

    Abstract Background Many consensus-based and Position Weight Matrix-based methods for recognizing transcription factor binding sites (TFBS) are not well suited to the variability in the lengths of binding sites. Besides, many methods discard known binding sites while building the model. Moreover, the impact of Information Content (IC) and the positional dependence of nucleotides within an aligned set of TFBS has not been well researched for modeling variable-length binding sites. In this pape...

  16. Computational Models for Analysis of Illicit Activities

    DEFF Research Database (Denmark)

    Nizamani, Sarwat

    Numerous illicit activities happen in our society, which, from time to time affect the population by harming individuals directly or indirectly. Researchers from different disciplines have contributed to developing strategies to analyze such activities, in order to help law enforcement agents dev...... population globally sensitive to specific world issues. The models discuss the dynamics of population in response to such issues. All the models presented in the thesis can be combined for a systematic analysis of illicit activities.......Numerous illicit activities happen in our society, which, from time to time affect the population by harming individuals directly or indirectly. Researchers from different disciplines have contributed to developing strategies to analyze such activities, in order to help law enforcement agents...... devise policies to minimize them. These activities include cybercrimes, terrorist attacks or violent actions in response to certain world issues. Beside such activities, there are several other related activities worth analyzing, for which computational models have been presented in this thesis...

  17. The complexities of measuring access to parks and physical activity sites in New York City: a quantitative and qualitative approach

    Directory of Open Access Journals (Sweden)

    Sohler Nancy L

    2009-06-01

    Full Text Available Abstract Background Proximity to parks and physical activity sites has been linked to an increase in active behaviors, and positive impacts on health outcomes such as lower rates of cardiovascular disease, diabetes, and obesity. Since populations with a low socio-economic status as well as racial and ethnic minorities tend to experience worse health outcomes in the USA, access to parks and physical activity sites may be an environmental justice issue. Geographic Information systems were used to conduct quantitative and qualitative analyses of park accessibility in New York City, which included kernel density estimation, ordinary least squares (global regression, geographically weighted (local regression, and longitudinal case studies, consisting of field work and archival research. Accessibility was measured by both density of park acreage and density of physical activity sites. Independent variables included percent non-Hispanic black, percent Hispanic, percent below poverty, percent of adults without high school diploma, percent with limited English-speaking ability, and population density. Results The ordinary least squares linear regression found weak relationships in both the park acreage density and the physical activity site density models (Ra2 = .11 and .23, respectively; AIC = 7162 and 3529, respectively. Geographically weighted regression, however, suggested spatial non-stationarity in both models, indicating disparities in accessibility that vary over space with respect to magnitude and directionality of the relationships (AIC = 2014 and -1241, respectively. The qualitative analysis supported the findings of the local regression, confirming that although there is a geographically inequitable distribution of park space and physical activity sites, it is not globally predicted by race, ethnicity, or socio-economic status. Conclusion The combination of quantitative and qualitative analyses demonstrated the complexity of the issues around

  18. AKAP9 regulates activation-induced retention of T lymphocytes at sites of inflammation.

    Science.gov (United States)

    Herter, Jan M; Grabie, Nir; Cullere, Xavier; Azcutia, Veronica; Rosetti, Florencia; Bennett, Paul; Herter-Sprie, Grit S; Elyaman, Wassim; Luscinskas, Francis W; Lichtman, Andrew H; Mayadas, Tanya N

    2015-01-01

    The mechanisms driving T cell homing to lymph nodes and migration to tissue are well described but little is known about factors that affect T cell egress from tissues. Here, we generate mice with a T cell-specific deletion of the scaffold protein A kinase anchoring protein 9 (AKAP9) and use models of inflammatory disease to demonstrate that AKAP9 is dispensable for T cell priming and migration into tissues and lymph nodes, but is required for T cell retention in tissues. AKAP9 deficiency results in increased T cell egress to draining lymph nodes, which is associated with impaired T cell re-activation in tissues and protection from organ damage. AKAP9-deficient T cells exhibit reduced microtubule-dependent recycling of TCRs back to the cell surface and this affects antigen-dependent activation, primarily by non-classical antigen-presenting cells. Thus, AKAP9-dependent TCR trafficking drives efficient T cell re-activation and extends their retention at sites of inflammation with implications for disease pathogenesis. PMID:26680259

  19. Direct Visualization of Catalytically Active Sites at the FeO-Pt(111) Interface.

    Science.gov (United States)

    Kudernatsch, Wilhelmine; Peng, Guowen; Zeuthen, Helene; Bai, Yunhai; Merte, Lindsay R; Lammich, Lutz; Besenbacher, Flemming; Mavrikakis, Manos; Wendt, Stefan

    2015-08-25

    Within the area of surface science, one of the "holy grails" is to directly visualize a chemical reaction at the atomic scale. Whereas this goal has been reached by high-resolution scanning tunneling microscopy (STM) in a number of cases for reactions occurring at flat surfaces, such a direct view is often inhibited for reaction occurring at steps and interfaces. Here we have studied the CO oxidation reaction at the interface between ultrathin FeO islands and a Pt(111) support by in situ STM and density functional theory (DFT) calculations. Time-lapsed STM imaging on this inverse model catalyst in O2 and CO environments revealed catalytic activity occurring at the FeO-Pt(111) interface and directly showed that the Fe-edges host the catalytically most active sites for the CO oxidation reaction. This is an important result since previous evidence for the catalytic activity of the FeO-Pt(111) interface is essentially based on averaging techniques in conjunction with DFT calculations. The presented STM results are in accord with DFT+U calculations, in which we compare possible CO oxidation pathways on oxidized Fe-edges and O-edges. We found that the CO oxidation reaction is more favorable on the oxidized Fe-edges, both thermodynamically and kinetically.

  20. Direct Visualization of Catalytically Active Sites at the FeO-Pt(111) Interface

    Energy Technology Data Exchange (ETDEWEB)

    Kudernatsch, Wilhelmine; Peng, Guowen; Zeuthen, Helene; Bai, Yunhai; Merte, L. R.; Lammich, Lutz; Besenbacher, Fleming; Mavrikakis, Manos; Wendt, Stefen

    2015-08-25

    Within the area of surface science, one of the “holy grails” is to directly visualize a chemical reaction at the atomic scale. Whereas this goal has been reached by high-resolution scanning tunneling microscopy (STM) in a number of cases for reactions occurring at flat surfaces, such a direct view is often inhibited for reaction occurring at steps and interfaces. Here we have studied the CO oxidation reaction at the interface between ultrathin FeO islands and a Pt(111) support by in situ STM and density functional theory (DFT) calculations. Time-lapsed STM imaging on this inverse model catalyst in O2 and CO environments revealed catalytic activity occurring at the FeO-Pt(111) interface and directly showed that the Fe-edges host the catalytically most active sites for the CO oxidation reaction. This is an important result since previous evidence for the catalytic activity of the FeO-Pt(111) interface is essentially based on averaging techniques in conjunction with DFT calculations. The presented STM results are in accord with DFTþU calculations, in which we compare possible CO oxidation pathways on oxidized Fe-edges and O-edges. We found that the CO oxidation reaction is more favorable on the oxidized Fe-edges, both thermodynamically and kinetically.

  1. AKAP9 regulates activation-induced retention of T lymphocytes at sites of inflammation

    Science.gov (United States)

    Herter, Jan M.; Grabie, Nir; Cullere, Xavier; Azcutia, Veronica; Rosetti, Florencia; Bennett, Paul; Herter-Sprie, Grit S.; Elyaman, Wassim; Luscinskas, Francis W.; Lichtman, Andrew H.; Mayadas, Tanya N.

    2015-01-01

    The mechanisms driving T cell homing to lymph nodes and migration to tissue are well described but little is known about factors that affect T cell egress from tissues. Here, we generate mice with a T cell-specific deletion of the scaffold protein A kinase anchoring protein 9 (AKAP9) and use models of inflammatory disease to demonstrate that AKAP9 is dispensable for T cell priming and migration into tissues and lymph nodes, but is required for T cell retention in tissues. AKAP9 deficiency results in increased T cell egress to draining lymph nodes, which is associated with impaired T cell re-activation in tissues and protection from organ damage. AKAP9-deficient T cells exhibit reduced microtubule-dependent recycling of TCRs back to the cell surface and this affects antigen-dependent activation, primarily by non-classical antigen-presenting cells. Thus, AKAP9-dependent TCR trafficking drives efficient T cell re-activation and extends their retention at sites of inflammation with implications for disease pathogenesis. PMID:26680259

  2. Water-rock interaction modelling and uncertainties of mixing modelling. SDM-Site Laxemar

    Energy Technology Data Exchange (ETDEWEB)

    Gimeno, Maria J.; Auque, Luis F.; Gomez, Javier B.; Acero, Patricia (Univ. of Zaragoza, Zaragoza (Spain))

    2009-01-15

    The overall objectives of hydrogeochemical description for Laxemar are to establish a detailed understanding of the hydrogeochemical conditions at the site and to develop models that fulfil the needs identified by the safety assessment groups during the site investigation phase. Issues of concern to safety assessment are radionuclide transport and technical barrier behaviour, both of which are dependent on the chemistry of groundwater and pore water and their evolution with time. The work has involved the development of descriptive and mathematical models for groundwaters in relation to rock domains, fracture domains and deformation zones. Past climate changes are the major driving force for hydrogeochemical changes and therefore of fundamental importance for understanding the palaeohydrogeological, palaeohydrogeochemical and present evolution of groundwater in the crystalline bedrock of the Fennoscandian Shield. Understanding current undisturbed hydrochemical conditions at the proposed repository site is important when predicting future changes in groundwater chemistry. The causes of copper corrosion and/or bentonite degradation are of particular interest as they may jeopardise the long-term integrity of the planned SKB repository system. Thus, the following variables are considered for the hydrogeochemical site descriptive modelling: pH, Eh, sulphur species, iron, manganese, carbonate, phosphate, nitrogen species, total dissolved solids (TDS), isotopes, colloids, fulvic and humic acids and microorganisms. In addition, dissolved gases (e.g. carbon dioxide, methane and hydrogen) are of interest because of their likely participation in microbial reactions. In this series of reports, the final hydrogeochemical evaluation work of the site investigation at the Laxemar site, is presented. The work was conducted by SKB's hydrogeochemical project group, ChemNet, which consists of independent consultants and Univ. researchers with expertise in geochemistry

  3. Ligninolytic Peroxidase-Like Activity of a Synthetic Metalloporphine Immobilized onto Mercapto-Grafted Crosslinked PVA Inspired by the Active Site of Cytochrome P450

    Institute of Scientific and Technical Information of China (English)

    Paolo ZUCCA; Antonio RESCIGNO; Enrico SANJUST

    2011-01-01

    A synthetic metalloporphine was immobilized onto a PVA-based and mercapto-grafted solid support,emulating the active site of cytochrome P450.Its ligninolytic peroxidase-like catalytic activity was studied.The coordinated mercapto ligand significantly affected the catalytic features of the catalyst because the oxidation of lignin-model compounds was very slow by comparison with imidazole- and pyridine-coordinated immobilized metalloporphines.Conversely,the catalyst efficiently bleached several industrial dyes and thus demonstrated promising activity for this application.Based on this altered substrate specificity the oxygen-donor catalytic route seems to be more favorable than a single electron oxidation pathway.

  4. Using Carbohydrate Interaction Assays to Reveal Novel Binding Sites in Carbohydrate Active Enzymes

    DEFF Research Database (Denmark)

    Cockburn, Darrell; Wilkens, Casper; Dilokpimol, Adiphol;

    2016-01-01

    Carbohydrate active enzymes often contain auxiliary binding sites located either on independent domains termed carbohydrate binding modules (CBMs) or as so-called surface binding sites (SBSs) on the catalytic module at a certain distance from the active site. The SBSs are usually critical...... for the activity of their cognate enzyme, though they are not readily detected in the sequence of a protein, but normally require a crystal structure of a complex for their identification. A variety of methods, including affinity electrophoresis (AE), insoluble polysaccharide pulldown (IPP) and surface plasmon...... resonance (SPR) have been used to study auxiliary binding sites. These techniques are complementary as AE allows monitoring of binding to soluble polysaccharides, IPP to insoluble polysaccharides and SPR to oligosaccharides. Here we show that these methods are useful not only for analyzing known binding...

  5. Brookhaven Regional Energy Facility Siting Model (REFS): model development and application

    Energy Technology Data Exchange (ETDEWEB)

    Meier, P.; Hobbs, B.; Ketcham, G.; McCoy, M.; Stern, R.

    1979-06-01

    A siting methodology developed specifically to bridge the gap between regional-energy-system scenarios and environmental transport models is documented. Development of the model is described in Chapter 1. Chapter 2 described the basic structure of such a model. Additional chapters on model development cover: generation, transmission, demand disaggregation, the interface to other models, computational aspects, the coal sector, water resource considerations, and air quality considerations. These subjects comprise Part I. Part II, Model Applications, covers: analysis of water resource constraints, water resource issues in the New York Power Pool, water resource issues in the New England Power Pool, water resource issues in the Pennsylvania-Jersey-Maryland Power Pool, and a summary of water resource constraint analysis. (MCW)

  6. The limnic ecosystems at Forsmark and Laxemar-Simpevarp. Site descriptive modelling SDM-Site

    International Nuclear Information System (INIS)

    the lakes are dominated by species resistant to low oxygen concentrations, mainly due to poor oxygen conditions during the winter. The streams in Forsmark are all very small, and long stretches of the streams are dry during summer. The downstream parts of some of the streams may function as passages for migrating fish, and extensive spawning migration between the sea and a downstream lake has been observed. Human activities in the area have affected the limnic ecosystem, and large parts of the streams in the Forsmark area consist of man-made ditches. Moreover, one of the lakes has been lowered and one has been divided into two basins. The ecosystem carbon models for the Forsmark area show that the lakes that contain a microbial mat have larger primary production than respiration, and thus show a positive net ecosystem production (NEP). In lakes that lack a microbial mat, respiration is similar in magnitude as primary production and net ecosystem production is close to zero. Carbon mass balance models for the Forsmark lakes indicate, in accordance with the ecosystem models, that the larger lakes (with a microbial mat) in the area have a positive NEP. However, in contrast to the ecosystem models, the mass balance models indicate that the smaller lakes in the area have negative NEP, regardless of the occurrence of a microbial mat. A low proportion (7-10%) of the carbon incorporated into primary producers in the lake is transported upwards in the food web, and instead most carbon is consumed by bacteria in the form of DOC and POC. The mass balances for a number of elements in Forsmark lakes show that the proportions of different fluxes to and from the lakes are dependent on lake size and position in the catchment, but also on the specific properties of the different elements. The Laxemar-Simpevarp lakes are small and all but one are characterized as brown-water lakes. The lakes have moderate phosphorus concentrations, whereas the concentrations of nitrogen and dissolved

  7. The limnic ecosystems at Forsmark and Laxemar-Simpevarp. Site descriptive modelling SDM-Site

    Energy Technology Data Exchange (ETDEWEB)

    Norden, Sara; Soederbaeck, Bjoern (Swedish Nuclear Fuel and Waste Management Co., Stockholm (Sweden)); Andersson, Eva (SWECO, Stockholm (Sweden))

    2008-11-15

    the lakes are dominated by species resistant to low oxygen concentrations, mainly due to poor oxygen conditions during the winter. The streams in Forsmark are all very small, and long stretches of the streams are dry during summer. The downstream parts of some of the streams may function as passages for migrating fish, and extensive spawning migration between the sea and a downstream lake has been observed. Human activities in the area have affected the limnic ecosystem, and large parts of the streams in the Forsmark area consist of man-made ditches. Moreover, one of the lakes has been lowered and one has been divided into two basins. The ecosystem carbon models for the Forsmark area show that the lakes that contain a microbial mat have larger primary production than respiration, and thus show a positive net ecosystem production (NEP). In lakes that lack a microbial mat, respiration is similar in magnitude as primary production and net ecosystem production is close to zero. Carbon mass balance models for the Forsmark lakes indicate, in accordance with the ecosystem models, that the larger lakes (with a microbial mat) in the area have a positive NEP. However, in contrast to the ecosystem models, the mass balance models indicate that the smaller lakes in the area have negative NEP, regardless of the occurrence of a microbial mat. A low proportion (7-10%) of the carbon incorporated into primary producers in the lake is transported upwards in the food web, and instead most carbon is consumed by bacteria in the form of DOC and POC. The mass balances for a number of elements in Forsmark lakes show that the proportions of different fluxes to and from the lakes are dependent on lake size and position in the catchment, but also on the specific properties of the different elements. The Laxemar-Simpevarp lakes are small and all but one are characterized as brown-water lakes. The lakes have moderate phosphorus concentrations, whereas the concentrations of nitrogen and dissolved

  8. A new insight into the nature of seasonal variations in coordinate time series of GPS sites located near active faults

    Science.gov (United States)

    Trofimenko, Sergey V.; Bykov, Victor G.; Shestakov, Nikolay V.; Grib, Nikolay N.; Takahashi, Hiroaki

    2016-09-01

    This study provides new insights into the nature of seasonal variations in coordinate time series of GPS sites located near active faults and methods of their modeling. Monthly averaged coordinate time series were analyzed for several pairs of collocated GPS sites situated near the active fault intersection area, in close proximity to the central part of the northern boundary of the Amurian plate and the vicinity of the San Andreas Fault zone. It is concluded that the observed seasonal variations are best described by a breather function which is one of the solutions of the well-known sine-Gordon equation. The obtained results suggest that, in this case, the source of seasonal variations may be caused by the appearance of solitary strain waves in the fault intersection system, which may be qualitatively treated as standing waves of compression-extension of the geological medium. Based on statistical testing, the limits of applicability of the suggested model have been established.

  9. Waste inventory and preliminary source term model for the Greater Confinement Disposal site at the Nevada Test Site

    Energy Technology Data Exchange (ETDEWEB)

    Chu, M.S.Y.; Bernard, E.A.

    1991-12-01

    Currently, there are several Greater Confinement Disposal (GCD) boreholes at the Radioactive Waste Management Site (RWMS) for the Nevada Test Site. These are intermediate-depth boreholes used for the disposal of special case wastes, that is, radioactive waste within the Department of Energy complex that do not meet the criteria established for disposal of high-level waste, transuranic waste, or low-level waste. A performance assessment is needed to evaluate the safety of the GCD site, and to examine the feasibility of the GCD disposal concept as a disposal solution for special case wastes in general. This report documents the effort in defining all the waste inventory presently disposed of at the GCD site, and the inventory and release model to be used in a performance assessment for compliance with the Environmental Protection Agency`s 40 CFR 191.

  10. Discursive Positionings and Emotions in Modelling Activities

    Science.gov (United States)

    Daher, Wajeeh

    2015-01-01

    Mathematical modelling is suggested as an activity through which students engage in meaningful mathematics. In the current research, the modelling activity of a group of four seventh-grade students was analysed using the discursive analysis framework. The research findings show that the positionings and emotions of the group members during their…

  11. Underground Test Area Activity Quality Assurance Plan Nevada National Security Site, Nevada. Revision 1

    Energy Technology Data Exchange (ETDEWEB)

    Farnham, Irene [Navarro-Intera, LLC (N-I), Las Vegas, NV (United States); Krenzien, Susan [Navarro-Intera, LLC (N-I), Las Vegas, NV (United States)

    2012-10-01

    This Quality Assurance Plan (QAP) provides the overall quality assurance (QA) requirements and general quality practices to be applied to the U.S. Department of Energy (DOE), National Nuclear Security Administration Nevada Site Office (NNSA/NSO) Underground Test Area (UGTA) activities. The requirements in this QAP are consistent with DOE Order 414.1C, Quality Assurance (DOE, 2005); U.S. Environmental Protection Agency (EPA) Guidance for Quality Assurance Project Plans for Modeling (EPA, 2002); and EPA Guidance on the Development, Evaluation, and Application of Environmental Models (EPA, 2009). NNSA/NSO, or designee, must review this QAP every two years. Changes that do not affect the overall scope or requirements will not require an immediate QAP revision but will be incorporated into the next revision cycle after identification. Section 1.0 describes UGTA objectives, participant responsibilities, and administrative and management quality requirements (i.e., training, records, procurement). Section 1.0 also details data management and computer software requirements. Section 2.0 establishes the requirements to ensure newly collected data are valid, existing data uses are appropriate, and environmental-modeling methods are reliable. Section 3.0 provides feedback loops through assessments and reports to management. Section 4.0 provides the framework for corrective actions. Section 5.0 provides references for this document.

  12. Students’ mathematical learning in modelling activities

    DEFF Research Database (Denmark)

    Kjeldsen, Tinne Hoff; Blomhøj, Morten

    2013-01-01

    involved. We argue that progress in students’ conceptual learning needs to be conceptualised separately from that of progress in their modelling competency. Findings are that modelling activities open a window to the students’ images of the mathematical concepts involved; that modelling activities can......Ten years of experience with analyses of students’ learning in a modelling course for first year university students, led us to see modelling as a didactical activity with the dual goal of developing students’ modelling competency and enhancing their conceptual learning of mathematical concepts...... create and help overcome hidden cognitive conflicts in students’ understanding; that reflections within modelling can play an important role for the students’ learning of mathematics. These findings are illustrated with a modelling project concerning the world population....

  13. Evaluating a Model of Youth Physical Activity

    Science.gov (United States)

    Heitzler, Carrie D.; Lytle, Leslie A.; Erickson, Darin J.; Barr-Anderson, Daheia; Sirard, John R.; Story, Mary

    2010-01-01

    Objective: To explore the relationship between social influences, self-efficacy, enjoyment, and barriers and physical activity. Methods: Structural equation modeling examined relationships between parent and peer support, parent physical activity, individual perceptions, and objectively measured physical activity using accelerometers among a…

  14. Modelling Typical Online Language Learning Activity

    Science.gov (United States)

    Montoro, Carlos; Hampel, Regine; Stickler, Ursula

    2014-01-01

    This article presents the methods and results of a four-year-long research project focusing on the language learning activity of individual learners using online tasks conducted at the University of Guanajuato (Mexico) in 2009-2013. An activity-theoretical model (Blin, 2010; Engeström, 1987) of the typical language learning activity was used to…

  15. Activity after Site-Directed Mutagenesis of CD59 on Complement-Mediated Cytolysis

    Institute of Scientific and Technical Information of China (English)

    Xinhong Zhu; Meihua Gao; Shurong Ren; Qiubo Wang; Cunzhi Lin

    2008-01-01

    CD59 may inhibit the cytolytic activity of complement by binding to C8/C9 and protect host cell membranes against homologous membrane attack complex (MAC). However, CD59 is widely overexpressed on tumor cells,which has been implicated in tumorigenesis. The active site of CD59 relative to MAC is still confused. As reported the MAC binding site is located in the vicinity of a hydrophobic groove on the membrane distal face of the protein centered around residue W40. Here two site-directed mutagenesis were performed by overlapping extension PCR to delete residue W40 site (Mutant 1, M1) or to change C39W40K41 to W39W40W41 (Mutant 2, M2). Then we constructed mutant CD59 eukaryotic expression system and investigated their biological function on CHO cells compared with wild-type CD59. Stable populations of CHO cells expressing recombinant proteins were screened by immunotechnique. After 30 passages culturing, proteins could be tested. Dye release assays suggest that M1CD59 loses the activity against complement, while M2CD59 increases the anti-complement activity slightly.Results indicate that W40 of human CD59 is important to its activity, and prohibition of this site may be a potential way to increase complement activity and to treat tumors.

  16. Using Carbohydrate Interaction Assays to Reveal Novel Binding Sites in Carbohydrate Active Enzymes.

    Science.gov (United States)

    Cockburn, Darrell; Wilkens, Casper; Dilokpimol, Adiphol; Nakai, Hiroyuki; Lewińska, Anna; Abou Hachem, Maher; Svensson, Birte

    2016-01-01

    Carbohydrate active enzymes often contain auxiliary binding sites located either on independent domains termed carbohydrate binding modules (CBMs) or as so-called surface binding sites (SBSs) on the catalytic module at a certain distance from the active site. The SBSs are usually critical for the activity of their cognate enzyme, though they are not readily detected in the sequence of a protein, but normally require a crystal structure of a complex for their identification. A variety of methods, including affinity electrophoresis (AE), insoluble polysaccharide pulldown (IPP) and surface plasmon resonance (SPR) have been used to study auxiliary binding sites. These techniques are complementary as AE allows monitoring of binding to soluble polysaccharides, IPP to insoluble polysaccharides and SPR to oligosaccharides. Here we show that these methods are useful not only for analyzing known binding sites, but also for identifying new ones, even without structural data available. We further verify the chosen assays discriminate between known SBS/CBM containing enzymes and negative controls. Altogether 35 enzymes are screened for the presence of SBSs or CBMs and several novel binding sites are identified, including the first SBS ever reported in a cellulase. This work demonstrates that combinations of these methods can be used as a part of routine enzyme characterization to identify new binding sites and advance the study of SBSs and CBMs, allowing them to be detected in the absence of structural data. PMID:27504624

  17. Cyanide does more to inhibit heme enzymes, than merely serving as an active-site ligand

    Energy Technology Data Exchange (ETDEWEB)

    Parashar, Abhinav [Center for Biomedical Research, VIT University, Vellore, Tamil Nadu, 632014 India (India); Venkatachalam, Avanthika [REDOx Lab, PSG Institute of Advanced Studies, Avinashi Road, Peelamedu, Coimbatore, Tamil Nadu, 641004 (India); Gideon, Daniel Andrew [Center for Biomedical Research, VIT University, Vellore, Tamil Nadu, 632014 India (India); Manoj, Kelath Murali, E-mail: satyamjayatu@yahoo.com [REDOx Lab, PSG Institute of Advanced Studies, Avinashi Road, Peelamedu, Coimbatore, Tamil Nadu, 641004 (India)

    2014-12-12

    Highlights: • Cyanide (CN) is a well-studied toxic principle, known to inhibit heme-enzymes. • Inhibition is supposed to result from CN binding at the active site as a ligand. • Diverse heme enzymes’ CN inhibition profiles challenge prevailing mechanism. • Poor binding efficiency of CN at low enzyme concentrations and ligand pressures. • CN-based diffusible radicals cause ‘non-productive electron transfers’ (inhibition). - Abstract: The toxicity of cyanide is hitherto attributed to its ability to bind to heme proteins’ active site and thereby inhibit their activity. It is shown herein that the long-held interpretation is inadequate to explain several observations in heme-enzyme reaction systems. Generation of cyanide-based diffusible radicals in heme-enzyme reaction milieu could shunt electron transfers (by non-active site processes), and thus be detrimental to the efficiency of oxidative outcomes.

  18. SITE-94. Discrete-feature modelling of the Aespoe Site: 3. Predictions of hydrogeological parameters for performance assessment

    Energy Technology Data Exchange (ETDEWEB)

    Geier, J.E. [Golder Associates AB, Uppsala (Sweden)

    1996-12-01

    A 3-dimensional, discrete-feature hydrological model is developed. The model integrates structural and hydrologic data for the Aespoe site, on scales ranging from semi regional fracture zones to individual fractures in the vicinity of the nuclear waste canisters. Predicted parameters for the near field include fracture spacing, fracture aperture, and Darcy velocity at each of forty canister deposition holes. Parameters for the far field include discharge location, Darcy velocity, effective longitudinal dispersion coefficient and head gradient, flow porosity, and flow wetted surface, for each canister source that discharges to the biosphere. Results are presented in the form of statistical summaries for a total of 42 calculation cases, which treat a set of 25 model variants in various combinations. The variants for the SITE-94 Reference Case model address conceptual and parametric uncertainty related to the site-scale hydrogeologic model and its properties, the fracture network within the repository, effective semi regional boundary conditions for the model, and the disturbed-rock zone around the repository tunnels and shafts. Two calculation cases simulate hydrologic conditions that are predicted to occur during future glacial episodes. 30 refs.

  19. SITE-94. Discrete-feature modelling of the Aespoe Site: 3. Predictions of hydrogeological parameters for performance assessment

    International Nuclear Information System (INIS)

    A 3-dimensional, discrete-feature hydrological model is developed. The model integrates structural and hydrologic data for the Aespoe site, on scales ranging from semi regional fracture zones to individual fractures in the vicinity of the nuclear waste canisters. Predicted parameters for the near field include fracture spacing, fracture aperture, and Darcy velocity at each of forty canister deposition holes. Parameters for the far field include discharge location, Darcy velocity, effective longitudinal dispersion coefficient and head gradient, flow porosity, and flow wetted surface, for each canister source that discharges to the biosphere. Results are presented in the form of statistical summaries for a total of 42 calculation cases, which treat a set of 25 model variants in various combinations. The variants for the SITE-94 Reference Case model address conceptual and parametric uncertainty related to the site-scale hydrogeologic model and its properties, the fracture network within the repository, effective semi regional boundary conditions for the model, and the disturbed-rock zone around the repository tunnels and shafts. Two calculation cases simulate hydrologic conditions that are predicted to occur during future glacial episodes. 30 refs

  20. Mechanistic pathways of mercury removal from the organomercurial lyase active site.

    Science.gov (United States)

    Silva, Pedro J; Rodrigues, Viviana

    2015-01-01

    protonation by solvent-provided H3O(+). Thiolate addition to the active site (prior to any attack by thiols) leads to pathways where the removal of the first cysteine becomes the rate-determining step, irrespective of whether Cys159 or Cys96 leaves first. Comparisons with the recently computed mechanism of the related enzyme MerA further underline the important role of Asp99 in the energetics of the MerB reaction. Kinetic simulation of the mechanism derived from our computations strongly suggests that in vivo the thiolate-only pathway is operative, and the Asp-assisted pathway (as well as the conversion of intermediates of the thiolate pathway into intermediates of the Cys-assisted pathway) is prevented by steric factors absent from our model and related to the precise geometry of the organomercurial binding-pocket. PMID:26246970

  1. Identification of potential sites for deep-ocean waste isolation with a geographic site-selection model

    Science.gov (United States)

    Fleischer, Peter; Bowles, Frederick A.; Richardson, Michael D.

    1998-05-01

    Identification of optimal sites for the isolation of waste on the abyssal seafloor was performed with two approaches: by the traditional method of map overlays of relevant attributes, and by a specially developed, automated Site-Selection Model (SSM). Five initial, Surrogate Sites, identified with the map-overlay approach, were then compared with the more rigorously produced scores from the SSM. The SSM, a process for optimization of site locations, accepts subjective, expert-based judgments and transforms them into a quantitative, reproducible, and documented product. The SSM is adaptable to any siting scenario. Forty-one factors relevant to the isolation scenario, including 21 weightable factors having a total of 123 scorable categories, have been entered into the SSM. Factors are grouped under project definition, unique environments, anthropogenic, geologic, biologic, weather, oceanographic and distance criteria. The factor scores are linked to a georeferenced database array of all factors, corresponding to 1°×1° latitude-longitude squares. The SSM includes a total of 2241 one-degree squares within 1000 n.m. of the U.S. coasts, including the western North Atlantic, the Gulf of Mexico, and the eastern North Pacific. Under a carefully weighted and scored scenario of isolation, the most favorable sites identified with the SSM are on the Hatteras and Nares Abyssal Plains in the Atlantic. High-scoring sites are also located in the Pacific abyssal hills province between the Murray and Molokai Fracture Zones. Acceptable 1° squares in the Gulf of Mexico are few and of lower quality, with the optimum location on the northern Sigsbee Abyssal Plain. Two of the five Surrogate Site locations, on the Hatteras and Sigsbee Abyssal Plains, correspond to the best SSM sites in each ocean area. Two Pacific and a second Atlantic Surrogate Site are located in low-scoring regions or excluded by the SSM. Site-selection results from the SSM, although robust, are an initial attempt

  2. The activity model of legal psychologist

    OpenAIRE

    N.V. Bogdanovich,; V.A. Chernushevich

    2014-01-01

    We propose an activity model of legal psychologist work. As a basis for the construction of the system of legal psychologist activity, we use trajectory of teenager living in the legal field. As the main activities within their respective specializations, we highlighted prevention, maintenance and rehabilitation. We define the main activities necessary for the development within the FGOSIII specialization 050407 “Pedagogy and Psychology of deviant behavior”: general and pathopsychologic diagn...

  3. Crystal structure of an avian influenza polymerase PA[subscript N] reveals an endonuclease active site

    Energy Technology Data Exchange (ETDEWEB)

    Yuan, Puwei; Bartlam, Mark; Lou, Zhiyong; Chen, Shoudeng; Zhou, Jie; He, Xiaojing; Lv, Zongyang; Ge, Ruowen; Li, Xuemei; Deng, Tao; Fodor, Ervin; Rao, Zihe; Liu, Yingfang; (NU Sinapore); (Nankai); (Oxford); (Chinese Aca. Sci.); (Tsinghua)

    2009-11-10

    The heterotrimeric influenza virus polymerase, containing the PA, PB1 and PB2 proteins, catalyses viral RNA replication and transcription in the nucleus of infected cells. PB1 holds the polymerase active site and reportedly harbours endonuclease activity, whereas PB2 is responsible for cap binding. The PA amino terminus is understood to be the major functional part of the PA protein and has been implicated in several roles, including endonuclease and protease activities as well as viral RNA/complementary RNA promoter binding. Here we report the 2.2 angstrom (A) crystal structure of the N-terminal 197 residues of PA, termed PA(N), from an avian influenza H5N1 virus. The PA(N) structure has an alpha/beta architecture and reveals a bound magnesium ion coordinated by a motif similar to the (P)DX(N)(D/E)XK motif characteristic of many endonucleases. Structural comparisons and mutagenesis analysis of the motif identified in PA(N) provide further evidence that PA(N) holds an endonuclease active site. Furthermore, functional analysis with in vivo ribonucleoprotein reconstitution and direct in vitro endonuclease assays strongly suggest that PA(N) holds the endonuclease active site and has critical roles in endonuclease activity of the influenza virus polymerase, rather than PB1. The high conservation of this endonuclease active site among influenza strains indicates that PA(N) is an important target for the design of new anti-influenza therapeutics.

  4. Modelling activity transport behavior in PWR plant

    International Nuclear Information System (INIS)

    The activation and transport of corrosion products around a PWR circuit is a major concern to PWR plant operators as these may give rise to high personnel doses. The understanding of what controls dose rates on ex-core surfaces and shutdown releases has improved over the years but still several questions remain unanswered. For example the relative importance of particle and soluble deposition in the core to activity levels in the plant is not clear. Wide plant to plant and cycle to cycle variations are noted with no apparent explanations why such variations are observed. Over the past few years this group have been developing models to simulate corrosion product transport around a PWR circuit. These models form the basis for the latest version of the BOA code and simulate the movement of Fe and Ni around the primary circuit. Part of this development is to include the activation and subsequent transport of radioactive species around the circuit and this paper describes some initial modelling work in this area. A simple model of activation, release and deposition is described and then applied to explain the plant behaviour at Sizewell B and Vandellos II. This model accounts for activation in the core, soluble and particulate activity movement around the circuit and for activity capture ex-core on both the inner and outer oxides. The model gives a reasonable comparison with plant observations and highlights what controls activity transport in these plants and importantly what factors can be ignored. (authors)

  5. Large zinc cation occupancy of octahedral sites in mechanically activated zinc ferrite powders

    International Nuclear Information System (INIS)

    The cation site occupancy of a mechanically activated nanocrystalline zinc ferrite powder was determined as (Zn0.552+Fe0.183+)tet[Zr0.452+Fe1.823+]octO4 through analysis of extended x-ray absorption fine structure measurements, showing a large redistribution of cations between sites compared to normal zinc ferrite samples. The overpopulation of cations in the octahedral sites was attributed to the ascendance in importance of the ionic radii over the crystal energy and bonding coordination in determining which interstitial sites are occupied in this structurally disordered powder. Slight changes are observed in the local atomic environment about the zinc cations, but not the iron cations, with respect to the spinel structure. The presence of Fe3+ on both sites is consistent with the measured room temperature magnetic properties. (c) 2000 American Institute of Physics

  6. The toponymy of communal activity: Anglo-Saxon assembly sites and their functions

    OpenAIRE

    Baker, John

    2014-01-01

    The paper builds on earlier discussion of the multiple functions of medieval judicial assembly sites, providing a comprehensive evaluation of relevant English hundred-names, and making reference to associated microtoponymy. While religious, military, commercial, and recreational activities may all have occurred at assembly-sites, it can be hard to delineate the evidence so clearly along these lines, and attempts to do so may be anachronistic in some instances; nevertheless, the analysis of di...

  7. Identification of essential histidine residues in the active site of Escherichia coli xylose (glucose) isomerase.

    OpenAIRE

    Batt, C A; Jamieson, A. C.; Vandeyar, M A

    1990-01-01

    Two conserved histidine residues (His-101 and His-271) appear to be essential components in the active site of the enzyme xylose (glucose) isomerase (EC 5.3.1.5). These amino acid residues were targeted for mutagenesis on the basis of sequence homology among xylose isomerases isolated from Escherichia coli, Bacillus subtilis, Ampullariella sp. strain 3876, and Streptomyces violaceus-niger. Each residue was selectively replaced by site-directed mutagenesis and shown to be essential for activit...

  8. Activity transport models for PWR primary circuits

    International Nuclear Information System (INIS)

    The corrosion products activated in the primary circuit form a major source of occupational radiation dose in the PWR reactors. Transport of corrosion activity is a complex process including chemistry, reactor physics, thermodynamics and hydrodynamics. All the mechanisms involved are not known and there is no comprehensive theory for the process, so experimental test loops and plant data are very important in research efforts. Several activity transport modelling attempts have been made to improve the water chemistry control and to minimise corrosion in PWR's. In this research report some of these models are reviewed with special emphasis on models designed for Soviet VVER type reactors. (51 refs., 16 figs., 4 tabs.)

  9. Modified Active Site Coordination in a Clinical Mutant of Sulfite Oxidase

    Energy Technology Data Exchange (ETDEWEB)

    Doonan, C.J.; Wilson, H.L.; Rajagopalan, K.V.; Garrett, R.M.; Bennett, B.; Prince, R.C.; George, G.N.

    2009-06-02

    The molybdenum site of the Arginine 160 {yields} Glutamine clinical mutant of the physiologically vital enzyme sulfite oxidase has been investigated by a combination of X-ray absorption spectroscopy and density functional theory calculations. We conclude that the mutant enzyme has a six-coordinate pseudo-octahedral active site with coordination of Glutamine O{sup {epsilon}} to molybdenum. This contrasts with the wild-type enzyme which is five-coordinate with approximately square-based pyramidal geometry. This difference in the structure of the molybdenum site explains many of the properties of the mutant enzyme which have previously been reported.

  10. Conformational Change in the Active Site of Streptococcal Unsaturated Glucuronyl Hydrolase Through Site-Directed Mutagenesis at Asp-115.

    Science.gov (United States)

    Nakamichi, Yusuke; Oiki, Sayoko; Mikami, Bunzo; Murata, Kousaku; Hashimoto, Wataru

    2016-08-01

    Bacterial unsaturated glucuronyl hydrolase (UGL) degrades unsaturated disaccharides generated from mammalian extracellular matrices, glycosaminoglycans, by polysaccharide lyases. Two Asp residues, Asp-115 and Asp-175 of Streptococcus agalactiae UGL (SagUGL), are completely conserved in other bacterial UGLs, one of which (Asp-175 of SagUGL) acts as a general acid and base catalyst. The other Asp (Asp-115 of SagUGL) also affects the enzyme activity, although its role in the enzyme reaction has not been well understood. Here, we show substitution of Asp-115 in SagUGL with Asn caused a conformational change in the active site. Tertiary structures of SagUGL mutants D115N and D115N/K370S with negligible enzyme activity were determined at 2.00 and 1.79 Å resolution, respectively, by X-ray crystallography. The side chain of Asn-115 is drastically shifted in both mutants owing to the interaction with several residues, including Asp-175, by formation of hydrogen bonds. This interaction between Asn-115 and Asp-175 probably prevents the mutants from triggering the enzyme reaction using Asp-175 as an acid catalyst. PMID:27402448

  11. Discursive positionings and emotions in modelling activities

    Science.gov (United States)

    Daher, Wajeeh

    2015-11-01

    Mathematical modelling is suggested as an activity through which students engage in meaningful mathematics. In the current research, the modelling activity of a group of four seventh-grade students was analysed using the discursive analysis framework. The research findings show that the positionings and emotions of the group members during their participation in the modelling activity changed as the activity proceeded. Overall, it can be said that three of the four group members acted as insiders, while the fourth acted as an outsider, and only, towards the end of the group's work on the activity, he acted as an insider. Moreover, the research findings point at four factors that affected the group members' positionings and emotions during the modelling activity: the member's characteristics, the member's history of learning experiences, the activity characteristics and the modelling phases. Furthermore, the different positionings of the group members in the different modelling phases were accompanied by different emotions experienced by them, where being an insider and a collaborator resulted in positive emotions, while being an outsider resulted in negative emotions.

  12. Water-rock interaction modelling and uncertainties of mixing modelling. SDM-Site Forsmark

    Energy Technology Data Exchange (ETDEWEB)

    Gimeno, Maria J.; Auque, Luis F.; Gomez, Javier B.; Acero, Patricia (Univ. of Zaragoza, Zaragoza (Spain))

    2008-08-15

    The overall objectives of the hydrogeochemical description for Forsmark are to establish a detailed understanding of the hydrogeochemical conditions at the site and to develop models that fulfil the needs identified by the safety assessment groups during the site investigation phase. Issues of concern to safety assessment are radionuclide transport and technical barrier behaviour, both of which are dependent on the chemistry of groundwater and pore water and their evolution with time. The work has involved the development of descriptive and mathematical models for groundwaters in relation to rock domains, fracture domains and deformation zones. Past climate changes are one of the major driving forces for hydrogeochemical changes and therefore of fundamental importance for understanding the palaeohydrogeological, palaeohydrogeochemical and present evolution of groundwater in the crystalline bedrock of the Fennoscandian Shield. Understanding current undisturbed hydrochemical conditions at the proposed repository site is important when predicting future changes in groundwater chemistry. The causes behind of copper corrosion and/or bentonite degradation are of particular interest as they may jeopardise the long-term integrity of the planned SKB repository system. Thus, the following variables are considered for the hydrogeochemical site descriptive modelling: pH, Eh, sulphur species, iron, manganese, carbonate, phosphate, nitrogen species, total dissolved solids (TDS), isotopes, colloids, fulvic and humic acids and microorganisms. In addition, dissolved gases (e.g. carbon dioxide, methane and hydrogen) are of interest because of their likely participation in microbial reactions. In this series of reports, the final hydrogeochemical evaluation work of the site investigation at the Forsmark site, is presented. The work was conducted by SKB's hydrogeochemical project group, ChemNet, which consists of independent consultants and university researchers with expertise

  13. Improving the neutral phytase activity from Bacillus amyloliquefaciens DSM 1061 by site-directed mutagenesis.

    Science.gov (United States)

    Xu, Wei; Shao, Rong; Wang, Zupeng; Yan, Xiuhua

    2015-03-01

    Neutral phytase is used as a feed additive for degradation of anti-nutritional phytate in aquatic feed industry. Site-directed mutagenesis of Bacillus amyloliquefaciens DSM 1061 phytase was performed with an aim to increase its activity. Mutation residues were chosen based on multiple sequence alignments and structure analysis of neutral phytsaes from different microorganisms. The mutation sites on surface (D148E, S197E and N156E) and around the active site (D52E) of phytase were selected. Analysis of the phytase variants showed that the specific activities of mutants D148E and S197E remarkably increased by about 35 and 13% over a temperature range of 40-75 °C at pH 7.0, respectively. The k cat of mutants D148E and S197E were 1.50 and 1.25 times than that of the wild-type phytase, respectively. Both D148E and S197E showed much higher thermostability than that of the wild-type phytase. However, mutants N156E and D52E led to significant loss of specific activity of the enzyme. Structural analysis revealed that these mutations may affect conformation of the active site of phytase. The present mutant phytases D148E and S197E with increased activities and thermostabilities have application potential as additives in aquaculture feed. PMID:25613522

  14. Stringency of the 2-His-1-Asp active-site motif in prolyl 4-hydroxylase.

    Directory of Open Access Journals (Sweden)

    Kelly L Gorres

    Full Text Available The non-heme iron(II dioxygenase family of enzymes contain a common 2-His-1-carboxylate iron-binding motif. These enzymes catalyze a wide variety of oxidative reactions, such as the hydroxylation of aliphatic C-H bonds. Prolyl 4-hydroxylase (P4H is an alpha-ketoglutarate-dependent iron(II dioxygenase that catalyzes the post-translational hydroxylation of proline residues in protocollagen strands, stabilizing the ensuing triple helix. Human P4H residues His412, Asp414, and His483 have been identified as an iron-coordinating 2-His-1-carboxylate motif. Enzymes that catalyze oxidative halogenation do so by a mechanism similar to that of P4H. These halogenases retain the active-site histidine residues, but the carboxylate ligand is replaced with a halide ion. We replaced Asp414 of P4H with alanine (to mimic the active site of a halogenase and with glycine. These substitutions do not, however, convert P4H into a halogenase. Moreover, the hydroxylase activity of D414A P4H cannot be rescued with small molecules. In addition, rearranging the two His and one Asp residues in the active site eliminates hydroxylase activity. Our results demonstrate a high stringency for the iron-binding residues in the P4H active site. We conclude that P4H, which catalyzes an especially demanding chemical transformation, is recalcitrant to change.

  15. Quantum delocalization of protons in the hydrogen bond network of an enzyme active site

    CERN Document Server

    Wang, Lu; Boxer, Steven G; Markland, Thomas E

    2015-01-01

    Enzymes utilize protein architectures to create highly specialized structural motifs that can greatly enhance the rates of complex chemical transformations. Here we use experiments, combined with ab initio simulations that exactly include nuclear quantum effects, to show that a triad of strongly hydrogen bonded tyrosine residues within the active site of the enzyme ketosteroid isomerase (KSI) facilitates quantum proton delocalization. This delocalization dramatically stabilizes the deprotonation of an active site tyrosine residue, resulting in a very large isotope effect on its acidity. When an intermediate analog is docked, it is incorporated into the hydrogen bond network, giving rise to extended quantum proton delocalization in the active site. These results shed light on the role of nuclear quantum effects in the hydrogen bond network that stabilizes the reactive intermediate of KSI, and the behavior of protons in biological systems containing strong hydrogen bonds.

  16. Contribution of physical modelling to climate-driven landslide hazard mapping: an alpine test site

    Science.gov (United States)

    Vandromme, R.; Desramaut, N.; Baills, A.; Hohmann, A.; Grandjean, G.; Sedan, O.; Mallet, J. P.

    2012-04-01

    The aim of this work is to develop a methodology for integrating climate change scenarios into quantitative hazard assessment and especially their precipitation component. The effects of climate change will be different depending on both the location of the site and the type of landslide considered. Indeed, mass movements can be triggered by different factors. This paper describes a methodology to address this issue and shows an application on an alpine test site. Mechanical approaches represent a solution for quantitative landslide susceptibility and hazard modeling. However, as the quantity and the quality of data are generally very heterogeneous at a regional scale, it is necessary to take into account the uncertainty in the analysis. In this perspective, a new hazard modeling method is developed and integrated in a program named ALICE. This program integrates mechanical stability analysis through a GIS software taking into account data uncertainty. This method proposes a quantitative classification of landslide hazard and offers a useful tool to gain time and efficiency in hazard mapping. However, an expertise approach is still necessary to finalize the maps. Indeed it is the only way to take into account some influent factors in slope stability such as heterogeneity of the geological formations or effects of anthropic interventions. To go further, the alpine test site (Barcelonnette area, France) is being used to integrate climate change scenarios into ALICE program, and especially their precipitation component with the help of a hydrological model (GARDENIA) and the regional climate model REMO (Jacob, 2001). From a DEM, land-cover map, geology, geotechnical data and so forth the program classifies hazard zones depending on geotechnics and different hydrological contexts varying in time. This communication, realized within the framework of Safeland project, is supported by the European Commission under the 7th Framework Programme for Research and Technological

  17. Mutations Closer to the Active Site Improve the Promiscuous Aldolase Activity of 4-Oxalocrotonate Tautomerase More Effectively than Distant Mutations.

    Science.gov (United States)

    Rahimi, Mehran; van der Meer, Jan-Ytzen; Geertsema, Edzard M; Poddar, Harshwardhan; Baas, Bert-Jan; Poelarends, Gerrit J

    2016-07-01

    The enzyme 4-oxalocrotonate tautomerase (4-OT), which catalyzes enol-keto tautomerization as part of a degradative pathway for aromatic hydrocarbons, promiscuously catalyzes various carbon-carbon bond-forming reactions. These include the aldol condensation of acetaldehyde with benzaldehyde to yield cinnamaldehyde. Here, we demonstrate that 4-OT can be engineered into a more efficient aldolase for this condensation reaction, with a >5000-fold improvement in catalytic efficiency (kcat /Km ) and a >10(7) -fold change in reaction specificity, by exploring small libraries in which only "hotspots" are varied. The hotspots were identified by systematic mutagenesis (covering each residue), followed by a screen for single mutations that give a strong improvement in the desired aldolase activity. All beneficial mutations were near the active site of 4-OT, thus underpinning the notion that new catalytic activities of a promiscuous enzyme are more effectively enhanced by mutations close to the active site. PMID:27238293

  18. Testing the applicability of rapid on-site enzymatic activity detection for surface water monitoring

    Science.gov (United States)

    Stadler, Philipp; Vogl, Wolfgang; Juri, Koschelnik; Markus, Epp; Maximilian, Lackner; Markus, Oismüller; Monika, Kumpan; Peter, Strauss; Regina, Sommer; Gabriela, Ryzinska-Paier; Farnleitner Andreas, H.; Matthias, Zessner

    2015-04-01

    On-site detection of enzymatic activities has been suggested as a rapid surrogate for microbiological pollution monitoring of water resources (e.g. using glucuronidases, galactosidases, esterases). Due to the possible short measuring intervals enzymatic methods have high potential as near-real time water quality monitoring tools. This presentation describes results from a long termed field test. For twelve months, two ColiMinder devices (Vienna Water Monitoring, Austria) for on-site determination of enzymatic activity were tested for stream water monitoring at the experimental catchment HOAL (Hydrological Open Air Laboratory, Center for Water Resource Systems, Vienna University of Technology). The devices were overall able to follow and reflect the diverse hydrological and microbiological conditions of the monitored stream during the test period. Continuous data in high temporal resolution captured the course of enzymatic activity in stream water during diverse rainfall events. The method also proofed sensitive enough to determine diurnal fluctuations of enzymatic activity in stream water during dry periods. The method was able to capture a seasonal trend of enzymatic activity in stream water that matches the results gained from Colilert18 analysis for E. coli and coliform bacteria of monthly grab samples. Furthermore the comparison of ColiMinder data with measurements gained at the same test site with devices using the same method but having different construction design (BACTcontrol, microLAN) showed consistent measuring results. Comparative analysis showed significant differences between measured enzymatic activity (modified fishman units and pmol/min/100ml) and cultivation based analyses (most probable number, colony forming unit). Methods of enzymatic activity measures are capable to detect ideally the enzymatic activity caused by all active target bacteria members, including VBNC (viable but nonculturable) while cultivation based methods cannot detect VBNC

  19. MODELES STRUCTURAUX ET FONTIONNELS DU SITE ACTIF DES HYDROGENASES [NIFE] : DE NOUVEAUX CATALYSEURS BIO-INSPIRES POUR LA PRODUCTION D'HYDROGENE

    OpenAIRE

    Oudart, Yohan

    2006-01-01

    Hydrogenase enzymes reversibly catalyse the oxidation and production of hydrogen in a range close to the thermodynamic potential. The [NiFe] hydrogenase active site contains an iron-cyano-carbonyl moiety linked to a nickel atom which is in an all sulphur environment. Both the active site originality and the potential development of an hydrogen economy make the synthesis of functional and structural models worthy.To take up this challenge, we have synthesised mononuclear ruthenium models and m...

  20. Fragment-based identification of determinants of conformational and spectroscopic change at the ricin active site

    Directory of Open Access Journals (Sweden)

    Soares Alexei S

    2007-11-01

    Full Text Available Abstract Background Ricin is a potent toxin and known bioterrorism threat with no available antidote. The ricin A-chain (RTA acts enzymatically to cleave a specific adenine base from ribosomal RNA, thereby blocking translation. To understand better the relationship between ligand binding and RTA active site conformational change, we used a fragment-based approach to find a minimal set of bonding interactions able to induce rearrangements in critical side-chain positions. Results We found that the smallest ligand stabilizing an open conformer of the RTA active site pocket was an amide group, bound weakly by only a few hydrogen bonds to the protein. Complexes with small amide-containing molecules also revealed a switch in geometry from a parallel towards a splayed arrangement of an arginine-tryptophan cation-pi interaction that was associated with an increase and red-shift in tryptophan fluorescence upon ligand binding. Using the observed fluorescence signal, we determined the thermodynamic changes of adenine binding to the RTA active site, as well as the site-specific binding of urea. Urea binding had a favorable enthalpy change and unfavorable entropy change, with a ΔH of -13 ± 2 kJ/mol and a ΔS of -0.04 ± 0.01 kJ/(K*mol. The side-chain position of residue Tyr80 in a complex with adenine was found not to involve as large an overlap of rings with the purine as previously considered, suggesting a smaller role for aromatic stacking at the RTA active site. Conclusion We found that amide ligands can bind weakly but specifically to the ricin active site, producing significant shifts in positions of the critical active site residues Arg180 and Tyr80. These results indicate that fragment-based drug discovery methods are capable of identifying minimal bonding determinants of active-site side-chain rearrangements and the mechanistic origins of spectroscopic shifts. Our results suggest that tryptophan fluorescence provides a sensitive probe for the

  1. Threatened and endangered wildlife species of the Hanford Site related to CERCLA characterization activities

    Energy Technology Data Exchange (ETDEWEB)

    Fitzner, R.E. [Pacific Northwest Lab., Richland, WA (United States); Weiss, S.G.; Stegen, J.A. [Westinghouse Hanford Co., Richland, WA (United States)

    1994-06-01

    The US Department of Energy`s (DOE) Hanford Site has been placed on the National Priorities List, which requires that it be remediated under the Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) or Superfund. Potentially contaminated areas of the Hanford Site were grouped into operable units, and detailed characterization and investigation plans were formulated. The DOE Richland Operations Office requested Westinghouse Hanford Company (WHC) to conduct a biological assessment of the potential impact of these characterization activities on the threatened, endangered, and sensitive wildlife species of the Hanford Site. Additional direction for WHC compliances with wildlife protection can be found in the Environmental Compliance Manual. This document is intended to meet these requirements, in part, for the CERCLA characterization activities, as well as for other work comparable in scope. This report documents the biological assessment and describes the pertinent components of the Hanford Site as well as the planned characterization activities. Also provided are accounts of endangered, threatened, and federal candidate wildlife species on the Hanford Site and information as to how human disturbances can affect these species. Potential effects of the characterization activities are described with recommendations for mitigation measures.

  2. Symmetrical 1-pyrrolidineacetamide showing anti-HIV activity through a new binding site on HIV-1 integrase

    Institute of Scientific and Technical Information of China (English)

    Li DU; Ya-xue ZHAO; Liu-meng YANG; Yong-tang ZHENG; Yun TANG; Xu SHEN; Hua-liang JIANG

    2008-01-01

    Aim:To characterize the functional and pharmacological features of a symmetrical 1-pyrrolidineacetamide,N,N'-(methylene-di-4,1-phenylene) bis-1-pyrrolidineacetamide,as a new anti-HIV compound which could competitively inhibit HIV-1 integrase (IN) binding to viral DNA.Methods:A surface plasma resonance (SPR)-based competitive assay was employed to determine the compound's inhibitory activity,and the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide cell assay was used to qualify the antiviral activity.The potential binding sites were predicted by molecular modeling and determined by site-directed mutagenesis and a SPR binding assay.Results:l-pyrrolidineacetamide,N,N'-(methylene-di-4,1-phenylene) bis-1-pyrrolidineacetamide could competitively inhibit IN binding to viral DNA with a 50% inhibitory concentration (IC50) value of 7.29±0.68 μmol/L as investigated by SPR-based investigation.Another antiretroviral activity assay showed that this compound exhibited inhibition against HⅣ-Ⅰ(ⅢB) replication with a 50% effective concentration (EC50) value of 40.54 μmol/L in C8166 cells,and cytotoxicity with a cytotoxic concentration value of 173.84 μmol/L in mock-infected C8166 cells.Molecular docking predicted 3 potential residues as 1-pyrrolidineacetamide,N,N'-(methylene-di-4,1-phenylene)bis-1-pyrrolidineacetamide binding sites.The importance of 3 key amino acid residues (Lys103,Lys173,and Thr174) involved in the binding was further identified by site-directed mutagenesis and a SPR binding assay.Conclusion:This present work identified a new anti-HIV compound through a new IN-binding site which is expected to supply new potential drug-binding site information for HIV-1 integrase inhibitor discovery and development.

  3. SABER: a computational method for identifying active sites for new reactions.

    Science.gov (United States)

    Nosrati, Geoffrey R; Houk, K N

    2012-05-01

    A software suite, SABER (Selection of Active/Binding sites for Enzyme Redesign), has been developed for the analysis of atomic geometries in protein structures, using a geometric hashing algorithm (Barker and Thornton, Bioinformatics 2003;19:1644-1649). SABER is used to explore the Protein Data Bank (PDB) to locate proteins with a specific 3D arrangement of catalytic groups to identify active sites that might be redesigned to catalyze new reactions. As a proof-of-principle test, SABER was used to identify enzymes that have the same catalytic group arrangement present in o-succinyl benzoate synthase (OSBS). Among the highest-scoring scaffolds identified by the SABER search for enzymes with the same catalytic group arrangement as OSBS were L-Ala D/L-Glu epimerase (AEE) and muconate lactonizing enzyme II (MLE), both of which have been redesigned to become effective OSBS catalysts, demonstrated by experiments. Next, we used SABER to search for naturally existing active sites in the PDB with catalytic groups similar to those present in the designed Kemp elimination enzyme KE07. From over 2000 geometric matches to the KE07 active site, SABER identified 23 matches that corresponded to residues from known active sites. The best of these matches, with a 0.28 Å catalytic atom RMSD to KE07, was then redesigned to be compatible with the Kemp elimination using RosettaDesign. We also used SABER to search for potential Kemp eliminases using a theozyme predicted to provide a greater rate acceleration than the active site of KE07, and used Rosetta to create a design based on the proteins identified.

  4. The active site of low-temperature methane hydroxylation in iron-containing zeolites

    Science.gov (United States)

    Snyder, Benjamin E. R.; Vanelderen, Pieter; Bols, Max L.; Hallaert, Simon D.; Böttger, Lars H.; Ungur, Liviu; Pierloot, Kristine; Schoonheydt, Robert A.; Sels, Bert F.; Solomon, Edward I.

    2016-08-01

    An efficient catalytic process for converting methane into methanol could have far-reaching economic implications. Iron-containing zeolites (microporous aluminosilicate minerals) are noteworthy in this regard, having an outstanding ability to hydroxylate methane rapidly at room temperature to form methanol. Reactivity occurs at an extra-lattice active site called α-Fe(II), which is activated by nitrous oxide to form the reactive intermediate α-O; however, despite nearly three decades of research, the nature of the active site and the factors determining its exceptional reactivity are unclear. The main difficulty is that the reactive species—α-Fe(II) and α-O—are challenging to probe spectroscopically: data from bulk techniques such as X-ray absorption spectroscopy and magnetic susceptibility are complicated by contributions from inactive ‘spectator’ iron. Here we show that a site-selective spectroscopic method regularly used in bioinorganic chemistry can overcome this problem. Magnetic circular dichroism reveals α-Fe(II) to be a mononuclear, high-spin, square planar Fe(II) site, while the reactive intermediate, α-O, is a mononuclear, high-spin Fe(IV)=O species, whose exceptional reactivity derives from a constrained coordination geometry enforced by the zeolite lattice. These findings illustrate the value of our approach to exploring active sites in heterogeneous systems. The results also suggest that using matrix constraints to activate metal sites for function—producing what is known in the context of metalloenzymes as an ‘entatic’ state—might be a useful way to tune the activity of heterogeneous catalysts.

  5. The active site of low-temperature methane hydroxylation in iron-containing zeolites.

    Science.gov (United States)

    Snyder, Benjamin E R; Vanelderen, Pieter; Bols, Max L; Hallaert, Simon D; Böttger, Lars H; Ungur, Liviu; Pierloot, Kristine; Schoonheydt, Robert A; Sels, Bert F; Solomon, Edward I

    2016-08-18

    An efficient catalytic process for converting methane into methanol could have far-reaching economic implications. Iron-containing zeolites (microporous aluminosilicate minerals) are noteworthy in this regard, having an outstanding ability to hydroxylate methane rapidly at room temperature to form methanol. Reactivity occurs at an extra-lattice active site called α-Fe(ii), which is activated by nitrous oxide to form the reactive intermediate α-O; however, despite nearly three decades of research, the nature of the active site and the factors determining its exceptional reactivity are unclear. The main difficulty is that the reactive species-α-Fe(ii) and α-O-are challenging to probe spectroscopically: data from bulk techniques such as X-ray absorption spectroscopy and magnetic susceptibility are complicated by contributions from inactive 'spectator' iron. Here we show that a site-selective spectroscopic method regularly used in bioinorganic chemistry can overcome this problem. Magnetic circular dichroism reveals α-Fe(ii) to be a mononuclear, high-spin, square planar Fe(ii) site, while the reactive intermediate, α-O, is a mononuclear, high-spin Fe(iv)=O species, whose exceptional reactivity derives from a constrained coordination geometry enforced by the zeolite lattice. These findings illustrate the value of our approach to exploring active sites in heterogeneous systems. The results also suggest that using matrix constraints to activate metal sites for function-producing what is known in the context of metalloenzymes as an 'entatic' state-might be a useful way to tune the activity of heterogeneous catalysts. PMID:27535535

  6. Conserved phosphorylation sites in the activation loop of the Arabidopsis phytosulfokine receptor PSKR1 differentially affect kinase and receptor activity.

    Science.gov (United States)

    Hartmann, Jens; Linke, Dennis; Bönniger, Christine; Tholey, Andreas; Sauter, Margret

    2015-12-15

    PSK (phytosulfokine) is a plant peptide hormone perceived by a leucine-rich repeat receptor kinase. Phosphosite mapping of epitope-tagged PSKR1 (phytosulfokine receptor 1) from Arabidopsis thaliana plants identified Ser(696) and Ser(698) in the JM (juxtamembrane) region and probably Ser(886) and/or Ser(893) in the AL (activation loop) as in planta phosphorylation sites. In vitro-expressed kinase was autophosphorylated at Ser(717) in the JM, and at Ser(733), Thr(752), Ser(783), Ser(864), Ser(911), Ser(958) and Thr(998) in the kinase domain. The LC-ESI-MS/MS spectra provided support that up to three sites (Thr(890), Ser(893) and Thr(894)) in the AL were likely to be phosphorylated in vitro. These sites are evolutionarily highly conserved in PSK receptors, indicative of a conserved function. Site-directed mutagenesis of the four conserved residues in the activation segment, Thr(890), Ser(893), Thr(894) and Thr(899), differentially altered kinase activity in vitro and growth-promoting activity in planta. The T899A and the quadruple-mutated TSTT-A (T890A/S893A/T894A/T899A) mutants were both kinase-inactive, but PSKR1(T899A) retained growth-promoting activity. The T890A and S893A/T894A substitutions diminished kinase activity and growth promotion. We hypothesize that phosphorylation within the AL activates kinase activity and receptor function in a gradual and distinctive manner that may be a means to modulate the PSK response. PMID:26472115

  7. Pipeline for Efficient Mapping of Transcription Factor Binding Sites and Comparison of Their Models

    KAUST Repository

    Ba alawi, Wail

    2011-06-01

    The control of genes in every living organism is based on activities of transcription factor (TF) proteins. These TFs interact with DNA by binding to the TF binding sites (TFBSs) and in that way create conditions for the genes to activate. Of the approximately 1500 TFs in human, TFBSs are experimentally derived only for less than 300 TFs and only in generally limited portions of the genome. To be able to associate TF to genes they control we need to know if TFs will have a potential to interact with the control region of the gene. For this we need to have models of TFBS families. The existing models are not sufficiently accurate or they are too complex for use by ordinary biologists. To remove some of the deficiencies of these models, in this study we developed a pipeline through which we achieved the following: 1. Through a comparison analysis of the performance we identified the best models with optimized thresholds among the four different types of models of TFBS families. 2. Using the best models we mapped TFBSs to the human genome in an efficient way. The study shows that a new scoring function used with TFBS models based on the position weight matrix of dinucleotides with remote dependency results in better accuracy than the other three types of the TFBS models. The speed of mapping has been improved by developing a parallelized code and shows a significant speed up of 4x when going from 1 CPU to 8 CPUs. To verify if the predicted TFBSs are more accurate than what can be expected with the conventional models, we identified the most frequent pairs of TFBSs (for TFs E4F1 and ATF6) that appeared close to each other (within the distance of 200 nucleotides) over the human genome. We show unexpectedly that the genes that are most close to the multiple pairs of E4F1/ATF6 binding sites have a co-expression of over 90%. This indirectly supports our hypothesis that the TFBS models we use are more accurate and also suggests that the E4F1/ATF6 pair is exerting the

  8. Native Plant Uptake Model for Radioactive Waste Disposal Areas at the Nevada Test Site

    International Nuclear Information System (INIS)

    This report defines and defends the basic framework, methodology, and associated input parameters for modeling plant uptake of radionuclides for use in Performance Assessment (PA) activities of Radioactive Waste Management Sites (RWMS) at the Nevada Test Site (NTS). PAs are used to help determine whether waste disposal configurations meet applicable regulatory standards for the protection of human health, the environment, or both. Plants adapted to the arid climate of the NTS are able to rapidly capture infiltrating moisture. In addition to capturing soil moisture, plant roots absorb nutrients, minerals, and heavy metals, transporting them within the plant to the above-ground biomass. In this fashion, plant uptake affects the movement of radionuclides. The plant uptake model presented reflects rooting characteristics important to plant uptake, biomass turnover rates, and the ability of plants to uptake radionuclides from the soil. Parameters are provided for modeling plant uptake and estimating surface contaminant flux due to plant uptake under both current and potential future climate conditions with increased effective soil moisture. The term ''effective moisture'' is used throughout this report to indicate the soil moisture that is available to plants and is intended to be inclusive of all the variables that control soil moisture at a site (e.g., precipitation, temperature, soil texture, and soil chemistry). Effective moisture is a concept used to simplify a number of complex, interrelated soil processes for which there are too little data to model actual plant available moisture. The PA simulates both the flux of radionuclides across the land surface and the potential dose to humans from that flux. Surface flux is modeled here as the amount of soil contamination that is transferred from the soil by roots and incorporated into aboveground biomass. Movement of contaminants to the surface is the only transport mechanism evaluated with the model presented here

  9. Native Plant Uptake Model for Radioactive Waste Disposal Areas at the Nevada Test Site

    Energy Technology Data Exchange (ETDEWEB)

    BROWN,THERESA J.; WIRTH,SHARON

    1999-09-01

    This report defines and defends the basic framework, methodology, and associated input parameters for modeling plant uptake of radionuclides for use in Performance Assessment (PA) activities of Radioactive Waste Management Sites (RWMS) at the Nevada Test Site (NTS). PAs are used to help determine whether waste disposal configurations meet applicable regulatory standards for the protection of human health, the environment, or both. Plants adapted to the arid climate of the NTS are able to rapidly capture infiltrating moisture. In addition to capturing soil moisture, plant roots absorb nutrients, minerals, and heavy metals, transporting them within the plant to the above-ground biomass. In this fashion, plant uptake affects the movement of radionuclides. The plant uptake model presented reflects rooting characteristics important to plant uptake, biomass turnover rates, and the ability of plants to uptake radionuclides from the soil. Parameters are provided for modeling plant uptake and estimating surface contaminant flux due to plant uptake under both current and potential future climate conditions with increased effective soil moisture. The term ''effective moisture'' is used throughout this report to indicate the soil moisture that is available to plants and is intended to be inclusive of all the variables that control soil moisture at a site (e.g., precipitation, temperature, soil texture, and soil chemistry). Effective moisture is a concept used to simplify a number of complex, interrelated soil processes for which there are too little data to model actual plant available moisture. The PA simulates both the flux of radionuclides across the land surface and the potential dose to humans from that flux. Surface flux is modeled here as the amount of soil contamination that is transferred from the soil by roots and incorporated into aboveground biomass. Movement of contaminants to the surface is the only transport mechanism evaluated with the model

  10. Activity-based resource capability modeling

    Institute of Scientific and Technical Information of China (English)

    CHENG Shao-wu; XU Xiao-fei; WANG Gang; SUN Xue-dong

    2008-01-01

    To analyse and optimize a enterprise process in a wide scope, an activity-based method of modeling resource capabilities is presented. It models resource capabilities by means of the same structure as an activity, that is, resource capabilities are defined by input objects, actions and output objects. A set of activity-based re-source capability modeling rules and matching rules between an activity and a resource are introduced. This method can not only be used to describe capability of manufacturing tools, but also capability of persons and applications, etc. It unifies methods of modeling capability of all kinds of resources in an enterprise and supports the optimization of the resource allocation of a process.

  11. Bedrock Hydrogeology - Groundwater flow modelling. Site investigation SFR

    Energy Technology Data Exchange (ETDEWEB)

    Oehman, Johan [Geosigma AB, Uppsala (Sweden); Follin, Sven [SF GeoLogic AB, Taeby (Sweden); Oden, Magnus [SKB, Stockholm (Sweden)

    2013-05-15

    The hydrogeological model developed for the SFR extension project (PSU) consists of 40 geologically modelled deformation zones (DZ) and 8 sub-horizontal structural-hydraulic features, called SBAstructures, not defined in the geological model. However, some of the SBA-structures coincide with what is defined as unresolved possible deformation zones (Unresolved PDZ) in the geological modelling. In addition, the hydrogeological model consists of a stochastic discrete fracture network (DFN) model intended for the less fractured rock mass volumes (fracture domains) between the zones and the SBA-structures, and a stochastic fracture model intended to handle remaining Unresolved PDZs in the geological modelling not modelled as SBA-structures in the hydrogeological modelling. The four structural components of the bedrock in the hydrogeological model, i.e. DZ, SBA, Unresolved PDZ and DFN, are assigned hydraulic properties in the hydrogeological model based on the transmissivities interpreted from single-hole hydraulic tests. The main objective of the present work is to present the characteristics of the hydrogeological model with regard to the needs of the forthcoming safety assessment SR-PSU. In concrete words, simulated data are compared with measured data, i.e. hydraulic heads in boreholes and tunnel inflow to the existing repository (SFR). The calculations suggest that the available data for flow model calibration cannot be used to motivate a substantial adjustment of the initial hydraulic parameterisation (assignment of hydraulic properties) of the hydrogeological model. It is suggested that uncertainties in the hydrogeological model are studied in the safety assessment SR-PSU by means of a large number of calculation cases. These should address hydraulic heterogeneity of deterministic structures (DZ and SBA) and realisations of stochastic fractures/fracture networks (Unresolved PDZ and DFN) within the entire SFR Regional model domain.

  12. Site investigation SFR. Hydrogeological modelling of SFR. Model version 0.2

    Energy Technology Data Exchange (ETDEWEB)

    Oehman, Johan (Golder Associates AB (Sweden)); Follin, Sven (SF GeoLogic (Sweden))

    2010-01-15

    The Swedish Nuclear Fuel and Waste Management Company (SKB) has conducted site investigations for a planned extension of the existing final repository for short-lived radioactive waste (SFR). A hydrogeological model is developed in three model versions, which will be used for safety assessment and design analyses. This report presents a data analysis of the currently available hydrogeological data from the ongoing Site Investigation SFR (KFR27, KFR101, KFR102A, KFR102B, KFR103, KFR104, and KFR105). The purpose of this work is to develop a preliminary hydrogeological Discrete Fracture Network model (hydro-DFN) parameterisation that can be applied in regional-scale modelling. During this work, the Geologic model had not yet been updated for the new data set. Therefore, all analyses were made to the rock mass outside Possible Deformation Zones, according to Single Hole Interpretation. Owing to this circumstance, it was decided not to perform a complete hydro-DFN calibration at this stage. Instead focus was re-directed to preparatory test cases and conceptual questions with the aim to provide a sound strategy for developing the hydrogeological model SFR v. 1.0. The presented preliminary hydro-DFN consists of five fracture sets and three depth domains. A statistical/geometrical approach (connectivity analysis /Follin et al. 2005/) was performed to estimate the size (i.e. fracture radius) distribution of fractures that are interpreted as Open in geologic mapping of core data. Transmissivity relations were established based on an assumption of a correlation between the size and evaluated specific capacity of geologic features coupled to inflows measured by the Posiva Flow Log device (PFL-f data). The preliminary hydro-DFN was applied in flow simulations in order to test its performance and to explore the role of PFL-f data. Several insights were gained and a few model technical issues were raised. These are summarised in Table 5-1

  13. Utility experiences in redevelopment of formerly used sites -- Wisconsin Electric's risk management and economic development activities

    International Nuclear Information System (INIS)

    Wisconsin Electric Power Company, which recently celebrated its 100th anniversary, has actively promoted the redevelopment of its former sites as well as those of its customers. Serving Milwaukee and southeast Wisconsin, Wisconsin Electric's (WE) sites include former power plants, landfills, right-of-ways, and manufactured gas plant sites. In setting an example for others, as well as seeking to maximize the economic value of these sites, WE has either redeveloped or promoted the redevelopment of these sites by others. Examples include the East Wells Power Plant (now home of the Milwaukee Repertory Theater), the Lakeside Power Plant Site (now the home of Harnischfeger Corporation's headquarters), and the Commerce Street Power Plant located on the Milwaukee River near downtown Milwaukee. In each case the company evaluated the potential environmental liabilities against the unrealized asset value derived from facility location, site size, architectural uniqueness, or other characteristics. At the Commerce Street Power Plant, walking distance to the downtown Milwaukee business district combined with river frontage, were significant site values leveraged against a $5 million asbestos and lead-based paint removal project done to prepare the plant for marketing. More recently, WE has used its experience in promoting the redevelopment of the Menomonee River Valley, the original core of Milwaukee's industrial community, and in advancing a more practical regulatory approach to redeveloping older sites. Finally, the company is working with a non-profit community health clinic, community groups and local foundations in linking these redevelopment activities with the economic and physical health of inner city residents

  14. Estimating nitrogen fluxes at the European scale by upscaling INTEGRATOR model outputs from selected sites

    OpenAIRE

    G. J. Reinds; Heuvelink, G.B.M.; T. Hoogland; J. Kros; de Vries, W.

    2012-01-01

    A comparison was made between upscaled model results of nitrogen (N) fluxes to air and water from 450 sites within the EU-27 and results derived for the entire EU-27 area using the model INTEGRATOR. The 450 sites were selected using stratified random sampling, dividing the EU-27 into 150 strata and selecting three sites at random within each stratum. The strata were based on important environmental factors influencing N fluxes. Hierarchical divisive cluster analysis was used to reduce the num...

  15. Models for siting repair parts inventories in support of a Naval Air Rework Facility

    OpenAIRE

    McMasters, Alan W.

    1981-01-01

    Trade-off models are developed for siting inventories of repair parts by Naval Supply Center (NSC) which must support a local Naval Air Rework Facility (NARF). Two strategies are considered; siting at the NSC with direct delivery alternatives which include both scheduled and unscheduled delivery schemes are modeled when siting is at the NSC. The measure of effectiveness for all alternatives is the expected total costs per time period. Cost elements include delivery costs and production delay ...

  16. Data Catalog for Models Simulating Release of Contaminants from Hanford Site Waste Sources

    International Nuclear Information System (INIS)

    This report is an update to the previously published catalog that summarized information published since 1987 on models that have been used to simulate release of chemical and radioactive contaminants from waste sources on the Hanford Site. Tables in this report provide links to data sources needed to implement release models. These links enable users to quickly locate the specific release model information and data they need to apply the models to future site assessments.

  17. Optimizing warehouse logistics operations through site selection models : Istanbul, Turkey

    OpenAIRE

    Erdemir, Ugur

    2003-01-01

    Approved for public release; distribution is unlimited This thesis makes a cost benefit analysis of relocating the outdated and earthquake damaged supply distribution center of the Turkish Navy. Given the dynamic environment surrounding the military operations, logistic sustainability requirements, rapid information technology developments, and budget-constrained Turkish DoD acquisition environment, the site selection of a supply distribution center is critical to the future operations and...

  18. Human Activities in Natura 2000 Sites: A Highly Diversified Conservation Network

    Science.gov (United States)

    Tsiafouli, Maria A.; Apostolopoulou, Evangelia; Mazaris, Antonios D.; Kallimanis, Athanasios S.; Drakou, Evangelia G.; Pantis, John D.

    2013-05-01

    The Natura 2000 network was established across the European Union's (EU) Member States with the aim to conserve biodiversity, while ensuring the sustainability of human activities. However, to what kind and to what extent Natura 2000 sites are subject to human activities and how this varies across Member States remains unspecified. Here, we analyzed 111,269 human activity records from 14,727 protected sites in 20 Member States. The frequency of occurrence of activities differs among countries, with more than 86 % of all sites being subjected to agriculture or forestry. Activities like hunting, fishing, urbanization, transportation, and tourism are more frequently recorded in south European sites than in northern or eastern ones. The observed variations indicate that Natura 2000 networks are highly heterogeneous among EU Member States. Our analysis highlights the importance of agriculture in European landscapes and indicates possible targets for policy interventions at national, European, or "sub-European" level. The strong human presence in the Natura 2000 network throughout Member States, shows that conservation initiatives could succeed only by combining social and ecological sustainability and by ensuring the integration of policies affecting biodiversity.

  19. Autocatalytic activation of the furin zymogen requires removal of the emerging enzyme's N-terminus from the active site.

    Directory of Open Access Journals (Sweden)

    Katarzyna Gawlik

    Full Text Available Before furin can act on protein substrates, it must go through an ordered process of activation. Similar to many other proteinases, furin is synthesized as a zymogen (profurin which becomes active only after the autocatalytic removal of its auto-inhibitory prodomain. We hypothesized that to activate profurin its prodomain had to be removed and, in addition, the emerging enzyme's N-terminus had to be ejected from the catalytic cleft.We constructed and analyzed the profurin mutants in which the egress of the emerging enzyme's N-terminus from the catalytic cleft was restricted. Mutants were autocatalytically processed at only the primary cleavage site Arg-Thr-Lys-Arg(107 downward arrowAsp(108, but not at both the primary and the secondary (Arg-Gly-Val-Thr-Lys-Arg(75 downward arrowSer(76 cleavage sites, yielding, as a result, the full-length prodomain and mature furins commencing from the N-terminal Asp108. These correctly processed furin mutants, however, remained self-inhibited by the constrained N-terminal sequence which continuously occupied the S' sub-sites of the catalytic cleft and interfered with the functional activity. Further, using the in vitro cleavage of the purified prodomain and the analyses of colon carcinoma LoVo cells with the reconstituted expression of the wild-type and mutant furins, we demonstrated that a three-step autocatalytic processing including the cleavage of the prodomain at the previously unidentified Arg-Leu-Gln-Arg(89 downward arrowGlu(90 site, is required for the efficient activation of furin.Collectively, our results show the restrictive role of the enzyme's N-terminal region in the autocatalytic activation mechanisms. In a conceptual form, our data apply not only to profurin alone but also to a range of self-activated proteinases.

  20. Gis-Based Wind Farm Site Selection Model Offshore Abu Dhabi Emirate, Uae

    Science.gov (United States)

    Saleous, N.; Issa, S.; Mazrouei, J. Al

    2016-06-01

    The United Arab Emirates (UAE) government has declared the increased use of alternative energy a strategic goal and has invested in identifying and developing various sources of such energy. This study aimed at assessing the viability of establishing wind farms offshore the Emirate of Abu Dhabi, UAE and to identify favourable sites for such farms using Geographic Information Systems (GIS) procedures and algorithms. Based on previous studies and on local requirements, a set of suitability criteria was developed including ocean currents, reserved areas, seabed topography, and wind speed. GIS layers were created and a weighted overlay GIS model based on the above mentioned criteria was built to identify suitable sites for hosting a new offshore wind energy farm. Results showed that most of Abu Dhabi offshore areas were unsuitable, largely due to the presence of restricted zones (marine protected areas, oil extraction platforms and oil pipelines in particular). However, some suitable sites could be identified, especially around Delma Island and North of Jabal Barakah in the Western Region. The environmental impact of potential wind farm locations and associated cables on the marine ecology was examined to ensure minimal disturbance to marine life. Further research is needed to specify wind mills characteristics that suit the study area especially with the presence of heavy traffic due to many oil production and shipping activities in the Arabian Gulf most of the year.

  1. The Oskarshamn model for public involvement in the siting of nuclear facilities

    Energy Technology Data Exchange (ETDEWEB)

    Aahagen, H. [Ahagen and Co (Sweden); CarIsson, Torsten [Mayor, Oskarshamn (Sweden); Hallberg, K. [Local Competence Building, Oskarshamn (Sweden); Andersson, Kjell [Karinta-Konsult, Taeby(Sweden)

    1999-12-01

    The Oskarshamn model has so far worked extremely well as a tool to achieve openness and public participation. The municipality involvement has been successful in several aspects, e.g.: It has been possible to influence the program, to a large extent, to meet certain municipality conditions and to ensure the local perspective. The local competence has increased to a considerable degree. The activities generated by the six working groups with a total of 40 members have generated a large number of contacts with various organisations, schools, mass media, individuals in the general public and interest groups. For the future, clarification of the disposal method and site selection criteria as well as the site selection process as such is crucial. The municipality has also emphasised the importance of SKB having shown the integration between site selection criteria, the feasibility study and the safety assessment. Furthermore, the programs for the encapsulation facility and the repository must be co-ordinated. For Oskarshamn it will be of utmost importance that the repository is well under way to be realised before the encapsulation facility can be built.

  2. The Oskarshamn model for public involvement in the siting of nuclear facilities

    International Nuclear Information System (INIS)

    The Oskarshamn model has so far worked extremely well as a tool to achieve openness and public participation. The municipality involvement has been successful in several aspects, e.g.: It has been possible to influence the program, to a large extent, to meet certain municipality conditions and to ensure the local perspective. The local competence has increased to a considerable degree. The activities generated by the six working groups with a total of 40 members have generated a large number of contacts with various organisations, schools, mass media, individuals in the general public and interest groups. For the future, clarification of the disposal method and site selection criteria as well as the site selection process as such is crucial. The municipality has also emphasised the importance of SKB having shown the integration between site selection criteria, the feasibility study and the safety assessment. Furthermore, the programs for the encapsulation facility and the repository must be co-ordinated. For Oskarshamn it will be of utmost importance that the repository is well under way to be realised before the encapsulation facility can be built

  3. A facile reflux procedure to increase active surface sites form highly active and durable supported palladium@platinum bimetallic nanodendrites

    Science.gov (United States)

    Wang, Qin; Li, Yingjun; Liu, Baocang; Xu, Guangran; Zhang, Geng; Zhao, Qi; Zhang, Jun

    2015-11-01

    A series of well-dispersed bimetallic Pd@Pt nanodendrites uniformly supported on XC-72 carbon black are fabricated by using different capping agents. These capping agents are essential for the branched morphology control. However, the surfactant adsorbed on the nanodendrites surface blocks the access of reactant molecules to the active surface sites, and the catalytic activities of these bimetallic nanodendrites are significantly restricted. Herein, a facile reflux procedure to effectively remove the capping agent molecules without significantly affecting their sizes is reported for activating supported nanocatalysts. More significantly, the structure and morphology of the nanodendrites can also be retained, enhancing the numbers of active surface sites, catalytic activity and stability toward methanol and ethanol electro-oxidation reactions. The as-obtained hot water reflux-treated Pd@Pt/C catalyst manifests superior catalytic activity and stability both in terms of surface and mass specific activities, as compared to the untreated catalysts and the commercial Pt/C and Pd/C catalysts. We anticipate that this effective and facile removal method has more general applicability to highly active nanocatalysts prepared with various surfactants, and should lead to improvements in environmental protection and energy production.

  4. Learning models of activities involving interacting objects

    DEFF Research Database (Denmark)

    Manfredotti, Cristina; Pedersen, Kim Steenstrup; Hamilton, Howard J.;

    2013-01-01

    We propose the LEMAIO multi-layer framework, which makes use of hierarchical abstraction to learn models for activities involving multiple interacting objects from time sequences of data concerning the individual objects. Experiments in the sea navigation domain yielded learned models that were t...

  5. POISONING OF ACTIVE SITES ON ZIEGLER-NATTA CATALYST FOR PROPYLENE POLYMERIZATION

    Institute of Scientific and Technical Information of China (English)

    Kitti Tangjituabun; Sang Yull Kim; Yuichi Hiraoka; Toshiaki Taniike; Minoru Terano; Bunjerd Jongsomjit; Piyasan Praserthdam

    2008-01-01

    The effects of poisoning materials on catalytic activity and isospecificity of the supported Ziegler-Natta catalyst were investigated.A minor amount of simple structure of Lewis base,i.e.,methanol,acetone,ethyl acetate,was introduced into the catalyst slurry for partial poisoning catalytic active centers.It was found that the variations in deactivation power were in the order of methanol>acetone>ethyl acetate.The kinetic investigation via stopped-flow polymerization showed that poisoning compounds caused a decrease in activity through the reduction of the number of active sites whereas no effect on the degree of isotacticity was observed.

  6. Active site diversification of P450cam with indole generates catalysts for benzylic oxidation reactions.

    Science.gov (United States)

    Kelly, Paul P; Eichler, Anja; Herter, Susanne; Kranz, David C; Turner, Nicholas J; Flitsch, Sabine L

    2015-01-01

    Cytochrome P450 monooxygenases are useful biocatalysts for C-H activation, and there is a need to expand the range of these enzymes beyond what is naturally available. A panel of 93 variants of active self-sufficient P450cam[Tyr96Phe]-RhFRed fusion enzymes with a broad diversity in active site amino acids was developed by screening a large mutant library of 16,500 clones using a simple, highly sensitive colony-based colorimetric screen against indole. These mutants showed distinct fingerprints of activity not only when screened in oxidations of substituted indoles but also for unrelated oxidations such as benzylic hydroxylations.

  7. Active site diversification of P450cam with indole generates catalysts for benzylic oxidation reactions

    Directory of Open Access Journals (Sweden)

    Paul P. Kelly

    2015-09-01

    Full Text Available Cytochrome P450 monooxygenases are useful biocatalysts for C–H activation, and there is a need to expand the range of these enzymes beyond what is naturally available. A panel of 93 variants of active self-sufficient P450cam[Tyr96Phe]-RhFRed fusion enzymes with a broad diversity in active site amino acids was developed by screening a large mutant library of 16,500 clones using a simple, highly sensitive colony-based colorimetric screen against indole. These mutants showed distinct fingerprints of activity not only when screened in oxidations of substituted indoles but also for unrelated oxidations such as benzylic hydroxylations.

  8. Active site diversification of P450cam with indole generates catalysts for benzylic oxidation reactions.

    Science.gov (United States)

    Kelly, Paul P; Eichler, Anja; Herter, Susanne; Kranz, David C; Turner, Nicholas J; Flitsch, Sabine L

    2015-01-01

    Cytochrome P450 monooxygenases are useful biocatalysts for C-H activation, and there is a need to expand the range of these enzymes beyond what is naturally available. A panel of 93 variants of active self-sufficient P450cam[Tyr96Phe]-RhFRed fusion enzymes with a broad diversity in active site amino acids was developed by screening a large mutant library of 16,500 clones using a simple, highly sensitive colony-based colorimetric screen against indole. These mutants showed distinct fingerprints of activity not only when screened in oxidations of substituted indoles but also for unrelated oxidations such as benzylic hydroxylations. PMID:26664590

  9. Geology Forsmark. Site descriptive modelling Forsmark - stage 2.2

    Energy Technology Data Exchange (ETDEWEB)

    Stephens, Michael B. [Geological Survey of Sweden, Uppsala (Sweden); Fox, Aaron; La Pointe, Paul [Golder Associates Inc (United States); Simeonov, Assen [Swedish Nuclear Fuel and Waste Management Co., Stockholm (Sweden); Isaksson, Hans [GeoVista AB, Luleaa (Sweden); Hermanson, Jan; Oehman, Johan [Golder Associates AB, Stockholm (Sweden)

    2007-10-15

    The geological work during stage 2.2 has involved the development of deterministic models for rock domains (RFM) and deformation zones (ZFM), the identification and deterministic modelling of fracture domains (FFM) inside the candidate volume, i.e. the parts of rock domains that are not affected by deformation zones, and the development of statistical models for fractures and minor deformation zones (geological discrete fracture network modelling or geological DFN modelling). The geological DFN model addresses brittle structures at a scale of less than 1 km, which is the lower cut-off in the deterministic modelling of deformation zones. In order to take account of variability in data resolution, deterministic models for rock domains and deformation zones are presented in both regional and local model volumes, while the geological DFN model is valid within specific fracture domains inside the north-western part of the candidate volume, including the target volume. The geological modelling work has evaluated and made use of: A revised bedrock geological map at the ground surface. Geological and geophysical data from 21 cored boreholes and 33 percussion boreholes. Detailed mapping of fractures and rock units along nine excavations or large surface outcrops. Data bearing on the characterisation (including kinematics) of deformation zones. Complementary geochronological and other rock and fracture analytical data. Lineaments identified on the basis of airborne and high-resolution ground magnetic data. A reprocessing of both surface and borehole reflection seismic data. Seismic refraction data. The outputs of the deterministic modelling work are geometric models in RVS format and detailed property tables for rock domains and deformation zones, and a description of fracture domains. The outputs of the geological DFN modelling process are recommended parameters or statistical distributions that describe fracture set orientations, radius sizes, volumetric intensities

  10. Geology Forsmark. Site descriptive modelling Forsmark - stage 2.2

    International Nuclear Information System (INIS)

    The geological work during stage 2.2 has involved the development of deterministic models for rock domains (RFM) and deformation zones (ZFM), the identification and deterministic modelling of fracture domains (FFM) inside the candidate volume, i.e. the parts of rock domains that are not affected by deformation zones, and the development of statistical models for fractures and minor deformation zones (geological discrete fracture network modelling or geological DFN modelling). The geological DFN model addresses brittle structures at a scale of less than 1 km, which is the lower cut-off in the deterministic modelling of deformation zones. In order to take account of variability in data resolution, deterministic models for rock domains and deformation zones are presented in both regional and local model volumes, while the geological DFN model is valid within specific fracture domains inside the north-western part of the candidate volume, including the target volume. The geological modelling work has evaluated and made use of: A revised bedrock geological map at the ground surface. Geological and geophysical data from 21 cored boreholes and 33 percussion boreholes. Detailed mapping of fractures and rock units along nine excavations or large surface outcrops. Data bearing on the characterisation (including kinematics) of deformation zones. Complementary geochronological and other rock and fracture analytical data. Lineaments identified on the basis of airborne and high-resolution ground magnetic data. A reprocessing of both surface and borehole reflection seismic data. Seismic refraction data. The outputs of the deterministic modelling work are geometric models in RVS format and detailed property tables for rock domains and deformation zones, and a description of fracture domains. The outputs of the geological DFN modelling process are recommended parameters or statistical distributions that describe fracture set orientations, radius sizes, volumetric intensities

  11. Modelling the Active Hearing Process in Mosquitoes

    Science.gov (United States)

    Avitabile, Daniele; Homer, Martin; Jackson, Joe; Robert, Daniel; Champneys, Alan

    2011-11-01

    A simple microscopic mechanistic model is described of the active amplification within the Johnston's organ of the mosquito species Toxorhynchites brevipalpis. The model is based on the description of the antenna as a forced-damped oscillator coupled to a set of active threads (ensembles of scolopidia) that provide an impulsive force when they twitch. This twitching is in turn controlled by channels that are opened and closed if the antennal oscillation reaches a critical amplitude. The model matches both qualitatively and quantitatively with recent experiments. New results are presented using mathematical homogenization techniques to derive a mesoscopic model as a simple oscillator with nonlinear force and damping characteristics. It is shown how the results from this new model closely resemble those from the microscopic model as the number of threads approach physiologically correct values.

  12. Mass discharge estimation from contaminated sites: Multi-model solutions for assessment of conceptual uncertainty

    DEFF Research Database (Denmark)

    Thomsen, Nanna Isbak; Troldborg, Mads; McKnight, Ursula S.;

    2012-01-01

    Mass discharge estimates are increasingly being used in the management of contaminated sites. Such estimates have proven useful for supporting decisions related to the prioritization of contaminated sites in a groundwater catchment. Potential management options can be categorised as follows: (1...... propose a method for quantifying the uncertainty of dynamic mass discharge estimates from contaminant point sources on the local scale. The method considers both parameter and conceptual uncertainty through a multi-model approach. The multi-model approach evaluates multiple conceptual models for the same...... the different conceptual models using Bayesian model averaging. The weight for each model is obtained by integrating available data and expert knowledge using Bayesian belief networks. The multi-model approach is applied to a contaminated site. At the site a DNAPL (dense non aqueous phase liquid) spill...

  13. Active catalytic sites in the ammoxidation of propane and propene over V-Sb-O catalysts

    Energy Technology Data Exchange (ETDEWEB)

    Buchholz, S.A.; Zanthoff, H.W. [Bochum Univ. (Germany). Lehrstuhl fuer Technische Chemie

    1998-12-31

    The ammoxidation of propane over VSb{sub y}O{sub x} catalysts (y=1, 2, 5) was investigated with respect to the role of different oxygen species in the selective and non selective reaction steps using transient experiments in the Temporal Analysis of Products (TAP) reactor. Only lattice oxygen is involved in the oxidation reactions. Using isotopic labelled oxygen it is shown that two different active sites exist on the surface. On site A, which can be reoxidized faster by gas phase oxygen compared to site B, mainly CO is formed. On site B CO{sub 2} and acrolein as well as NO and N{sub 2}O in the presence of ammonia in the feed gas are formed and reoxidation mainly occurs with bulk lattice oxygen. (orig.)

  14. Mechanochemical coupling in the myosin motor domain. I. Insights from equilibrium active-site simulations.

    Directory of Open Access Journals (Sweden)

    Haibo Yu

    2007-02-01

    Full Text Available Although the major structural transitions in molecular motors are often argued to couple to the binding of Adenosine triphosphate (ATP, the recovery stroke in the conventional myosin has been shown to be dependent on the hydrolysis of ATP. To obtain a clearer mechanistic picture for such "mechanochemical coupling" in myosin, equilibrium active-site simulations with explicit solvent have been carried out to probe the behavior of the motor domain as functions of the nucleotide chemical state and conformation of the converter/relay helix. In conjunction with previous studies of ATP hydrolysis with different active-site conformations and normal mode analysis of structural flexibility, the results help establish an energetics-based framework for understanding the mechanochemical coupling. It is proposed that the activation of hydrolysis does not require the rotation of the lever arm per se, but the two processes are tightly coordinated because both strongly couple to the open/close transition of the active site. The underlying picture involves shifts in the dominant population of different structural motifs as a consequence of changes elsewhere in the motor domain. The contribution of this work and the accompanying paper [] is to propose the actual mechanism behind these "population shifts" and residues that play important roles in the process. It is suggested that structural flexibilities at both the small and large scales inherent to the motor domain make it possible to implement tight couplings between different structural motifs while maintaining small free-energy drops for processes that occur in the detached states, which is likely a feature shared among many molecular motors. The significantly different flexibility of the active site in different X-ray structures with variable level arm orientations supports the notation that external force sensed by the lever arm may transmit into the active site and influence the chemical steps (nucleotide

  15. Identification and characterization of radioactively contaminated sites in Ukraine and planning for environmental restoration activities

    International Nuclear Information System (INIS)

    In the Pridniprovsk-Krivoy Rog region uranium, titanium, iron and manganese ores were mined and milled beginning in the 1950s. These activities have caused radioactive contamination of the environment at some sites. In recent times intensive works concerning the surveying of contaminated areas and substantiating the need for remediation have been initiated. The research methodologies applied and the results from radiation surveys are presented for the site of the first uranium mine in the Ukraine, for tailings originating from the Pridniprovsk Chemical Plant (PChP), for the recultivated dump-site of the former 'O'-mine, as well as for the wastes, raw materials and production of the Nicopol Ferro-Alloy Plant. The planning procedure for the remediation activities at the town of Zhovty Vody is described. (author)

  16. Geological discrete fracture network model for the Olkiluoto site, Eurajoki, Finland. Version 2.0

    Energy Technology Data Exchange (ETDEWEB)

    Fox, A.; Forchhammer, K.; Pettersson, A. [Golder Associates AB, Stockholm (Sweden); La Pointe, P.; Lim, D-H. [Golder Associates Inc. (Finland)

    2012-06-15

    This report describes the methods, analyses, and conclusions of the modeling team in the production of the 2010 revision to the geological discrete fracture network (DFN) model for the Olkiluoto Site in Finland. The geological DFN is a statistical model for stochastically simulating rock fractures and minor faults at a scale ranging from approximately 0.05 m to approximately 565m; deformation zones are expressly excluded from the DFN model. The DFN model is presented as a series of tables summarizing probability distributions for several parameters necessary for fracture modeling: fracture orientation, fracture size, fracture intensity, and associated spatial constraints. The geological DFN is built from data collected during site characterization (SC) activities at Olkiluoto, which is selected to function as a final deep geological repository for spent fuel and nuclear waste from the Finnish nuclear power program. Data used in the DFN analyses include fracture maps from surface outcrops and trenches, geological and structural data from cored drillholes, and fracture information collected during the construction of the main tunnels and shafts at the ONKALO laboratory. Unlike the initial geological DFN, which was focused on the vicinity of the ONKALO tunnel, the 2010 revisions present a model parameterization for the entire island. Fracture domains are based on the tectonic subdivisions at the site (northern, central, and southern tectonic units) presented in the Geological Site Model (GSM), and are further subdivided along the intersection of major brittle-ductile zones. The rock volume at Olkiluoto is dominated by three distinct fracture sets: subhorizontally-dipping fractures striking north-northeast and dipping to the east that is subparallel to the mean bedrock foliation direction, a subvertically-dipping fracture set striking roughly north-south, and a subvertically-dipping fracture set striking approximately east-west. The subhorizontally-dipping fractures

  17. Study on the active sites of Cu-ZSM-5 in trichloroethylene catalytic combustion with air

    Institute of Scientific and Technical Information of China (English)

    Cheng Hua Xu; Chuan Qi Liu; Yan Zhong; Xiu Zhou Yang; Jian Ying Liu; Ying Chun Yang; Zhi Xiang Ye

    2008-01-01

    The catalytic activity of Cu-ZSM-5 in trichloroethylene (TCE) combustion increases with the increasing skeletal Cu amount and however decreases with the increase of surface amorphous CuO,which is detected by infrared spectroscopy (IR) and diffuse reflectance ultraviolet-visible spectroscopy (DRS-UV-vis),therefore the skeletal Cu species are concluded to be the active sites for the TCE combustion.

  18. Variants of the cell recognition site of fibronectin that retain attachment-promoting activity

    OpenAIRE

    1985-01-01

    A tetrapeptide sequence, Arg-Gly-Asp-Ser, is the minimal structure recognized by cells in the large, adhesive glycoprotein fibronectin. We now have defined the structural requirements for this cell recognition site by testing several synthetic variants of the active tetrapeptide sequence. The conservative substitutions of lysine for arginine, alanine for glycine, or glutamic acid for aspartic acid each resulted in abrogation of the cell attachment-promoting activity characteristic of the natu...

  19. Receptor modelling of secondary particulate matter at UK sites

    Directory of Open Access Journals (Sweden)

    A. Charron

    2012-10-01

    Full Text Available Complementary approaches have been taken to better understand the sources and their spatial distribution for secondary inorganic (nitrate and sulphate and secondary organic aerosol sampled at a rural site (Harwell in the southern United Kingdom. A concentration field map method was applied to 1581 daily samples of chloride, nitrate and sulphate from 2006 to 2010, and 982 samples for organic carbon and elemental carbon from 2007 to 2010. This revealed a rather similar pattern of sources for nitrate, sulphate and secondary organic carbon within western/central Europe, which in the case of nitrate and sulphate, correlated significantly with EMEP emissions maps of NOx and SO2. A slightly more southerly source emphasis for secondary organic carbon may reflect the contribution of biogenic sources. Trajectory clusters confirm this pattern of behaviour with a major contribution from mainland European sources. Similar behaviours of, on the one hand, sulphate and organic carbon and, on the other hand, EC and nitrate showed that the former are more subject to regional influence than the latter in agreement with the slower atmospheric formation of sulphate and secondary organic aerosol than for nitrate, and the local/mesoscale influences upon primary EC. In a separate study, measurements of sulphate, nitrate, elemental and organic carbon were made in 100 simultaneously collected samples at Harwell and at a suburban site in Birmingham (UK. This showed a significant correlation in concentrations between the two sites for all of the secondary constituents, further indicating secondary organic aerosol to be a regional pollutant behaving similarly to sulphate and nitrate.

  20. Active Gel Model of Amoeboid Cell Motility

    CERN Document Server

    Callan-Jones, A C

    2013-01-01

    We develop a model of amoeboid cell motility based on active gel theory. Modeling the motile apparatus of a eukaryotic cell as a confined layer of finite length of poroelastic active gel permeated by a solvent, we first show that, due to active stress and gel turnover, an initially static and homogeneous layer can undergo a contractile-type instability to a polarized moving state in which the rear is enriched in gel polymer. This agrees qualitatively with motile cells containing an actomyosin-rich uropod at their rear. We find that the gel layer settles into a steadily moving, inhomogeneous state at long times, sustained by a balance between contractility and filament turnover. In addition, our model predicts an optimal value of the gel-susbstrate adhesion leading to maximum layer speed, in agreement with cell motility assays. The model may be relevant to motility of cells translocating in complex, confining environments that can be mimicked experimentally by cell migration through microchannels.

  1. Uncertainty Analysis Framework - Hanford Site-Wide Groundwater Flow and Transport Model

    Energy Technology Data Exchange (ETDEWEB)

    Cole, Charles R.; Bergeron, Marcel P.; Murray, Christopher J.; Thorne, Paul D.; Wurstner, Signe K.; Rogers, Phillip M.

    2001-11-09

    Pacific Northwest National Laboratory (PNNL) embarked on a new initiative to strengthen the technical defensibility of the predictions being made with a site-wide groundwater flow and transport model at the U.S. Department of Energy Hanford Site in southeastern Washington State. In FY 2000, the focus of the initiative was on the characterization of major uncertainties in the current conceptual model that would affect model predictions. The long-term goals of the initiative are the development and implementation of an uncertainty estimation methodology in future assessments and analyses using the site-wide model. This report focuses on the development and implementation of an uncertainty analysis framework.

  2. Modeling of Activated Sludge Floc Characteristics

    Directory of Open Access Journals (Sweden)

    Ibrahim H. Mustafa

    2009-01-01

    Full Text Available Problem Statement: The activated sludge system needs to improve the operational performance and to achieve more effective control. To realize this, a better quantitative understanding of the biofloc characteristics is required. The objectives of this study were to: (i Study the biofloc characteristics from kinetics-mass transfer interaction point of view by quantification of the weight of the aerobic portion of the activated sludge floc to the total floc weight. (ii Study the effect of bulk concentrations of oxygen and nitrates, power input and substrates diffusivity on the portion aerobic portion of the floc. Approach: An appropriate mathematical model based on heterogeneous modeling is developed for activated sludge flocs. The model was taking into account three growth processes: Carbon oxidation, nitrification and de-nitrification in terms of four components: substrate, nitrate, ammonia, and oxygen. The model accounts for the internal and external mass transfer limitations and relates the external mass transfer resistance with power input. The floc model equations were two- point boundary value differential equations. Therefore a central finite difference method is employed. Results: The percentage aerobic portion increased with increasing with oxygen bulk concentrations and power input and decreases when the bulk concentration of ammonia and substrate increases. Both will compete to consume the internal oxygen by autotrophic and heterotrophic bacteria through aerobic growth processes. The biofloc activity through the profiles was either totally active or partially active. The totally active biofloc is either totally aerobic or aerobic and anoxic together. Conclusions: The heterogeneous floc model was able to describe the biofloc characteristics and reflects the real phenomena existing in the activated sludge processes.

  3. Spectroscopic studies on the active site of hydroperoxide lyase : the influence of detergents on its conformation

    NARCIS (Netherlands)

    Vliegenthart, J.F.G.; Noordermeer, M.A.; Veldink, G.A.

    2001-01-01

    Expression of high quantities of alfalfa hydroperoxide lyase in Escherichia coli made it possible to study its active site and structure in more detail. Circular dichroism (CD) spectra showed that hydroperoxide lyase consists for about 75% of alpha-helices. Electron paramagnetic resonance (EPR) spec

  4. Biosynthesis of selenosubtilisin: A novel way to target selenium into the active site of subtilisin

    Institute of Scientific and Technical Information of China (English)

    LI Jing; LIU XiaoMan; JI YueTong; QI ZhenHui; GE Yan; XU JiaYun; LIU JunQiu; LUO GuiMin; SHEN JiaCong

    2008-01-01

    Glutathione peroxidase (GPx,EC1.11.1.9),an important anti-oxidative selenoenzyme,can catalyze the reduction of harmful hydroperoxides with concomitant glutathione,thereby protecting cells and other biological issues against oxidative damage.It captures considerable interest in redesign of its function for either the mechanism study or the pharmacological development as an antioxidant.In order to de-velop a general strategy for specifically targeting and operating selenium in active sites of enzymes,the catalytically essential residue selenocysteine (Sec) was first successfully bioincorporated into the catalytic center of subtilisin by using an auxotrophic expression system.The studies of the catalytic activity and the steady-state kinetics demonstrated that selenosubtilisin is an excellent GPx-like bio-catalyst.In comparison with the chemically modified method,biosynthesis exhibits obvious advan-tages:Sec could be site-directly incorporated into active sites of enzymes to overcome the non-speci-ficity generated by chemical modification.This study provides an important strategy for specifically targeting and operating selenium in the active site of an enzyme.

  5. 76 FR 51391 - Commercial Wind Lease Issuance and Site Characterization Activities on the Atlantic Outer...

    Science.gov (United States)

    2011-08-18

    ..., geotechnical, archeological, and biological surveys), and reasonably foreseeable site assessment scenarios... characterization activities (i.e., geological and geophysical surveys and core samples), a lessee must submit the results of such surveys before BOEMRE can consider its COP. See 30 CFR 285.626. 2. Proposed Action...

  6. Aberration-corrected imaging of active sites on industrial catalyst nanoparticles

    DEFF Research Database (Denmark)

    Gontard, Lionel Cervera; Chang, L-Y; Hetherington, CJD;

    2007-01-01

    Picture perfect: Information about the local topologies of active sites on commercial nanoparticles can be gained with atomic resolution through spherical-aberration-corrected transmission electron microscopy (TEM). A powder of Pt nanoparticles on carbon black was examined with two advanced TEM t...

  7. Comparative active-site mutation study of human and Caenorhabditis elegans thymidine kinase 1

    DEFF Research Database (Denmark)

    Skovgaard, Tine; Uhlin, Ulla; Munch-Petersen, Birgitte

    2012-01-01

    ligands. To improve our understanding of TK1 substrate specificity, we performed a detailed, mutation-based comparative structure-function study of the active sites of two thymidine kinases: HuTK1 and Caenorhabditis elegans TK1 (CeTK1). Specifically, mutations were introduced into the hydrophobic pocket...

  8. Molecular Interactions Between the Active Sites of RGD (Arg-Gly-Asp with its Receptor (Integrine

    Directory of Open Access Journals (Sweden)

    E. Jauregui

    2000-03-01

    Full Text Available A study of the molecular interactions between the active sites of RGD (Arg-Gly-Asp with it Receptor using simultaions is reported. Our calculations indicate that the guanidine-carboxylate complex is energetically favourd with respect to the guanidine-methyl tetrazole complex.

  9. Artificial Metalloenzymes for Asymmetric Catalysis by Creation of Novel Active Sites in Protein and DNA Scaffolds

    NARCIS (Netherlands)

    Drienovska, Ivana; Roelfes, Gerard

    2015-01-01

    Artificial metalloenzymes have emerged as a promising new approach to asymmetric catalysis. In our group, we are exploring novel artificial metalloenzyme designs involving creation of a new active site in a protein or DNA scaffold that does not have an existing binding pocket. In this review, we giv

  10. 78 FR 8190 - Commercial Wind Leasing and Site Assessment Activities on the Atlantic Outer Continental Shelf...

    Science.gov (United States)

    2013-02-05

    ... published the Notice in the Federal Register (77 FR 74218) inviting Federal, state, local government... Bureau of Ocean Energy Management Commercial Wind Leasing and Site Assessment Activities on the Atlantic... Notice of Intent to Prepare an Environmental Assessment (EA) for Commercial Wind Leasing and...

  11. 77 FR 5830 - Commercial Wind Leasing and Site Assessment Activities on the Atlantic Outer Continental Shelf...

    Science.gov (United States)

    2012-02-06

    ... (NOA) in the Federal Register (72 FR 62,672) of the Programmatic EIS for Alternative Energy Development... FR 30,616) of the EA for Issuance of Leases for Wind Resource Data Collection on the Outer... Bureau of Ocean Energy Management Commercial Wind Leasing and Site Assessment Activities on the...

  12. Domestic activities at the Linear Pottery site of Elsloo (Netherlands) : a look from under the microscoop

    NARCIS (Netherlands)

    Gijn, van A.L.; Mazzucco, N.; Hamon, C.; Allard, P.; Ilett, M.

    2013-01-01

    Use-wear analysis of a sample of flint tools from the site of Elsloo, situated in the Graetheide cluster (NL), has shed light on the domestic activities carried out within the settlement. It was shown that hide processing predominates. The extent and character of the wear on the hide working impleme

  13. A comparative study of drug resistance mechanism associated with active site and non-active site mutations: I388N and D425G mutants of acetyl-coenzyme-A carboxylase.

    Science.gov (United States)

    Zhu, Xiao-Lei; Yang, Guang-Fu

    2012-03-01

    A major concern in the development of acetyl-CoA carboxylase-inhibiting (ACCase; EC 6.4.1.2) herbicides is the emergence of resistance as a result of the selection of distinct mutations within the CT domain. Mutations associated with resistance have been demonstrated to include both active sites and non-active sites, including Ile-1781-Leu, Trp- 2027-Cys, Ile-2041-Asn, Asp-2078-Gly, and Gly-2096-Ala (numbered according to the Alopecurus myosuroides plastid ACCase). In the present study, extensive computational simulations, including molecular dynamics (MD) simulations and molecular mechanics-Poisson-Boltzmann surface area (MM/PBSA) calculations, were carried out to compare the molecular mechanisms of active site mutation (I388N) and non-active site mutation (D425G) in Alopecurus myosuroides resistance to some commercial herbicides targeting ACCase, including haloxyfop (HF), diclofop (DF) and fenoxaprop (FR). All of the computational model and energetic results indicated that both I388N and D425G mutations have effects on the conformational change of the binding pocket. The π-π interaction between ligand and Phe377 and Tyr161' residues, which make an important contribution to the binding affinity, was decreased after mutation. As a result, the mutant-type ACCase has a lower affinity for the inhibitor than the wild-type enzyme, which accounts for the molecular basis of herbicidal resistance. The structural and mechanistic insights obtained from the present study will deepen our understanding of the interactions between ACCase and herbicides, which provides a molecular basis for the future design of a promising inhibitor with low resistance risk. PMID:22242795

  14. Effect of active site of Xiangsha Liujunzitang on behavior and injury of hippocampal neurons in depression model mice%香砂六君子汤对抑郁模型小鼠行为及海马神经元损伤的影响

    Institute of Scientific and Technical Information of China (English)

    周本宏; 刘敏; 郭志磊; 黄付伟

    2009-01-01

    目的:探究香砂六君子汤对慢性应激抑郁模型小鼠行为、海马神经元损伤及海马突触体内游离Ca~(2+)浓度的影响.方法:60只昆明雄性小鼠平均分为正常组、模型组、香砂六君子汤活性部位高、中、低剂量组(800,600,400 mg·kg~(-1)).采用长期不可预见性慢性应激小鼠抑郁模型,测定各组小鼠体重变化,Open-field法和糖水消耗实验测定各组小鼠的行为变化;Nissl染色法观察海马CA1,CA3区神经元形态及锥体细胞数目;以Fura-2负载及荧光分光光度计检测海马突触体内游离Ca~(2+)浓度.结果:与正常组比较,模型组小鼠呈现明显的抑郁样症状.香砂六君子汤活性部位高、中、低剂量组小鼠在第14,21天体重增长明显高于模型组,其中高、中剂量能增加抑郁小鼠的爬格数(P<0.05),但与剂量无对应关系;高剂量能增加抑郁小鼠的站立次数(P<0.001);低、中、高剂量能明显增加抑郁小鼠的糖水消耗量(P<0.01,P<0.01,P<0.001),并呈现一定的量效关系.高,中剂量组小鼠海马CA3区空泡明显减少,且锥体细胞数量显著增多(P<0.001);高、中剂量能明显降低抑郁小鼠海马突触体内游离Ca~(2+)浓度(P<0.01,P<0.001).结论:香砂六君子汤活性部位能改善小鼠的抑郁样行为;保护抑郁模型小鼠海马神经元损伤,其可能与香砂六君子汤活性部位抑制海马神经细胞外Ca~(2+)内流,阻止Ca~(2+)超载相关.%Objective: To observe the effect of the active site of Xiangshia Liujunzitang on behavior, injury of hippocampal neurons and Ca~(2+) ion in hippocampal synaptic in the depression model mice. Method: Sixty male Kunming mice were randomly dividbody weight). The model was established by separation and chronic unpredictable mild stimulation. The increased weight and crossing scores, rearing scores were measured by open-field and sweet water consumption of mice. Cone cell and configuration of neuron in CA1, CA3 region of

  15. The role of the catalysts with highly dispersed and isolated active sites in the selective oxidation of light hydrocarbons

    Institute of Scientific and Technical Information of China (English)

    WANG Hongxuan; ZHAO Zhen

    2005-01-01

    This review summarizes the role of catalysts with highly dispersed and isolated active sites (active sites: supported atoms f≤0.5 % ) in the selective oxidation of light hydrocarbons, such as methane, ethane and propane, into oxygenatesand the epoxidation of olefins. The plausible structures of the highly dispersed and isolated active species, as well as their effects on the catalytic performances are discussed. The special physico-chemical properties and the functional mechanism of the catalysts with highly dispersed and isolated active sites, as well as the preparation, characterization of the catalysts with highly dispersed and isolated active sites and their applications in other types of reactions of lower hydrocarbons are summarized.

  16. Conversion of the Bayou Choctaw geological site characterization report to a three-dimensional model.

    Energy Technology Data Exchange (ETDEWEB)

    Stein, Joshua S. (Sandia National Laboratories, Carlsbad, NM); Rautman, Christopher Arthur

    2004-02-01

    The geologic model implicit in the original site characterization report for the Bayou Choctaw Strategic Petroleum Reserve Site near Baton Rouge, Louisiana, has been converted to a numerical, computer-based three-dimensional model. The original site characterization model was successfully converted with minimal modifications and use of new information. The geometries of the salt diapir, selected adjacent sedimentary horizons, and a number of faults have been modeled. Models of a partial set of the several storage caverns that have been solution-mined within the salt mass are also included. Collectively, the converted model appears to be a relatively realistic representation of the geology of the Bayou Choctaw site as known from existing data. A small number of geometric inconsistencies and other problems inherent in 2-D vs. 3-D modeling have been noted. Most of the major inconsistencies involve faults inferred from drill hole data only. Modem computer software allows visualization of the resulting site model and its component submodels with a degree of detail and flexibility that was not possible with conventional, two-dimensional and paper-based geologic maps and cross sections. The enhanced visualizations may be of particular value in conveying geologic concepts involved in the Bayou Choctaw Strategic Petroleum Reserve site to a lay audience. A Microsoft WindowsTM PC-based viewer and user-manipulable model files illustrating selected features of the converted model are included in this report.

  17. Computer models used to support cleanup decision-making at hazardous and radioactive waste sites

    International Nuclear Information System (INIS)

    Massive efforts are underway to cleanup hazardous and radioactive waste sites located throughout the US To help determine cleanup priorities, computer models are being used to characterize the source, transport, fate and effects of hazardous chemicals and radioactive materials found at these sites. Although, the US Environmental Protection Agency (EPA), the US Department of Energy (DOE), and the US Nuclear Regulatory Commission (NRC) have provided preliminary guidance to promote the use of computer models for remediation purposes, no Agency has produced directed guidance on models that must be used in these efforts. To identify what models are actually being used to support decision-making at hazardous and radioactive waste sites, a project jointly funded by EPA, DOE and NRC was initiated. The purpose of this project was to: (1) Identify models being used for hazardous and radioactive waste site assessment purposes; and (2) describe and classify these models. This report presents the results of this study

  18. A MULTI-SITE SHEEP MODEL FOR CANCELLOUS BONE HEALING

    OpenAIRE

    MatthewhenryPelletier

    2014-01-01

    Appropriate, well characterized bone defect animal models remain essential for preclinical research. This pilot study demonstrates a relevant animal model for cancellous bone defect healing. Three different defect diameters (8, 11, 14mm) of fixed depth (25mm) were compared in both skeletally immature (18 month old) and aged sheep (5 year old). In each animal, four defects were surgically created and placed in the cancellous bone of the medial distal femoral and proximal tibial epiphyses bi...

  19. SITE-94. Development of a geological and a structural model of Aespoe, southeastern Sweden

    International Nuclear Information System (INIS)

    The objective of the present study is to construct three-dimensional geological and structural models to be used within the SKI SITE-94 project as a base for modelling hydrogeological, hydrochemical, and rock mechanical bedrock conditions, mass transport and layout of a hypothetical repository. The basic input data in the SITE-94 geological and structural models are restricted to geological and structural readings and geophysical measurements made prior to building the Hard Rock Laboratory. 114 refs, 82 figs, 28 tabs

  20. Asymmetry of the Active Site Loop Conformation between Subunits of Glutamate-1-semialdehyde Aminomutase in Solution

    Directory of Open Access Journals (Sweden)

    Barbara Campanini

    2013-01-01

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

  1. A split active site couples cap recognition by Dcp2 to activation

    OpenAIRE

    Floor, Stephen N.; Jones, Brittnee N.; Hernandez, Gail A.; Gross, John D.

    2010-01-01

    Decapping by Dcp2 is an essential step in 5′-3′ mRNA decay. In yeast, decapping requires an open-to-closed transition in Dcp2, though the link between closure and catalysis remains elusive. Here we show using NMR that cap binds conserved residues on both the catalytic and regulatory domains of Dcp2. Lesions in the cap-binding site on the regulatory domain reduce the catalytic step two orders of magnitude and block formation of the closed state whereas Dcp1 enhances the catalytic step by a fac...

  2. Integral Public Activities as a Support to the Site Selection Process for LILW Repository

    International Nuclear Information System (INIS)

    The first site selection process for low and intermediate level radioactive waste (LILW) repository took place between 1990 and 1993 in Slovenia was stopped unsuccessfully with very strong public opposition at local level, followed by political withdrawal on national level. As one of the consequences ARAO started to develop new approach to the site selection based also on the findings from sociology, psychology and other human sciences. The recommendations on public involvement and transparency were so strong that ARAO started with first limited public relation (PR) activities which later grew to the PR process which supports all technical activities in ARAO. Presently the PR process covers communication, information and research activities and assures careful planning, prompt responds and involvement of the highest responsible persons at ARAO. Integral public relation activities are divided in several parts. Majority of activities support the on-going site selection process where activities are presently focused on functioning of local partnerships developed as a basic communication tool to involve as much citizens and public as possible on local level. Presently two local partnerships are working in Krsko and Brezice community with clear role to enhance public involvement according to Aarchus convention. Each of the partnerships is organized in a specific way adjusted to the local needs. Communication activities are organized also for different other projects and are preparing the necessary basis for the work with different groups of stake holders and in different situations. As a foundation very broad information material, such as books, leaflets, reports, magazines, video cassettes, CD and DVD on the radioactive waste management is prepared and used for different purposes. We also try to be proactive with web pages and have a well organized visitors' center. Improvement of public relation process is achieved through constant survey and feed-back information

  3. Pacemaker activity in a sensory ending with multiple encoding sites : The cat muscle spindle primary ending

    NARCIS (Netherlands)

    Banks, RW; Hulliger, M; Scheepstra, KA; Otten, E

    1997-01-01

    1. A combined physiological, histological and computer modelling study was carried out on muscle spindles of the cat tenuissimus muscle to examine whether there was any correlation between the functional interaction of putative encoding sites, operated separately by static and dynamic fusimotor neur

  4. Ionizing Groups at the Active Site of the Alkaline Phosphatase from Ostrea cucullate

    Institute of Scientific and Technical Information of China (English)

    CHEN Qiao; WANG Qin; LIAO Jinhua; CHEN Qingxi

    2006-01-01

    The ionizing groups at the active site of alkaline phosphatase (ALP, EC 3.1.3.1) from Ostrea cucullate were studied using kinetic methods. The ionization constant, pKe, of the ionizing groups at the active site of the enzyme was found to be 10.11 at 37.0℃ and the organic solvent, dioxin, had no effect on the pKe. The standard dissociation enthalpy (△Ho) was determined to be 10.57 kcal/mol (1 cal=4.18 J). The results show that the dissociation group of the enzyme active center is the з-NH3+ of lysine. Chemical modification of the enzyme by acetic anhydride and succinic anhydride demonstrates that the amino group is one of the enzyme's functional groups.

  5. Multiple transport-active binding sites are available for a single substrate on human P-glycoprotein (ABCB1).

    Science.gov (United States)

    Chufan, Eduardo E; Kapoor, Khyati; Sim, Hong-May; Singh, Satyakam; Talele, Tanaji T; Durell, Stewart R; Ambudkar, Suresh V

    2013-01-01

    P-glycoprotein (Pgp, ABCB1) is an ATP-Binding Cassette (ABC) transporter that is associated with the development of multidrug resistance in cancer cells. Pgp transports a variety of chemically dissimilar amphipathic compounds using the energy from ATP hydrolysis. In the present study, to elucidate the binding sites on Pgp for substrates and modulators, we employed site-directed mutagenesis, cell- and membrane-based assays, molecular modeling and docking. We generated single, double and triple mutants with substitutions of the Y307, F343, Q725, F728, F978 and V982 residues at the proposed drug-binding site with cys in a cysless Pgp, and expressed them in insect and mammalian cells using a baculovirus expression system. All the mutant proteins were expressed at the cell surface to the same extent as the cysless wild-type Pgp. With substitution of three residues of the pocket (Y307, Q725 and V982) with cysteine in a cysless Pgp, QZ59S-SSS, cyclosporine A, tariquidar, valinomycin and FSBA lose the ability to inhibit the labeling of Pgp with a transport substrate, [(125)I]-Iodoarylazidoprazosin, indicating these drugs cannot bind at their primary binding sites. However, the drugs can modulate the ATP hydrolysis of the mutant Pgps, demonstrating that they bind at secondary sites. In addition, the transport of six fluorescent substrates in HeLa cells expressing triple mutant (Y307C/Q725C/V982C) Pgp is also not significantly altered, showing that substrates bound at secondary sites are still transported. The homology modeling of human Pgp and substrate and modulator docking studies support the biochemical and transport data. In aggregate, our results demonstrate that a large flexible pocket in the Pgp transmembrane domains is able to bind chemically diverse compounds. When residues of the primary drug-binding site are mutated, substrates and modulators bind to secondary sites on the transporter and more than one transport-active binding site is available for each

  6. Multiple transport-active binding sites are available for a single substrate on human P-glycoprotein (ABCB1.

    Directory of Open Access Journals (Sweden)

    Eduardo E Chufan

    Full Text Available P-glycoprotein (Pgp, ABCB1 is an ATP-Binding Cassette (ABC transporter that is associated with the development of multidrug resistance in cancer cells. Pgp transports a variety of chemically dissimilar amphipathic compounds using the energy from ATP hydrolysis. In the present study, to elucidate the binding sites on Pgp for substrates and modulators, we employed site-directed mutagenesis, cell- and membrane-based assays, molecular modeling and docking. We generated single, double and triple mutants with substitutions of the Y307, F343, Q725, F728, F978 and V982 residues at the proposed drug-binding site with cys in a cysless Pgp, and expressed them in insect and mammalian cells using a baculovirus expression system. All the mutant proteins were expressed at the cell surface to the same extent as the cysless wild-type Pgp. With substitution of three residues of the pocket (Y307, Q725 and V982 with cysteine in a cysless Pgp, QZ59S-SSS, cyclosporine A, tariquidar, valinomycin and FSBA lose the ability to inhibit the labeling of Pgp with a transport substrate, [(125I]-Iodoarylazidoprazosin, indicating these drugs cannot bind at their primary binding sites. However, the drugs can modulate the ATP hydrolysis of the mutant Pgps, demonstrating that they bind at secondary sites. In addition, the transport of six fluorescent substrates in HeLa cells expressing triple mutant (Y307C/Q725C/V982C Pgp is also not significantly altered, showing that substrates bound at secondary sites are still transported. The homology modeling of human Pgp and substrate and modulator docking studies support the biochemical and transport data. In aggregate, our results demonstrate that a large flexible pocket in the Pgp transmembrane domains is able to bind chemically diverse compounds. When residues of the primary drug-binding site are mutated, substrates and modulators bind to secondary sites on the transporter and more than one transport-active binding site is available

  7. Active space decomposition with multiple sites: Density matrix renormalization group algorithm

    CERN Document Server

    Parker, Shane M

    2014-01-01

    We extend the active space decomposition method, recently developed by us, to more than two active sites using the density matrix renormalization group algorithm. The fragment wave functions are described by complete or restricted active-space wave functions. Numerical results are shown on a benzene pentamer and a perylene diimide trimer. It is found that the truncation errors in our method decrease almost exponentially with respect to the number of renormalization states M, allowing for numerically exact calculations (to a few {\\mu}Eh or less) with M = 128 in both cases, which is in contrast to conventional ab initio density matrix renormalization group.

  8. Mapping Topoisomerase IV Binding and Activity Sites on the E. coli Genome.

    Science.gov (United States)

    El Sayyed, Hafez; Le Chat, Ludovic; Lebailly, Elise; Vickridge, Elise; Pages, Carine; Cornet, Francois; Cosentino Lagomarsino, Marco; Espéli, Olivier

    2016-05-01

    Catenation links between sister chromatids are formed progressively during DNA replication and are involved in the establishment of sister chromatid cohesion. Topo IV is a bacterial type II topoisomerase involved in the removal of catenation links both behind replication forks and after replication during the final separation of sister chromosomes. We have investigated the global DNA-binding and catalytic activity of Topo IV in E. coli using genomic and molecular biology approaches. ChIP-seq revealed that Topo IV interaction with the E. coli chromosome is controlled by DNA replication. During replication, Topo IV has access to most of the genome but only selects a few hundred specific sites for its activity. Local chromatin and gene expression context influence site selection. Moreover strong DNA-binding and catalytic activities are found at the chromosome dimer resolution site, dif, located opposite the origin of replication. We reveal a physical and functional interaction between Topo IV and the XerCD recombinases acting at the dif site. This interaction is modulated by MatP, a protein involved in the organization of the Ter macrodomain. These results show that Topo IV, XerCD/dif and MatP are part of a network dedicated to the final step of chromosome management during the cell cycle. PMID:27171414

  9. AECL strategy for surface-based investigations of potential disposal sites and the development of a geosphere model for a site

    International Nuclear Information System (INIS)

    The objective of this report is to summarize AECL's strategy for surface-based geotechnical site investigations used in screening and evaluating candidate areas and candidate sites for a nuclear fuel waste repository and for the development of geosphere models of sites. The report is one of several prepared by national nuclear fuel waste management programs for the Swedish Nuclear Fuel and Waste Management Co. (SKB) to provide international background on site investigations for SKB's R and D programme on siting.The scope of the report is limited to surface-based investigations of the geosphere, those done at surface or in boreholes drilled from surface. The report discusses AECL's investigation strategy and the methods proposed for use in surface-based reconnaissance and detailed site investigations at potential repository sites. Site investigations done for AECL's Underground Research Laboratory are used to illustrate the approach. The report also discusses AECL's strategy for developing conceptual and mathematical models of geological conditions at sites and the use of these models in developing a model (Geosphere Model) for use in assessing the performance of the disposal system after a repository is closed. Models based on the site data obtained at the URL are used to illustrate the approach. Finally, the report summarizes the lessons learned from AECL's R and D program on site investigations and mentions some recent developments in the R and D program. 120 refs, 33 figs, 7 tabs

  10. Regulatory inspection activities on nuclear power plant sites during construction in the United Kingdom

    International Nuclear Information System (INIS)

    The work of regulatory inspection of the construction of the plant on the site is performed not only by the inspector who has been allocated to inspection duties for that site but also by the specialist staff who are involved with the safety assessment of the plant. The coordination of this work is described in the paper and examples are given of inspection activities associated with the enforcement requirements of license conditions as well as those related to the inspection of the plant itself

  11. Technical basis for classification of low-activity waste fraction from Hanford site tanks

    Energy Technology Data Exchange (ETDEWEB)

    Petersen, C.A., Westinghouse Hanford

    1996-07-17

    The overall objective of this report is to provide a technical basis to support a U.S. Nuclear Regulatory Commission determination to classify the low-activity waste from the Hanford Site single-shell and double-shell tanks as `incidental` wastes after removal of additional radionuclides and immobilization.The proposed processing method, in addition to the previous radionuclide removal efforts, will remove the largest practical amount of total site radioactivity, attributable to high-level wastes, for disposal in a deep geologic repository. The remainder of the waste would be considered `incidental` waste and could be disposed onsite.

  12. Water-rock interaction modelling and uncertainties of mixing modelling. SDM-Site Forsmark

    International Nuclear Information System (INIS)

    The overall objectives of the hydrogeochemical description for Forsmark are to establish a detailed understanding of the hydrogeochemical conditions at the site and to develop models that fulfil the needs identified by the safety assessment groups during the site investigation phase. Issues of concern to safety assessment are radionuclide transport and technical barrier behaviour, both of which are dependent on the chemistry of groundwater and pore water and their evolution with time. The work has involved the development of descriptive and mathematical models for groundwaters in relation to rock domains, fracture domains and deformation zones. Past climate changes are one of the major driving forces for hydrogeochemical changes and therefore of fundamental importance for understanding the palaeohydrogeological, palaeohydrogeochemical and present evolution of groundwater in the crystalline bedrock of the Fennoscandian Shield. Understanding current undisturbed hydrochemical conditions at the proposed repository site is important when predicting future changes in groundwater chemistry. The causes behind of copper corrosion and/or bentonite degradation are of particular interest as they may jeopardise the long-term integrity of the planned SKB repository system. Thus, the following variables are considered for the hydrogeochemical site descriptive modelling: pH, Eh, sulphur species, iron, manganese, carbonate, phosphate, nitrogen species, total dissolved solids (TDS), isotopes, colloids, fulvic and humic acids and microorganisms. In addition, dissolved gases (e.g. carbon dioxide, methane and hydrogen) are of interest because of their likely participation in microbial reactions. In this series of reports, the final hydrogeochemical evaluation work of the site investigation at the Forsmark site, is presented. The work was conducted by SKB's hydrogeochemical project group, ChemNet, which consists of independent consultants and university researchers with expertise in

  13. Water-rock interaction modelling and uncertainties of mixing modelling. SDM-Site Forsmark

    Energy Technology Data Exchange (ETDEWEB)

    Gimeno, Maria J.; Auque, Luis F.; Gomez, Javier B.; Acero, Patricia (Univ. of Zaragoza, Zaragoza (Spain))

    2008-08-15

    The overall objectives of the hydrogeochemical description for Forsmark are to establish a detailed understanding of the hydrogeochemical conditions at the site and to develop models that fulfil the needs identified by the safety assessment groups during the site investigation phase. Issues of concern to safety assessment are radionuclide transport and technical barrier behaviour, both of which are dependent on the chemistry of groundwater and pore water and their evolution with time. The work has involved the development of descriptive and mathematical models for groundwaters in relation to rock domains, fracture domains and deformation zones. Past climate changes are one of the major driving forces for hydrogeochemical changes and therefore of fundamental importance for understanding the palaeohydrogeological, palaeohydrogeochemical and present evolution of groundwater in the crystalline bedrock of the Fennoscandian Shield. Understanding current undisturbed hydrochemical conditions at the proposed repository site is important when predicting future changes in groundwater chemistry. The causes behind of copper corrosion and/or bentonite degradation are of particular interest as they may jeopardise the long-term integrity of the planned SKB repository system. Thus, the following variables are considered for the hydrogeochemical site descriptive modelling: pH, Eh, sulphur species, iron, manganese, carbonate, phosphate, nitrogen species, total dissolved solids (TDS), isotopes, colloids, fulvic and humic acids and microorganisms. In addition, dissolved gases (e.g. carbon dioxide, methane and hydrogen) are of interest because of their likely participation in microbial reactions. In this series of reports, the final hydrogeochemical evaluation work of the site investigation at the Forsmark site, is presented. The work was conducted by SKB's hydrogeochemical project group, ChemNet, which consists of independent consultants and university researchers with expertise

  14. Assessment of national systems for obtaining local acceptance of nuclear waste management siting activities

    International Nuclear Information System (INIS)

    On behalf of the United States Department of Energy (DOE), International Energy Associates Limited (IEAL) of Washington, D.C. has conducted surveys and analyses of fourteen countries' plans and approaches for dealing with the problems of obtaining local siting acceptance for nuclear waste management facilities. It was determined that the following elements of the formal systems generally facilitate and/or expedite waste management siting decisions: (1) a clear-cut pro-nuclear power position on the part of the government; (2) a willingness on the part of the central government to exert (with prudence and restraint) its pre-emptive rights in nuclear matters; (3) political structures in which the heads of regional or provincial governments are appointed by the central government; (4) national laws that link reactor licensing with a detailed plan for waste management; (5) an established and stable policy with regard to reprocessing. In contrast, it was determined that the following elements of the formal system generally hinder waste management siting activities: (1) historically strong local land used veto laws; (2) the use of national referenda for making nuclear decisions; (3) requirements for public hearings. The informal approaches fall into the following five categories: (1) political: e.g. assertion of will by political leaders, activities to enlist support of local politicians, activities to broaden involvement in decision-making; (2) economic: e.g. emphasis on normal benefits, provision for additional economic benefits; (3) siting: e.g. at or near existing nuclear facilities, on government or utility property, at multiple locations to spread the political burden; (4) timing: e.g. decoupling drilling activities from ultimate repository site decision, deliberate deferral to (long-range) future; (5) education: e.g. creation of special government programmes, enlisting of media support

  15. Systematic Site Characterization at Seismic Stations combined with Empirical Spectral Modeling: critical data for local hazard analysis

    Science.gov (United States)

    Michel, Clotaire; Hobiger, Manuel; Edwards, Benjamin; Poggi, Valerio; Burjanek, Jan; Cauzzi, Carlo; Kästli, Philipp; Fäh, Donat

    2016-04-01

    The Swiss Seismological Service operates one of the densest national seismic networks in the world, still rapidly expanding (see http://www.seismo.ethz.ch/monitor/index_EN). Since 2009, every newly instrumented site is characterized following an established procedure to derive realistic 1D VS velocity profiles. In addition, empirical Fourier spectral modeling is performed on the whole network for each recorded event with sufficient signal-to-noise ratio. Besides the source characteristics of the earthquakes, statistical real time analyses of the residuals of the spectral modeling provide a seamlessly updated amplification function w.r. to Swiss rock conditions at every station. Our site characterization procedure is mainly based on the analysis of surface waves from passive experiments and includes cross-checks of the derived amplification functions with those obtained through spectral modeling. The systematic use of three component surface-wave analysis, allowing the derivation of both Rayleigh and Love waves dispersion curves, also contributes to the improved quality of the retrieved profiles. The results of site characterisation activities at recently installed strong-motion stations depict the large variety of possible effects of surface geology on ground motion in the Alpine context. Such effects range from de-amplification at hard-rock sites to amplification up to a factor of 15 in lacustrine sediments with respect to the Swiss reference rock velocity model. The derived velocity profiles are shown to reproduce observed amplification functions from empirical spectral modeling. Although many sites are found to exhibit 1D behavior, our procedure allows the detection and qualification of 2D and 3D effects. All data collected during the site characterization procedures in the last 20 years are gathered in a database, implementing a data model proposed for community use at the European scale through NERA and EPOS (www.epos-eu.org). A web stationbook derived from it

  16. Three-Dimensional Site Characterization Model of Bangalore Using Support Vector Machine

    OpenAIRE

    Samui, Pijush

    2012-01-01

    The main objective of site characterization is the prediction of in situ soil properties at any half-space point at a site based on limited tests. In this study, the Support Vector Machine (SVM) has been used to develop a three dimensional site characterization model for Bangalore, India based on large amount of Standard Penetration Test. SVM is a novel type of learning machine based on statistical learning theory, uses regression technique by introducing ε-insensitive loss function. The data...

  17. Assessment of Nucleation Site Density Models for CFD Simulations of Subcooled Flow Boiling

    International Nuclear Information System (INIS)

    The framework of a CFD simulation of subcooled flow boiling basically includes a block of wall boiling models communicating with governing equations of a two-phase flow via parameters like temperature, rate of phasic change, etc. In the block of wall boiling models, a heat flux partitioning model, which describes how the heat is taken away from a heated surface, is combined with models quantifying boiling parameters, i.e. nucleation site density, and bubble departure diameter and frequency. It is realized that the nucleation site density is an important parameter for predicting the subcooled flow boiling. The number of nucleation sites per unit area decides the influence region of each heat transfer mechanism. The variation of the nucleation site density will mutually change the dynamics of vapor bubbles formed at these sites. In addition, the nucleation site density is needed as one initial and boundary condition to solve the interfacial area transport equation. A lot of effort has been devoted to mathematically formulate the nucleation site density. As a consequence, numerous correlations of the nucleation site density are available in the literature. These correlations are commonly quite different in their mathematical form as well as application range. Some correlations of the nucleation site density have been applied successfully to CFD simulations of several specific subcooled boiling flows, but in combination with different correlations of the bubble departure diameter and frequency. In addition, the values of the nucleation site density, and bubble departure diameter and frequency obtained from simulations for a same problem are relatively different, depending on which models are used, even when global characteristics, e.g., void fraction and mean bubble diameter, agree well with experimental values. It is realized that having a good CFD simulations of the subcooled flow boiling requires a detailed validations of all the models used. Owing to the importance

  18. Scavenging of ultrafine particles by rainfall at a boreal site: observations and model estimations

    Directory of Open Access Journals (Sweden)

    C. Andronache

    2006-05-01

    Full Text Available Values of the scavenging coefficient were determined from observations of ultrafine particles (with diameters in the range 10–510 nm during rain events at a boreal forest site in Southern Finland between 1996 and 2001. The estimated range of values of the scavenging coefficient was [7×10−6–4×10−5] s−1, which is generally higher than model calculations based only on below-cloud processes (Brownian diffusion, interception, and typical charge effects. A new model that includes below-cloud scavenging processes, mixing of ultrafine particles from the boundary layer (BL into cloud, followed by cloud condensation nuclei activation and in-cloud removal by rainfall, is presented. The effective scavenging coefficients estimated from this new model have values comparable with those obtained from observations. Results show that ultrafine particle removal by rain depends on aerosol size, rainfall intensity, mixing processes between BL and cloud elements, in-cloud scavenged fraction, in-cloud collection efficiency, and in-cloud coagulation with cloud droplets. Implications for the treatment of scavenging of BL ultrafine particles in numerical models are discussed.

  19. A model of visual, aesthetic communication focusing on web sites

    DEFF Research Database (Denmark)

    Thorlacius, Lisbeth

    2002-01-01

    in the eyes of the media producers even though the most outstanding media products often obtained their success due to aesthetic phenomena. The formal aesthetic function and the inexpressible aesthetic function have therefore been prioritised in the model in regard to the construction and analysis of media...

  20. Risk Prediction Models for Other Cancers or Multiple Sites

    Science.gov (United States)

    Developing statistical models that estimate the probability of developing other multiple cancers over a defined period of time will help clinicians identify individuals at higher risk of specific cancers, allowing for earlier or more frequent screening and counseling of behavioral changes to decrease risk.

  1. Thermal properties. Site descriptive modelling Forsmark - stage 2.2

    Energy Technology Data Exchange (ETDEWEB)

    Back, Paer-Erik; Wrafter, John; Sundberg, Jan [Geo Innova AB (Sweden); Rosen, L ars [Sweco Viak AB (Sweden)

    2007-09-15

    The lithological data acquired from boreholes and mapping of the rock surface need to be reclassified into thermal rock classes, TRCs. The main reason is to simplify the simulations. The lithological data are used to construct models of the transition between different TRCs, thus describing the spatial statistical structure of each TRC. The result is a set of transition probability models that are used in the simulation of TRCs. The intermediate result of this first stochastic simulation is a number of realisations of the geology, each one equally probable. Based on the thermal data, a spatial statistical thermal model is constructed for each TRC. It consists of a statistical distribution and a variogram for each TRC. These are used in the stochastic simulation of thermal conductivity and the result is a number of equally probable realisations of thermal conductivity for the domain. In the next step, the realisations of TRCs (lithology) and thermal conductivity are merged, i.e. each realisation of geology is filled with simulated thermal conductivity values. The result is a set of realisations of thermal conductivity that considers both the difference in thermal properties between different TRCs, and the variability within each TRC. If the result is desired in a scale different from the simulation scale, i.e. the canister scale, upscaling of the realisations can be performed. The result is a set of equally probable realisations of thermal properties. The presented methodology was applied to rock domain RFM029 and RFM045. The main results are sets of realisations of thermal properties that can be used for further processing, most importantly for statistical analysis and numerical temperature simulations for the design of repository layout (distances between deposition holes). The main conclusions of the thermal modelling are: The choice of scale has a profound influence on the distribution of thermal conductivity values. The variance decreases and the lower tail

  2. Modeling the active site of [FeFe]-hydrogenase: Electro-catalytic hydrogen evolution from acetic acid catalysed by [Fe2(-L)(CO)6] and [Fe2(-L)(CO)5(PPh3)] (L=pyrazine-2, 3-dithiolate, quinoxaline-2, 3-dithiolate and pyrido[2,3-b] pyrazine-2, 3-dithiolate)

    Indian Academy of Sciences (India)

    Gummadi Durgaprasad; Samar K Das

    2015-02-01

    Compounds [Fe2{-pydt}(CO)6] (pydt = pyrazine-2,3-dithiolate) (1), [Fe2{-qdt}(CO)6] (qdt = quinoxaline-2,3-dithiolate) (2), [Fe2{-ppdt}CO)6] (ppdt = pyrido[2,3-b]pyrazine-2,3-dithiolate) (3), [Fe2{-pydt}(CO)5PPh3] (4), [Fe2{-qdt}(CO)5PPh3] (5) and [Fe2{-ppdt}(CO)5PPh3] (6) have been synthesized in order to model the active sites of `[FeFe]-hydrogenase’. Compounds 1–6 have been characterized by routine spectral studies and unambiguously by single crystal X-ray crystallography. Supramolecular chemistry of compounds 1–6 have been described in terms of intermolecular interactions, observed in their respective crystal structures. Electro-catalytic hydrogen evaluation studies (from acetic acid) have been performed using compounds 1–6 as electro-catalysts. The mechanistic aspects of relevant electro–catalytic proton reductions have been discussed in detail.

  3. Sensitivity of wetland methane emissions to model assumptions: application and model testing against site observations

    Directory of Open Access Journals (Sweden)

    L. Meng

    2012-07-01

    Full Text Available Methane emissions from natural wetlands and rice paddies constitute a large proportion of atmospheric methane, but the magnitude and year-to-year variation of these methane sources are still unpredictable. Here we describe and evaluate the integration of a methane biogeochemical model (CLM4Me; Riley et al., 2011 into the Community Land Model 4.0 (CLM4CN in order to better explain spatial and temporal variations in methane emissions. We test new functions for soil pH and redox potential that impact microbial methane production in soils. We also constrain aerenchyma in plants in always-inundated areas in order to better represent wetland vegetation. Satellite inundated fraction is explicitly prescribed in the model, because there are large differences between simulated fractional inundation and satellite observations, and thus we do not use CLM4-simulated hydrology to predict inundated areas. A rice paddy module is also incorporated into the model, where the fraction of land used for rice production is explicitly prescribed. The model is evaluated at the site level with vegetation cover and water table prescribed from measurements. Explicit site level evaluations of simulated methane emissions are quite different than evaluating the grid-cell averaged emissions against available measurements. Using a baseline set of parameter values, our model-estimated average global wetland emissions for the period 1993–2004 were 256 Tg CH4 yr−1 (including the soil sink and rice paddy emissions in the year 2000 were 42 Tg CH4 yr−1. Tropical wetlands contributed 201 Tg CH4 yr−1, or 78% of the global wetland flux. Northern latitude (>50 N systems contributed 12 Tg CH4 yr−1. However, sensitivity studies show a large range (150–346 Tg CH4 yr−1 in predicted global methane emissions (excluding emissions from rice paddies. The large range is

  4. Sensitivity of wetland methane emissions to model assumptions: application and model testing against site observations

    Directory of Open Access Journals (Sweden)

    L. Meng

    2011-06-01

    Full Text Available Methane emissions from natural wetlands and rice paddies constitute a large proportion of atmospheric methane, but the magnitude and year-to-year variation of these methane sources is still unpredictable. Here we describe and evaluate the integration of a methane biogeochemical model (CLM4Me; Riley et al., 2011 into the Community Land Model 4.0 (CLM4CN in order to better explain spatial and temporal variations in methane emissions. We test new functions for soil pH and redox potential that impact microbial methane production in soils. We also constrain aerenchyma in plants in always-inundated areas in order to better represent wetland vegetation. Satellite inundated fraction is explicitly prescribed in the model because there are large differences between simulated fractional inundation and satellite observations. A rice paddy module is also incorporated into the model, where the fraction of land used for rice production is explicitly prescribed. The model is evaluated at the site level with vegetation cover and water table prescribed from measurements. Explicit site level evaluations of simulated methane emissions are quite different than evaluating the grid cell averaged emissions against available measurements. Using a baseline set of parameter values, our model-estimated average global wetland emissions for the period 1993–2004 were 256 Tg CH4 yr−1, and rice paddy emissions in the year 2000 were 42 Tg CH4 yr−1. Tropical wetlands contributed 201 Tg CH4 yr−1, or 78 % of the global wetland flux. Northern latitude (>50 N systems contributed 12 Tg CH4 yr−1. We expect this latter number may be an underestimate due to the low high-latitude inundated area captured by satellites and unrealistically low high-latitude productivity and soil carbon predicted by CLM4. Sensitivity analysis showed a large range (150–346 Tg CH4 yr−1 in

  5. Hydrogeologic Model for the Gable Gap Area, Hanford Site

    Energy Technology Data Exchange (ETDEWEB)

    Bjornstad, Bruce N.; Thorne, Paul D.; Williams, Bruce A.; Last, George V.; Thomas, Gregory S.; Thompson, Michael D.; Ludwig, Jami L.; Lanigan, David C.

    2010-09-30

    Gable Gap is a structural and topographic depression between Gable Mountain and Gable Butte within the central Hanford Site. It has a long and complex geologic history, which includes tectonic uplift synchronous with erosional downcutting associated with the ancestral Columbia River during both Ringold and Cold Creek periods, and by the later Ice Age (mostly glacial Lake Missoula) floods. The gap was subsequently buried and partially backfilled by mostly coarse-grained, Ice Age flood deposits (Hanford formation). Erosional remnants of both the Ringold Formation and Cold Creek unit locally underlie the high-energy flood deposits. A large window exists in the gap where confined basalt aquifers are in contact with the unconfined suprabasalt aquifer. Several paleochannels, of both Hanford and Ringold Formation age, were eroded into the basalt bedrock across Gable Gap. Groundwater from the Central Plateau presently moves through Gable Gap via one or more of these shallow paleochannels. As groundwater levels continue to decline in the region, groundwater flow may eventually be cut off through Gable Gap.

  6. Adaptive Work Strategy for Evaluating a Conceptual Site Model

    Science.gov (United States)

    Dietrich, P.; Utom, A. U.; Werban, U.

    2015-12-01

    A comprehensive, diagnostic, procedural and adaptive scheme involving a combination of geophysical and direct push methods was developed and applied in the Wurmlingen study site situated within the region of Baden-Württemberg (southwest Germany). The goal of the study was to test the applicability of electrical resistivity method in imaging resistivity contrasts, and mapping the depth to and lateral extent of field-scale subsurface structures and existence of flow paths that may control concentration gradients of groundwater solution contents. Based on a relatively fast and cost-effective areal mapping with vertical electrical sounding technique, a northwest-southeast trending stream-channel-like depression (low apparent resistivity feature) through a Pleistocene aquifer was detected. For a more detailed characterization, we implemented electrical resistivity tomography method followed by direct push (DP) technologies. Beside the use of DP for verification of structures identified by geophysical tools, we used it for multi-level groundwater sampling. Results from groundwater chemistry indicate zones of steep nitrate concentration gradients associated with the feature.

  7. Linde FUSRAP Site Remediation: Engineering Challenges and Solutions of Remedial Activities on an Active Industrial Facility - 13506

    International Nuclear Information System (INIS)

    The Linde FUSRAP Site (Linde) is located in Tonawanda, New York at a major research and development facility for Praxair, Inc. (Praxair). Successful remediation activities at Linde combines meeting cleanup objectives of radiological contamination while minimizing impacts to Praxair business operations. The unique use of Praxair's property coupled with an array of active and abandoned utilities poses many engineering and operational challenges; each of which has been overcome during the remedial action at Linde. The U.S. Army Corps of Engineers - Buffalo District (USACE) and CABRERA SERVICES, INC. (CABRERA) have successfully faced engineering challenges such as relocation of an aboveground structure, structural protection of an active water line, and installation of active mechanical, electrical, and communication utilities to perform remediation. As remediation nears completion, continued success of engineering challenges is critical as remaining activities exist in the vicinity of infrastructure essential to business operations; an electrical substation and duct bank providing power throughout the Praxair facility. Emphasis on engineering and operations through final remediation and into site restoration will allow for the safe and successful completion of the project. (authors)

  8. The activity model of legal psychologist

    Directory of Open Access Journals (Sweden)

    N.V. Bogdanovich,

    2014-08-01

    Full Text Available We propose an activity model of legal psychologist work. As a basis for the construction of the system of legal psychologist activity, we use trajectory of teenager living in the legal field. As the main activities within their respective specializations, we highlighted prevention, maintenance and rehabilitation. We define the main activities necessary for the development within the FGOSIII specialization 050407 “Pedagogy and Psychology of deviant behavior”: general and pathopsychologic diagnostics, development activity and psychological education, psycho-correction, psychological counseling. Accordingly, we define the types of psychological practices. We highlight the motivational and integrative practice (teaching introductory and trainee. We propose a system of training modules, ensuring the formation of the necessary competencies. The modules feature is their focus on practice (the association of training courses with the main types of psychological practice.

  9. Novel active comb-shaped dry electrode for EEG measurement in hairy site.

    Science.gov (United States)

    Huang, Yan-Jun; Wu, Chung-Yu; Wong, Alice May-Kuen; Lin, Bor-Shyh

    2015-01-01

    Electroencephalography (EEG) is an important biopotential, and has been widely applied in clinical applications. The conventional EEG electrode with conductive gels is usually used for measuring EEG. However, the use of conductive gel also encounters with the issue of drying and hardening. Recently, many dry EEG electrodes based on different conductive materials and techniques were proposed to solve the previous issue. However, measuring EEG in the hairy site is still a difficult challenge. In this study, a novel active comb-shaped dry electrode was proposed to measure EEG in hairy site. Different form other comb-shaped or spike-shaped dry electrodes, it can provide more excellent performance of avoiding the signal attenuation, phase distortion, and the reduction of common mode rejection ratio. Even under walking motion, it can effectively acquire EEG in hairy site. Finally, the experiments for alpha rhythm and steady-state visually evoked potential were also tested to validate the proposed electrode.

  10. The Path to Graduation: A Model Interactive Web Site Design Supporting Doctoral Students

    Science.gov (United States)

    Simmons-Johnson, Nicole

    2012-01-01

    Objective. This 2-phase mixed method study assessed 2nd-year doctoral students' and dissertation students' perceptions of the current Graduate School of Education dissertation support Web site, with implications for designing a model dissertation support Web site. Methods. Phase 1 collected quantitative and qualitative data through an…

  11. The combination of Forest Site Maps, Site specific Growth Models and Nutrient Balance Models as a Basis for Sustainable Management in the Northern Limestone Alps

    Science.gov (United States)

    Ettmayer, C.; Katzensteiner, K.; Eckmüllner, O.

    2012-04-01

    The demand for biomass from forests is rising continuously. Decision support tools for managers and forest authorities should help to avoid negative consequences of increased biomass extraction on ecosystem processes and the sustainable supply of forest services. Those tools have to be site and stand specific. In Alpine regions shallow soils with high organic matter content are widespread on calcareous bedrock. There is increasing evidence that those soils are particularly vulnerable and intensive harvest leads to rapid humus and nutrient losses and a decline of water storage capacity. Such soils may rely on the existence of a continuous forest cover and/or a minimum input of coarse woody debris. For a test region in Tyrol management scenarios will be modelled to predict management effects on sites with calcareous bedrock. Site specific growth and yield models for biomass fractions are developed based on existing inventory data, site maps and high resolution digital surface and terrain models, complemented by stratified biomass and nutrient inventories, and are used for the calculation of different production scenarios. Nutrient balance models taking into account nutrient extraction via harvest, leaching losses as well as gains via atmospheric deposition, and fertilization are used to calculate the potential sustainable harvest intensity. In addition humus dynamics of the frequently shallow rendzic Leptosols is taken into account. Concepts for long term carbon and nutrient management experiments as a basis for adaptive forest management in the Calacareous Alps are developed.

  12. Evolution in random fitness landscapes: the infinite sites model

    International Nuclear Information System (INIS)

    We consider the evolution of an asexually reproducing population in an uncorrelated random fitness landscape in the limit of infinite genome size, which implies that each mutation generates a new fitness value drawn from a probability distribution g(w). This is the finite population version of Kingman's house of cards model (Kingman 1978 J. Appl. Probab. 15 1). In contrast to Kingman's work, the focus here is on unbounded distributions g(w) which lead to an indefinite growth of the population fitness. The model is solved analytically in the limit of infinite population size N→∞ and simulated numerically for finite N. When the genome-wide mutation probability U is small, the long-time behavior of the model reduces to a point process of fixation events, which is referred to as a diluted record process (DRP). The DRP is similar to the standard record process except that a new record candidate (a number that exceeds all previous entries in the sequence) is accepted only with a certain probability that depends on the values of the current record and the candidate. We develop a systematic analytic approximation scheme for the DRP. At finite U the fitness frequency distribution of the population decomposes into a stationary part due to mutations and a traveling wave component due to selection, which is shown to imply a reduction of the mean fitness by a factor of 1−U compared to the U→0 limit

  13. Genome-wide prediction, display and refinement of binding sites with information theory-based models

    Directory of Open Access Journals (Sweden)

    Leeder J Steven

    2003-09-01

    . Conclusions Delila-Genome was used to scan the human genome sequence with information weight matrices of transcription factor binding sites, including PXR/RXRα, AHR and NF-κB p50/p65, and matrices for RNA binding sites including splice donor, acceptor, and SC35 recognition sites. Comparisons of genome scans with the original and refined PXR/RXRα information weight matrices indicate that the refined model more accurately predicts the strengths of known binding sites and is more sensitive for detection of novel binding sites.

  14. Radar Monitoring: Modelling of Undeclared Activities

    International Nuclear Information System (INIS)

    A feasibility study in the framework of the German Support Programme investigates the applicability of the 3D radar method for the monitoring of a geological repository. The aim of technical solution is the detection and localization of clandestine underground mining activities. The radar system should form a kind of protective shield around a repository to detect and localize possible activities in an early stage and in a sufficient distance. To date radar monitoring in the context of geotechnical engineering is restricted to few applications, mainly in form of repetitive linear measurements. Repetitive surveys out of boreholes or drifts are conducted with disadvantages concerning safeguards requirements as high maintenance and positioning inaccuracie