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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. Resonant active sites in catalytic ammonia synthesis: A structural model

    Science.gov (United States)

    Cholach, Alexander R.; Bryliakova, Anna A.; Matveev, Andrey V.; Bulgakov, Nikolai N.

    2016-03-01

    Adsorption sites Mn consisted of n adjacent atoms M, each bound to the adsorbed species, are considered within a realistic model. The sum of bonds Σ lost by atoms in a site in comparison with the bulk atoms was used for evaluation of the local surface imperfection, while the reaction enthalpy at that site was used as a measure of activity. The comparative study of Mn sites (n = 1-5) at basal planes of Pt, Rh, Ir, Fe, Re and Ru with respect to heat of N2 dissociative adsorption QN and heat of Nad + Had → NHad reaction QNH was performed using semi-empirical calculations. Linear QN(Σ) increase and QNH(Σ) decrease allowed to specify the resonant Σ for each surface in catalytic ammonia synthesis at equilibrium Nad coverage. Optimal Σ are realizable for Ru2, Re2 and Ir4 only, whereas other centers meet steric inhibition or unreal crystal structure. Relative activity of the most active sites in proportion 5.0 × 10- 5: 4.5 × 10- 3: 1: 2.5: 3.0: 1080: 2270 for a sequence of Pt4, Rh4, Fe4(fcc), Ir4, Fe2-5(bcc), Ru2, Re2, respectively, is in agreement with relevant experimental data. Similar approach can be applied to other adsorption or catalytic processes exhibiting structure sensitivity.

  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. 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

  6. Cernavoda Unit 2: - BOP 3D model proposal for a possible organization of site activities

    International Nuclear Information System (INIS)

    The scope of this activity is to define characteristics and advantages of the 3D model of Cernavoda BOP to this set up at site for engineering and construction activities. This model will provide a modern and proven tool able to strongly support the site activities with particular regard to the following: 1. engineering activities, - plant arrangement 'double check' for resolution of clashing; - easy management of future design changes; - real time plant configuration updating as soon as any design modification is approved and integrated in the model; - preparation of high quality documentation for procurement, construction and commissioning; - prompt availability of the as built configuration of the plant as soon as the last modification is frozen; 2. material procurement activities, - definition of the priorities in the construction material procurement according to the construction planning by area; - inventory list of equipment, pipes, fittings, valves, cable trays and ventilation ducts to be installed in each construction area; 3. construction activities, - definition of construction sequences, with particular reference in the congested areas, for piping cable trays (electrical and C-and-I) and ventilations ducts; - definition of piping spools by construction contractors; - follow-up of the activities in each area (i.e. construction, painting, insulation, flushing, pressure testing, etc); 4. turn-over and commissioning, - check of the progress. The success of this approach is based on the following: i) proper management of the remote workstations providing easy and reliable access to the model; ii) subdivision of the Integrated Building in construction areas, whose detail design may be allotted to Romanian organizations with multidisciplinary tasks; iii) integration in the model of the remote developed engineering in order to validate the details of the design. (authors)

  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. 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

    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...

  9. 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.

  10. Remote auroral activity detection and modeling using low frequency transmitter signal reception at a midlatitude site

    Directory of Open Access Journals (Sweden)

    E. D. Schmitter

    2010-09-01

    Full Text Available The low frequency propagation conditions along the path from Iceland to Germany (52° N 8° E using the NRK/TFK 37.5 kHz transmitter (63.9° N 22.5° W prove as an easy to monitor and reliable proxy for north auroral activity. Signal processing using wavelet decomposition allows for quantitative activity level estimations. Calibration is based upon NOAA POES auroral activity data. Using an auroral oval model for the local intensity distribution of solar energetic particle precipitation and a wave propagation model ionospheric D-layer height decreases along the path can be derived. This in turn gives a hint to the low latitude extension and intensity of the auroral electrojet currents that can be responsible for communication and power systems failures.

  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. Low temperature syntheses and reactivity of Cu2O2 active-site models.

    Science.gov (United States)

    Citek, Cooper; Herres-Pawlis, Sonja; Stack, T Daniel P

    2015-08-18

    Nature's facility with dioxygen outmatches modern chemistry in the oxidation and oxygenation of materials and substrates for biosynthesis and cellular metabolism. The Earth's most abundant naturally occurring oxidant is-frankly-poorly understood and controlled, and thus underused. Copper-based enzyme metallocofactors are ubiquitous to the efficient consumption of dioxygen by all domains of life. Over the last several decades, we have joined many research groups in the study of copper- and dioxygen-dependent enzymes through close investigation of synthetically derived, small-molecule active-site analogs. Simple copper-dioxygen clusters bearing structural and spectroscopic similarity to dioxygen-activating enzymes can be probed for their fundamental geometrical, electronic, and reactive properties using the tools available to inorganic and synthetic chemistry. Our exploration of the copper-dioxygen arena has sustained product evaluation of the key dynamics and reactivity of binuclear Cu2O2 compounds. Almost exclusively operating at low temperatures, from -78 °C to solution characterization even at -125 °C, we have identified numerous compounds supported by simple and easily accessed, low molecular weight ligands-chiefly families of bidentate diamine chelates. We have found that by stripping away complexity in comparison to extended protein tertiary structures or sophisticated, multinucleating architectures, we can experimentally manipulate activated compounds and open pathways of reactivity toward exogenous substrates that both inform on and extend fundamental mechanisms of oxygenase enzymes. Our recent successes have advanced understanding of the tyrosinase enzyme, and related hemocyanin and NspF, and the copper membrane monooxygenases, specifically particulate methane monooxygenase (pMMO) and ammonia monooxygenase (AMO). Tyrosinase, ubiquitously distributed throughout life, is fundamental to the copper-based oxidation of phenols and the production of chromophores

  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. DOE site performance assessment activities

    International Nuclear Information System (INIS)

    Information on performance assessment capabilities and activities was collected from eight DOE sites. All eight sites either currently dispose of low-level radioactive waste (LLW) or plan to dispose of LLW in the near future. A survey questionnaire was developed and sent to key individuals involved in DOE Order 5820.2A performance assessment activities at each site. The sites surveyed included: Hanford Site (Hanford), Idaho National Engineering Laboratory (INEL), Los Alamos National Laboratory (LANL), Nevada Test Site (NTS), Oak Ridge National Laboratory (ORNL), Paducah Gaseous Diffusion Plant (Paducah), Portsmouth Gaseous Diffusion Plant (Portsmouth), and Savannah River Site (SRS). The questionnaire addressed all aspects of the performance assessment process; from waste source term to dose conversion factors. This report presents the information developed from the site questionnaire and provides a comparison of site-specific performance assessment approaches, data needs, and ongoing and planned activities. All sites are engaged in completing the radioactive waste disposal facility performance assessment required by DOE Order 5820.2A. Each site has achieved various degrees of progress and have identified a set of critical needs. Within several areas, however, the sites identified common needs and questions

  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. Spatial modeling of receptor species for ecological risk assessment activities on the Department of Energy's Savannah River Site

    Science.gov (United States)

    Gaines, Karen Frances

    To assist risk assessors on the Department of Energy's Savannah River Site (SRS), a Geographic Information System (GIS) was developed to provide relevant information about specific receptor species that can be used for ecological risk assessment (ERA). Although this GIS is a useful tool, it is limited in that it can only provide information about a species if it was studied in that particular area and does not describe the site-wide spatial distribution or life history of a receptor species, which may be crucial when developing an ecological impact assessment. The GIS was expanded by modeling wildlife species on the SRS to provide information regarding their over-all distribution (probability of being in an area) and habitat utilization. Each model is a stand-alone tool consisting of algorithms that are applied within a GIS and therefore dynamic enough to respond to stochastic events such as natural and anthropogenic habitat disturbances and/or long-term changes such as natural succession. Spatial analyses suggest toxicant exposure and accumulation risk in relation to the species probability of occurrence in the area. This modeling effort provides the tools that are crucial for the Department of Energy to conduct ERA activities for specific contaminants on the SRS. Further, it serves as a template for DOE managed lands and other large government facilities to establish a framework for site-specific ecological impact assessments that use wildlife species as endpoints. Predictive distribution models for the raccoon (Procyon lotor) and wild hog (Sus scrofa ) are used to demonstrate the construction and utilization of these models to: (1) estimate wildlife toxicant exposure, (2) identify possible contaminant vectors, and (3) construct human-based risk assessments from consuming wild game.

  17. Modeling emissions and dispersion of contaminants from cleanup activities at a mixed waste site to estimate air impacts and risks

    International Nuclear Information System (INIS)

    The transport and dispersion of contaminants via the air pathway is a major concern during cleanup of contaminated sites. Impacts to air quality and human health during cleanup were evaluated for the Weldon Spring site by using site-specific information for source areas, activities, and receptor locations. In order to ensure protection of human health and the environment, results are being used to focus on those cleanup activities for which release controls should be emphasized

  18. 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.

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

    OpenAIRE

    Lalida Shank; Vannajan Sanghiran Lee; Prontipa Nokthai

    2010-01-01

    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 ...

  20. Adjuvant activity of ambient particulate matter of different sites, sizes, and seasons in a respiratory allergy mouse model

    International Nuclear Information System (INIS)

    In the framework of an EU project entitled, 'Respiratory Allergy and Inflammation due to Ambient Particles (RAIAP)', various ambient particulate matter samples were tested for their adjuvant potency in an animal allergy model to ovalbumin. Coarse (2.5-10 μm) and fine (0.15-2.5 μm) particles were collected during the spring, summer, and winter in Rome, Oslo, Lodz, and Amsterdam. Coarse and fine particles were also collected near a seaside location in the Netherlands, where prevailing winds are westerly. These latter particles served as a control, with a minimum contribution by traffic. Ottawa dust (EHC-93) was used as a standard reference sample. Immunoglobulins (IgE, IgG1, and IgG2a), histopathological changes in the lung, cytokines, and the number of cells and their differentiation in lung lavages were used as effect parameters to study the adjuvant potency of these particles. The particles (3 mg/ml) were mixed with ovalbumin (0.4 mg/ml) and intranasally administered during the sensitization or the challenge phase. Intranasal administration of ovalbumin only induced very little antibody response, but introduced a minor inflammatory response in the lung or BAL during the sensitization and challenge phase. On the contrary, after coexposure to EHC-93 and ovalbumin, a major increase was found in immunoglobulin levels specific for ovalbumin, and a major inflammatory response in lung and BAL was induced. Coexposure to ovalbumin with 4 out of 12 collected PM samples (3 mg/ml) resulted in an increase of mainly IgE and IgG1. The histopathological changes consisted of a small to severe peribronchial and perivascular inflammatory response, a hypertrophy of bronchiolar mucous cells and an increase in eosinophils and neutrophils in the BAL. Statistical evaluation of the above-mentioned parameters showed associations with PMx (coarse and fine), site, season, season x PMx, season x site and PMx x site. In addition, adjuvant activity of the PMx can be ranked as Lodz > Rome

  1. In silico Modeling of 1A-Adrenoceptor: Interaction of its Normal and Mutated Active Sites with Noradrenaline as well as its Agonist and Antagonist

    Directory of Open Access Journals (Sweden)

    Ramchandran Vijayan

    2007-01-01

    Full Text Available Noradrenaline, like most other neurotransmitters, acts through various adrenoceptor subtypes. The structure and active site of adrenoceptors for the binding of noradrenaline were unknown, however, such information are crucial for understanding the molecular mechanism of action of neurotransmitters, including noradrenaline, in health and disease as well as for drug designing. In this in silico study, we modeled the α1A-adrenoceptor; a G protein coupled receptor and defined its active site. Further, molecular docking and interaction of noradrenaline and its agonist as well as antagonist with the so defined active site of the receptor was studied before and after in silico site directed mutation of several amino acid residues forming the active site. Our results indicate that the ARG166 is the most crucial residue for binding of noradrenaline and methoxamine to α1A-adrenoceptor and ILE178 is the most important residue for binding of prazosin to it. Thus, the observations provide new insights into the structure function relationship of α1A-adrenoceptor. A significant finding of this study is that the same residue of the active site may not be necessary for binding of a receptor with its natural ligand and its pharmacologically active known agonist and antagonist.

  2. A structural model for across membrane coupling between the Qo and Qi active sites of cytochrome bc1.

    Science.gov (United States)

    Cooley, Jason W

    2010-12-01

    The two spatially distant quinone-binding sites of the ubihydroquinone: cytochrome c oxidoreductase (cyt bc(1)) complex have been shown to influence one another in some fashion. This transmembrane communication alters cofactor and redox partner binding interactions and could potentially influence the timing or 'concerted' steps involved in the steady-state turnover of the homodimeric enzymes. Yet, despite several lines of evidence corroborating the coupling of the quinone binding active sites to one another, little to no testable hypothesis has been offered to explain how such a "signal" might be transmitted across the presumably rigid hydrophobic domain of the enzyme. Recently, it has been shown that this interquinone binding sites communication influences the steady-state position of the mobile [2Fe-2S] cluster containing iron sulfur protein (Sarewicz M., Dutka M., Froncisz W., Osyczka A. (2009) Biochemistry 48, 5708-5720) as mediated by at least one transmembrane helix of the b-type cyt containing subunit (Cooley, J. W., Lee, D. W., and Daldal, F. (2009) Biochemistry 48, 1988-1999). Here we provide an overview of the evidence supporting the structural coupling of these sites and provide a theoretical framework for how the redox state of a quinone at one cofactor binding site might influence the cofactor-, inhibitor-, and/or protein-protein interactions at the structurally distant opposing Q binding site. PMID:20513347

  3. Active Site Engineering in Electrocatalysis

    DEFF Research Database (Denmark)

    Verdaguer Casadevall, Arnau; Stephens, Ifan; Chorkendorff, Ib

    The overall goal of this thesis has been to design better catalysts for electrochemical reactions through a fundamental understanding of the materials at atomic scale. This has been achieved by combining electrochemical measurements with a variety of characterization techniques, often in ultra high...... under reaction conditions, which is ultimately controlled by the crystal structure of the underlying alloy.• Oxygen reduction to hydrogen peroxide has been investigated on single site catalysts, mainly alloys of noble metals with Hg. This resulted in a very special structure with isolated atoms of Pt or......, inexistent in other forms of Cu. The presence of strong CO binding sites correlates well with electrochemical activity, which paves the way for the rational development of even better electrocatalysts....

  4. 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...

  5. Efficient oxygen electrocatalysis on special active sites

    DEFF Research Database (Denmark)

    Halck, Niels Bendtsen

    Oxygen electrocatalysis will be pivotal in future independent of fossil fuels. Renewable energy production will rely heavily on oxygen electrocatalysis as a method for storing energy from intermittent energy sources such as the wind and sun in the form of chemical bonds and to release the energy ...... electrocatalysis (ORR and OER) using organic functional groups on another class of catalysts. These consist of graphene sheets modified to have a local porphyrine site with different transition metals ions as model systems....... stored in these bonds in an eco-friendly fashion in fuel cells. This thesis explores catalysts for oxygen electrocatalysis and how carefully designed local structures on catalysts surfaces termed special active sites can influence the activity. Density functional theory has been used as a method...... throughout this thesis to understand these local structure effects and their influence on surface reactions. The concept of these special active sites is used to explain how oxygen evolution reaction (OER) catalysts can have activities beyond the limits of what was previously thought possible. The concept is...

  6. 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 ...

  7. 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;

    a Danish context, it must be considered that ecological models also should be site-specific to capture local and cultural aspects related to PA. Methods: Three major multi-level intervention studies are carried out in Denmark with the objective to promote PA in 17 local communities. 1) The SPACE...... studies clarifies different local and cultural aspects with specific effect on PA behavior. This finding is closely related to the fact that the new outdoor PA facilities in the 17 local communities have different size, composition and are targeted to different subgroups with different organizational...... setup to support the use of the facilities. Despite the conceptual and contextual differences PA behavior is also affected by cultural and social values related to the specific site which not alone can be explained by intrapersonal, interpersonal or organizational factors. Discussion: The Ecological...

  8. 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

  9. 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

  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. 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...

  12. 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...

  13. 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

  14. 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

  15. 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.

  16. 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

  17. 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

  18. Modelling the active site of NiFe hydrogenases: new catalysts for the electro-production of H2 and mechanistic studies

    International Nuclear Information System (INIS)

    NiFe hydrogenases are unique metalloenzymes that catalyze H+/H2 interconversion with remarkable efficiency close to the thermodynamic potential. Their active site consists of a hetero-bimetallic complex containing a nickel ion in a sulphur-rich environment connected by two thiolate bridges to an organometallic cyano-carbonyl iron moiety. In order to improve the understanding of the enzymatic mechanism and to obtain new base-metal electrocatalysts for H2 production, we synthesized a series of bio-inspired low molecular weight model complexes with the butterfly structure Ni(μ-S2)M (M= Ru, Mn and Fe). All these compounds displayed a catalytic activity of hydrogen production. Modulating the electronic and steric properties of the ruthenium center allowed optimizing the catalytic performances of these compounds in terms of stability, catalytic rate and overpotential. Mechanistic studies of the catalytic cycle of the Ni-Ru complexes have also been carried out. They allowed us to suggest a bio-relevant bridging hydride as the catalytic intermediate. Finally, we synthesized one of the first Ni-Fe complexes that is both a structural and a functional model of NiFe hydrogenase. (author)

  19. 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

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

    International Nuclear Information System (INIS)

    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: FSMC, FSMEW007, FSMN, FSMNE005, FSMS, and FSMW. 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 alternative model and the P32 of the

  1. 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

  2. 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

  3. 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

  4. 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

  5. Managing Siting Activities for Nuclear Power Plants

    International Nuclear Information System (INIS)

    One of the IAEA's statutory objectives is to ''seek to accelerate and enlarge the contribution of atomic energy to peace, health and prosperity throughout the world''. One way this objective is achieved is through the publication of a range of technical series. Two of these are the IAEA Nuclear Energy Series and the IAEA Safety Standards Series. According to Article III.A.6 of the IAEA Statute, the safety standards establish 'standards of safety for protection of health and minimization of danger to life and property.' The safety standards include the Safety Fundamentals, Safety Requirements and Safety Guides. These standards are written primarily in a regulatory style, and are binding on the IAEA for its own programmes. The principal users are the regulatory bodies in Member States and other national authorities. The IAEA Nuclear Energy Series comprises reports designed to encourage and assist R and D on, and application of, nuclear energy for peaceful uses. This includes practical examples to be used by owners and operators of utilities in Member States, implementing organizations, academia, and government officials, among others. This information is presented in guides, reports on technology status and advances, and best practices for peaceful uses of nuclear energy based on inputs from international experts. The IAEA Nuclear Energy Series complements the IAEA Safety Standards Series. The introduction of nuclear power brings new challenges to States - one of them being the selection of appropriates sites. It is a project that needs to begin early, be well managed, and deploy good communications with all stakeholders; including regulators. This is important, not just for those States introducing nuclear power for the first time, but for any State looking to build a new nuclear power plant. The purpose of the siting activities goes beyond choosing a suitable site and acquiring a licence. A large part of the project is about producing and maintaining a validated

  6. Klipperaas 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 rpogramme will be to perform detailed characterisation, 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 any of the study sites will be selected as a site for detailed characterization. Other sites with geological and/or socio-economical characteristics judged more favorable 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 concern the Klipperaas study site. The main topics are the scope of activities, geologic model, geohydrological model, groundwater chemistry, assessment of solute transport, and rock mechanics

  7. Efficient oxygen electrocatalysis on special active sites

    DEFF Research Database (Denmark)

    Halck, Niels Bendtsen

    cobalt incorporated in ruthenium dioxide at high overpotentials during the oxygen reduction reaction (ORR). Density functional theory calculations were used to explain this phenomenon. The special active sites concepts are used to propose a general unified approach to increase the efficiency for oxygen...

  8. 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.

  9. Contaminant transport modeling studies of Russian sites

    International Nuclear Information System (INIS)

    Lawrence Berkeley Laboratory (LBL) established mechanisms that promoted cooperation between U.S. and Russian scientists in scientific research as well as environmental technology transfer. Using Russian experience and U.S technology, LBL developed approaches for field investigations, site evaluation, waste disposal, and remediation at Russian contaminated sites. LBL assessed a comprehensive database as well as an actual, large-scale contaminated site to evaluate existing knowledge of and test mathematical models used for the assessment of U.S. contaminated sites

  10. 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.

  11. 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...

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

    International Nuclear Information System (INIS)

    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

  13. 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.

  14. 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

  15. 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)

  16. 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

  17. Active Player Modelling

    OpenAIRE

    Togelius, Julian; Shaker, Noor; Yannakakis, Georgios N.

    2013-01-01

    We argue for the use of active learning methods for player modelling. In active learning, the learning algorithm chooses where to sample the search space so as to optimise learning progress. We hypothesise that player modelling based on active learning could result in vastly more efficient learning, but will require big changes in how data is collected. Some example active player modelling scenarios are described. A particular form of active learning is also equivalent to an influential forma...

  18. 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

  19. 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

  20. 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

  1. 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

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

    International Nuclear Information System (INIS)

    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

  3. 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

  4. 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

  5. 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

  6. 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...

  7. Transport properties site descriptive model. Guidelines for evaluation and modelling

    International Nuclear Information System (INIS)

    This report describes a strategy for the development of Transport Properties Site Descriptive Models within the SKB Site Investigation programme. Similar reports have been produced for the other disciplines in the site descriptive modelling (Geology, Hydrogeology, Hydrogeochemistry, Rock mechanics, Thermal properties, and Surface ecosystems). These reports are intended to guide the site descriptive modelling, but also to provide the authorities with an overview of modelling work that will be performed. The site descriptive modelling of transport properties is presented in this report and in the associated 'Strategy for the use of laboratory methods in the site investigations programme for the transport properties of the rock', which describes laboratory measurements and data evaluations. Specifically, the objectives of the present report are to: Present a description that gives an overview of the strategy for developing Site Descriptive Models, and which sets the transport modelling into this general context. Provide a structure for developing Transport Properties Site Descriptive Models that facilitates efficient modelling and comparisons between different sites. Provide guidelines on specific modelling issues where methodological consistency is judged to be of special importance, or where there is no general consensus on the modelling approach. The objectives of the site descriptive modelling process and the resulting Transport Properties Site Descriptive Models are to: Provide transport parameters for Safety Assessment. Describe the geoscientific basis for the transport model, including the qualitative and quantitative data that are of importance for the assessment of uncertainties and confidence in the transport description, and for the understanding of the processes at the sites. Provide transport parameters for use within other discipline-specific programmes. Contribute to the integrated evaluation of the investigated sites. The site descriptive modelling of

  8. 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

  9. 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...

  10. 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.

  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. 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

  13. 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

  14. 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

  15. 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

  16. 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.

  17. Promoter proximal polyadenylation sites reduce transcription activity

    DEFF Research Database (Denmark)

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

    2012-01-01

    transcription requires promoter proximity, as demonstrated using artificial constructs and supported by a genome-wide data set. Importantly, transcription down-regulation can be recapitulated in a gene context devoid of splice sites by placing a functional bona fide pA site/transcription terminator within ∼500...

  18. 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.

  19. Brownian aggregation rate of colloid particles with several active sites

    International Nuclear Information System (INIS)

    We theoretically analyze the aggregation kinetics of colloid particles with several active sites. Such particles (so-called “patchy particles”) are well known as chemically anisotropic reactants, but the corresponding rate constant of their aggregation has not yet been established in a convenient analytical form. Using kinematic approximation for the diffusion problem, we derived an analytical formula for the diffusion-controlled reaction rate constant between two colloid particles (or clusters) with several small active sites under the following assumptions: the relative translational motion is Brownian diffusion, and the isotropic stochastic reorientation of each particle is Markovian and arbitrarily correlated. This formula was shown to produce accurate results in comparison with more sophisticated approaches. Also, to account for the case of a low number of active sites per particle we used Monte Carlo stochastic algorithm based on Gillespie method. Simulations showed that such discrete model is required when this number is less than 10. Finally, we applied the developed approach to the simulation of immunoagglutination, assuming that the formed clusters have fractal structure

  20. Activities on the site during construction phase

    International Nuclear Information System (INIS)

    A survey is given of the work done on the site from site-opening till turn over of the plant to the client. After a short introduction to time schedules, manpower on site, site facilities and civil work and constructions, the commissioning and trial operation phase is discussed in detail. This phase begins with finishing the assembly of individual systems and components and ends with the trial operation and the acceptance measurement. During this period the subsystems are started-up in a useful sequence, first from cold, then from hot conditions and are finally operated as a total with nuclear energy. The single steps are: a) commissioning of indivudal systems; b) hot functional test 1 (without fuels) c) baseline inspection at the reactor pressure vessel; d) hot functional test 2 (with fuels); e) preparation for first criticality; f) postcriticality test program; g) trial operation: h) acceptance measurement. (HP)

  1. DSEM, Radioactive Waste Disposal Site Economic Model

    International Nuclear Information System (INIS)

    1 - Description of program or function: The Disposal Site Economic Model calculates the average generator price, or average price per cubic foot charged by a disposal facility to a waste generator, one measure of comparing the economic attractiveness of different waste disposal site and disposal technology combinations. The generator price is calculated to recover all costs necessary to develop, construct, operate, close, and care for a site through the end of the institutional care period and to provide the necessary financial returns to the site developer and lender (when used). Six alternative disposal technologies, based on either private or public financing, can be considered - shallow land disposal, intermediate depth disposal, above or below ground vaults, modular concrete canister disposal, and earth mounded concrete bunkers - based on either private or public development. 2 - Method of solution: The economic models incorporate default cost data from the Conceptual Design Report (DOE/LLW-60T, June 1987), a study by Rodgers Associates Engineering Corporation. Because all costs are in constant 1986 dollars, the figures must be modified to account for inflation. Interest during construction is either capitalized for the private developer or rolled into the loan for the public developer. All capital costs during construction are depreciated over the operation life of the site using straight-line depreciation for the private sector. 3 - Restrictions on the complexity of the problem: Maxima of - 100 years post-operating period, 30 years operating period, 15 years pre-operating period. The model should be used with caution outside the range of 1.8 to 10.5 million cubic feet of total volume. Depreciation is not recognized with public development

  2. 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.

  3. Site characterization techniques used in environmental remediation activities

    International Nuclear Information System (INIS)

    As a result of decades of nuclear energy research, weapons production, as well as ongoing operations, a significant amount of radioactive contamination has occurred throughout the United States Department of Energy (DOE) complex. DOE facility are in the process of assessing and potentially remediating various sites according to the regulations imposed by a Federal Facility Agreement and Consent order (FFA/CO) between DOE, the state in which the facility is located, and the U.S. Environmental Protection Agency (EPA). In support of these active site remediation efforts, the DOE has devoted considerable resources towards the development of innovative site characterization techniques that support environmental restoration activities. These resources and efforts have focused on various aspects of this complex problem. Research and technology development conducted at the Idaho National Engineering and Environmental Laboratory (INEEL) has resulted in the ability and state-of-the-art equipment required to obtain real-time, densely spaced, in situ characterization data (i.e. detection, speciation, and location) of various radionuclides and contaminants. The Remedial Action Monitoring System (RAMS), developed by the INEEL, consists of enhanced sensor technology, measurement modeling and interpretation techniques, and a suite of deployment platforms which can be interchanged to directly support remedial cleanup and site verification operations. In situ characterization techniques have advanced to the point where they are being actively deployed in support of remedial operations. The INEEL has deployed its system at various DOE and international sites. The deployment of in situ characterization systems during environmental restoration operations has shown that this approach results in several significant benefits versus conventional sampling techniques. A flexible characterization system permits rapid modification to satisfy physical site conditions, available site resources

  4. Evaluating Conceptual Site Models with Multicomponent Reactive Transport Modeling

    Science.gov (United States)

    Dai, Z.; Heffner, D.; Price, V.; Temples, T. J.; Nicholson, T. J.

    2005-05-01

    Modeling ground-water flow and multicomponent reactive chemical transport is a useful approach for testing conceptual site models and assessing the design of monitoring networks. A graded approach with three conceptual site models is presented here with a field case of tetrachloroethene (PCE) transport and biodegradation near Charleston, SC. The first model assumed a one-layer homogeneous aquifer structure with semi-infinite boundary conditions, in which an analytical solution of the reactive solute transport can be obtained with BIOCHLOR (Aziz et al., 1999). Due to the over-simplification of the aquifer structure, this simulation cannot reproduce the monitoring data. In the second approach we used GMS to develop the conceptual site model, a layer-cake multi-aquifer system, and applied a numerical module (MODFLOW and RT3D within GMS) to solve the flow and reactive transport problem. The results were better than the first approach but still did not fit the plume well because the geological structures were still inadequately defined. In the third approach we developed a complex conceptual site model by interpreting log and seismic survey data with Petra and PetraSeis. We detected a major channel and a younger channel, through the PCE source area. These channels control the local ground-water flow direction and provide a preferential chemical transport pathway. Results using the third conceptual site model agree well with the monitoring concentration data. This study confirms that the bias and uncertainty from inadequate conceptual models are much larger than those introduced from an inadequate choice of model parameter values (Neuman and Wierenga, 2003; Meyer et al., 2004). Numerical modeling in this case provides key insight into the hydrogeology and geochemistry of the field site for predicting contaminant transport in the future. Finally, critical monitoring points and performance indicator parameters are selected for future monitoring to confirm system

  5. 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

  6. 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.

  7. Integrated Site Model Process Model Report No.20

    International Nuclear Information System (INIS)

    The 20th semiannual report of the Yucca Mountain Site Characterization Project (YMP) summarizes activities during the period from October 1, 1998 through March 31, 1999. YMP activities are aimed at evaluating Yucca Mountain as a suitable site for permanent geologic disposal of nuclear materials, as directed by the Nuclear Waste Policy Act (NWPA). The progress report documents activities this period that contributed to completing the YMP's near-term programmatic and statutory objectives. These objectives include completing the Viability Assessment of a Repository at Yucca Mountain (VA), the Environmental Impact Statement (EIS), a possible U.S. Department of Energy (DOE) Secretarial Site Recommendation to the President, and, if the recommendation is approved, submittal of a license application to the U.S. Nuclear Regulatory Commission (NRC). The first of these objectives was attained with submittal of the VA (DOE 1998) to the President and the Congress. The other objectives are scheduled for completion in the next several years. The YMP's science and engineering work is now focused on supporting a decision on a site recommendation. YMP work this period continued to be concentrated in three integrated activities: site characterization, engineering design and construction, and repository performance. Accomplishments this period and their relation to near-term objectives are briefly summarized below. The near-term objectives and the three integrated activities are presented in more detail in Sections 2 through 6

  8. 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

  9. 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

  10. 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.

  11. Study the active site of flavonoid applying radiation chemistry

    International Nuclear Information System (INIS)

    Flavonoid are a large and important class of naturally occurring, low molecular weight benzo-γ-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)

  12. SITE-94. Discrete-feature modelling of the Aespoe site: 2. Development of the integrated site-scale model

    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. Hydrologic properties of the large-scale structures are initially estimated from cross-hole hydrologic test data, and automatically calibrated by numerical simulation of network flow, and comparison with undisturbed heads and observed drawdown in selected cross-hole tests. The calibrated model is combined with a separately derived fracture network model, to yield the integrated model. This model is partly validated by simulation of transient responses to a long-term pumping test and a convergent tracer test, based on the LPT2 experiment at Aespoe. The integrated model predicts that discharge from the SITE-94 repository is predominantly via fracture zones along the eastern shore of Aespoe. Similar discharge loci are produced by numerous model variants that explore uncertainty with regard to effective semi regional boundary conditions, hydrologic properties of the site-scale structures, and alternative structural/hydrological interpretations. 32 refs

  13. 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.

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

    International Nuclear Information System (INIS)

    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

  15. Are nest sites actively chosen? Testing a common assumption for three non-resource limited birds

    Science.gov (United States)

    Goodenough, A. E.; Elliot, S. L.; Hart, A. G.

    2009-09-01

    Many widely-accepted ecological concepts are simplified assumptions about complex situations that remain largely untested. One example is the assumption that nest-building species choose nest sites actively when they are not resource limited. This assumption has seen little direct empirical testing: most studies on nest-site selection simply assume that sites are chosen actively (and seek explanations for such behaviour) without considering that sites may be selected randomly. We used 15 years of data from a nestbox scheme in the UK to test the assumption of active nest-site choice in three cavity-nesting bird species that differ in breeding and migratory strategy: blue tit ( Cyanistes caeruleus), great tit ( Parus major) and pied flycatcher ( Ficedula hypoleuca). Nest-site selection was non-random (implying active nest-site choice) for blue and great tits, but not for pied flycatchers. We also considered the relative importance of year-specific and site-specific factors in determining occupation of nest sites. Site-specific factors were more important than year-specific factors for the tit species, while the reverse was true for pied flycatchers. Our results show that nest-site selection, in birds at least, is not always the result of active choice, such that choice should not be assumed automatically in studies of nesting behaviour. We use this example to highlight the need to test key ecological assumptions empirically, and the importance of doing so across taxa rather than for single "model" species.

  16. The active site behaviour of electrochemically synthesised gold nanomaterials.

    Science.gov (United States)

    Plowman, Blake J; O'Mullane, Anthony P; Bhargava, Suresh K

    2011-01-01

    Even though gold is the noblest of metals, a weak chemisorber and is regarded as being quite inert, it demonstrates significant electrocatalytic activity in its nanostructured form. It is demonstrated here that nanostructured and even evaporated thin films of gold are covered with active sites which are responsible for such activity. The identification of these sites is demonstrated with conventional electrochemical techniques such as cyclic voltammetry as well as a large amplitude Fourier transformed alternating current (FT-ac) method under acidic and alkaline conditions. The latter technique is beneficial in determining if an electrode process is either Faradaic or capacitive in nature. The observed behaviour is analogous to that observed for activated gold electrodes whose surfaces have been severely disrupted by cathodic polarisation in the hydrogen evolution region. It is shown that significant electrochemical oxidation responses occur at discrete potential values well below that for the formation of the compact monolayer oxide of bulk gold and are attributed to the facile oxidation of surface active sites. Several electrocatalytic reactions are explored in which the onset potential is determined by the presence of such sites on the surface. Significantly, the facile oxidation of active sites is used to drive the electroless deposition of metals such as platinum, palladium and silver from their aqueous salts on the surface of gold nanostructures. The resultant surface decoration of gold with secondary metal nanoparticles not only indicates regions on the surface which are rich in active sites but also provides a method to form interesting bimetallic surfaces. PMID:22455038

  17. Nicotinamide Cofactors Suppress Active-Site Labeling of Aldehyde Dehydrogenases.

    Science.gov (United States)

    Stiti, Naim; Chandrasekar, Balakumaran; Strubl, Laura; Mohammed, Shabaz; Bartels, Dorothea; van der Hoorn, Renier A L

    2016-06-17

    Active site labeling by (re)activity-based probes is a powerful chemical proteomic tool to globally map active sites in native proteomes without using substrates. Active site labeling is usually taken as a readout for the active state of the enzyme because labeling reflects the availability and reactivity of active sites, which are hallmarks for enzyme activities. Here, we show that this relationship holds tightly, but we also reveal an important exception to this rule. Labeling of Arabidopsis ALDH3H1 with a chloroacetamide probe occurs at the catalytic Cys, and labeling is suppressed upon nitrosylation and oxidation, and upon treatment with other Cys modifiers. These experiments display a consistent and strong correlation between active site labeling and enzymatic activity. Surprisingly, however, labeling is suppressed by the cofactor NAD(+), and this property is shared with other members of the ALDH superfamily and also detected for unrelated GAPDH enzymes with an unrelated hydantoin-based probe in crude extracts of plant cell cultures. Suppression requires cofactor binding to its binding pocket. Labeling is also suppressed by ALDH modulators that bind at the substrate entrance tunnel, confirming that labeling occurs through the substrate-binding cavity. Our data indicate that cofactor binding adjusts the catalytic Cys into a conformation that reduces the reactivity toward chloroacetamide probes. PMID:26990764

  18. 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

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

    International Nuclear Information System (INIS)

    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 promoted. The

  20. Finnsjoen study site. Scope of activities and main results

    International Nuclear Information System (INIS)

    The Finnsjoen study site was selected in 1977 to provide input to the KBS-1 and KBS-2 performance assessments. The site was later used as a test site for testing new instruments and new site characterization methods, as well as a research site for studying mainly groundwater flow and groundwater transport. All together, the Finnsjoen studies have involved 11 cored boreholes, down to max 700 m depth, and extensive borehole geophysical, geochemical and geohydraulic measurements, as well as rock stress measurements and tracer tests. This report presents the scope of the Finnsjoen studies together with main results. Conceptual uncertainties in assumptions and models are discussed with emphasis on the models used for the performance assessment SKB91. Of special interest for the Finnsjoen study site is the strong influence caused by a subhorizontal fracture zone on groundwater flow, transport and chemistry

  1. Hydrogeological structure model of the Olkiluoto Site. Update in 2010

    International Nuclear Information System (INIS)

    As part of the programme for the final disposal of spent nuclear fuel, a hydrogeological structure model containing the hydraulically significant zones on Olkiluoto Island has been compiled. The structure model describes the deterministic site scale zones that dominate the groundwater flow. The main objective of the study is to provide the geometry and the hydrogeological properties related to the groundwater flow for the zones and the sparsely fractured bedrock to be used in the numerical modelling of groundwater flow and geochemical transport and thereby in the safety assessment. Also, these zones should be taken into account in the repository layout and in the construction of the disposal facility and they have a long-term impact on the evolution of the site and the safety of the disposal repository. The previous hydrogeological model was compiled in 2008 and this updated version is based on data available at the end of May 2010. The updating was based on new hydrogeological observations and a systematic approach covering all drillholes to assess measured fracture transmissivities typical of the site-scale hydrogeological zones. New data consisted of head observations and interpreted pressure and flow responses caused by field activities. Essential background data for the modelling included the ductile deformation model and the site scale brittle deformation zones modelled in the geological model version 2.0. The GSM combine both geological and geophysical investigation data on the site. As a result of the modelling campaign, hydrogeological zones HZ001, HZ008, HZ19A, HZ19B, HZ19C, HZ20A, HZ20B, HZ21, HZ21B, HZ039, HZ099, OL-BFZ100, and HZ146 were included in the structure model. Compared with the previous model, zone HZ004 was replaced with zone HZ146 and zone HZ039 was introduced for the first time. Alternative zone HZ21B was included in the basic model. For the modelled zones, both the zone intersections, describing the fractures with dominating groundwater

  2. 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...

  3. Identification of essential residues for binding and activation in the human 5-HT7(a receptor by molecular modeling and site-directed mutagenesis

    Directory of Open Access Journals (Sweden)

    Agata Antonina Rita Impellizzeri

    2015-05-01

    We examined molecular determinants of ligand binding and G protein activation by the human 5-HT7(a receptor. The role of several key residues in the 7th transmembrane domain and helix 8 were elucidated combining in silico and experimental mutagenesis. Several single and two double point mutations of the 5-HT7(a wild type receptor were made (W7.33V, E7.35T, E7.35R, E7.35D, E7.35A, R7.36V, Y7.43A, Y7.43F, Y7.43T, R8.52D, D8.53K; E7.35T-R7.36V, R8.52D-D8.53K, and their effects upon ligand binding were assessed by radioligand binding using a potent agonist (5-CT and a potent antagonist (SB269970. In addition, the ability of the mutated 5-HT7(a receptors to activate G protein after 5-HT-stimulation was determined through activation of adenylyl cyclase. In silico investigation on mutated receptors substantiated the predicted importance of TM7 and showed critical roles of residues E7.35, W7.33, R7.36 and Y7.43 in agonist and antagonist binding and conformational changes of receptor structure affecting adenylyl cyclase activation. Experimental data showed that mutants E7.35T and E7.35R were incapable of ligand binding and adenylyl cyclase activation, consistent with a requirement for a negatively charged residue at this position. The mutant R8.52D was unable to activate adenylyl cyclase, despite unaffected ligand binding, consistent with the R8.52 residue playing an important role in the receptor-G protein interface. The mutants Y7.43A and Y7.43T displayed reduced agonist binding and AC agonist potency, not seen in Y7.43F, consistent with a requirement for an aromatic residue at this position. Knowledge of the molecular interactions important in h5-HT7 receptor ligand binding and G protein activation will aid the design of selective h5-HT7 receptor ligands for potential pharmacological use.

  4. A geosphere transport model for risk evaluation: Calculation of maximum concentration of activity at given distances from the waste disposal site due to water invasion

    International Nuclear Information System (INIS)

    A simplified model for the calculation of radioactivity concentration in water due to invasion of water in an underground disposal area of radioactive waste is described. The methodological framework for computation is based on processes like leaching, hydrodynamic dispersion and diffusion and physico-chemical sorption. A computer program LEDIRE is written in FORTRAN language for the purpose of a parametric study. The results of an example calculation are given and some limits of such calculations are shown

  5. 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.

  6. 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.; Tuxen, Nina; Bjerg, Poul Løgstrup; Troldborg, Mads

    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 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...

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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)

  12. Fjaellveden 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 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 sites 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 for complementary investigations. This report concerns the Fjaellveden study site. (au)

  13. Kamlunge 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 sites with geological and/or socio-economical characteristics judged more favourable may very well be 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 Kamlunge study site. (79 refs.) (au)

  14. '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

  15. Active Sites Environmental Monitoring Program: Mid-FY 1991 report

    Energy Technology Data Exchange (ETDEWEB)

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

    1991-10-01

    This report summarizes the activities of the Active Sites Environmental Monitoring Program (ASEMP) from October 1990 through March 1991. The ASEMP was established in 1989 by Solid Waste Operations and the Environmental Sciences Division to provide early detection and performance monitoring at active low-level radioactive waste (LLW) disposal sites in Solid Waste Storage Area (SWSA) 6 and transuranic (TRU) waste storage sites in SWSA 5 as required by chapters II and III of US Department of Energy Order 5820.2A. Monitoring results continue to demonstrate the no LLW is being leached from the storage vaults on the tumulus pads. Loading of vaults on Tumulus II began during this reporting period and 115 vaults had been loaded by the end of March 1991.

  16. 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.

  17. 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

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

    International Nuclear Information System (INIS)

    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

  19. 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

  20. 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

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

    International Nuclear Information System (INIS)

    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 reduced in order to reach

  2. Thermal Site Descriptive Model. A strategy for the model development during site investigations. Version 1.0

    International Nuclear Information System (INIS)

    Site investigations are in progress for the siting of a deep repository for spent nuclear fuel. As part of the planning work, strategies are developed for site descriptive modelling regarding different disciplines, amongst them the thermal conditions. The objective of the strategy for a thermal site descriptive model is to guide the practical implementation of evaluating site specific data during the site investigations. It is understood that further development may be needed. The model describes the thermal properties and other thermal parameters of intact rock, fractures and fracture zones, and of the rock mass. The methodology is based on estimation of thermal properties of intact rock and discontinuities, using both empirical and theoretical/numerical approaches, and estimation of thermal processes using mathematical modelling. The methodology will be used and evaluated for the thermal site descriptive modelling at the Aespoe Hard Rock Laboratory

  3. 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...

  4. 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…

  5. 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.

  6. 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, and...

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

    International Nuclear Information System (INIS)

    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

  8. 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.

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

    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 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. Locomotor activity influences muscle architecture and bone growth but not muscle attachment site morphology

    OpenAIRE

    Rabey, Karyne N.; Green, David J; Taylor, Andrea B.; Begun, David R.; Richmond, Brian G.; McFarlin, Shannon C.

    2014-01-01

    The ability to make behavioural inferences from skeletal remains is critical to understanding the lifestyles and activities of past human populations and extinct animals. Muscle attachment site (enthesis) morphology has long been assumed to reflect muscle strength and activity during life, but little experimental evidence exists to directly link activity patterns with muscle development and the morphology of their attachments to the skeleton. We used a mouse model to experimentally test how t...

  11. Reactive Transport Modeling of the Yucca Mountain Site, Nevada

    International Nuclear Information System (INIS)

    The Yucca Mountain site has a dry climate and deep water table, with the repository located in the middle of an unsaturated zone approximately 600 m thick. Radionuclide transport processes from the repository to the water table are sensitive to the unsaturated zone flow field, as well as to sorption, matrix diffusion, radioactive decay, and colloid transport mechanisms. The unsaturated zone flow and transport models are calibrated against both physical and chemical data, including pneumatic pressure, liquid saturation, water potential, temperature, chloride, and calcite. The transport model predictions are further compared with testing specific to unsaturated zone transport: at Alcove 1 in the Exploratory Studies Facility (ESF), at Alcove 8 and Niche 3 of the ESF, and at the Busted Butte site. The models are applied to predict the breakthroughs at the water table for nonsorbing and sorbing radionuclides, with faults shown as the important paths for radionuclide transport. Daughter products of some important radionuclides, such as 239Pu and 241Am, have faster transport than the parents and must be considered in the unsaturated zone transport model. Colloid transport is significantly affected by colloid size, but only negligibly affected by lunetic declogging (reverse filtering) mechanisms. Unsaturated zone model uncertainties are discussed, including the sensitivity of breakthrough to the active fracture model parameter, as an example of uncertainties related to detailed flow characteristics and fracture-matrix interaction. It is expected that additional benefits from the unsaturated zone barrier for transport can be achieved by full implementation of the shadow zone concept immediately below the radionuclide release points in the waste emplacement drifts

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

    International Nuclear Information System (INIS)

    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

  13. 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

  14. 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

  15. 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...

  16. 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

  17. 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

  18. 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

  19. 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...

  20. Methodology for contaminated sites of military activity territories restoration

    International Nuclear Information System (INIS)

    Major part of Eastern Europe countries meet environmental problems related to sites of military activity. Major part of these sites is characterised with degradation of natural landscapes and contamination of geological environment with toxic and hazardous waste representing actual and potential danger for population and environment. Actual danger is caused with localisation of toxic waste, hazardous materials and waste which are preventing normal land use. Potential danger is related to successive dispersion of contamination in biosphere as well as origin of new derivatives and products having toxic and hazardous properties. The list of such sites and objects comprises bases of land, air and naval forces. These objects include a network of infrastructures: storages of fuels and lubricants (surface, underground), filling stations, pipe lines, reparation stations, garages, decontamination stations, underground storages of different purposes, depots (for ammunition, chemical products), hospitals, constructions, firing grounds (tank, artillery, aircraft bombing etc.) and waste disposal sites. Special programs aimed at military industries and bases contaminated sites remediation have been carrying out in developed countries (USA, United Kingdom, Germany etc.). This experience was used in the frames of joint programs having been founded in several countries of Central and Eastern Europe (Chesh Republic, Slovakia, Lithuania etc.). (author)

  1. In silico analysis of Pycnoporus cinnabarinus laccase active site with toxic industrial dyes.

    Science.gov (United States)

    Prasad, Nirmal K; Vindal, Vaibhav; Narayana, Siva Lakshmi; Ramakrishna, V; Kunal, Swaraj Priyaranjan; Srinivas, M

    2012-05-01

    Laccases belong to multicopper oxidases, a widespread class of enzymes implicated in many oxidative functions in various industrial oxidative processes like production of fine chemicals to bioremediation of contaminated soil and water. In order to understand the mechanisms of substrate binding and interaction between substrates and Pycnoporus cinnabarinus laccase, a homology model was generated. The resulted model was further validated and used for docking studies with toxic industrial dyes- acid blue 74, reactive black 5 and reactive blue 19. Interactions of chemical mediators with the laccase was also examined. The docking analysis showed that the active site always cannot accommodate the dye molecules, due to constricted nature of the active site pocket and steric hindrance of the residues whereas mediators are relatively small and can easily be accommodated into the active site pocket, which, thereafter leads to the productive binding. The binding properties of these compounds along with identification of critical active site residues can be used for further site-directed mutagenesis experiments in order to identify their role in activity and substrate specificity, ultimately leading to improved mutants for degradation of these toxic compounds. PMID:21877154

  2. A Discrete Choice Model for Web Site Work Results

    OpenAIRE

    Pavlyuk, Dmitry

    2008-01-01

    Currently a corporate web site is not considered as a necessary business attribute, but as a marketing tool which should yield results. In this study we consider a web site as an instrument for attraction of new partners (customers, suppliers). Web site outputs are a number of visitors interested in contact information (reached the contact info page) and a number of visitors who sent a request via a special form on the web site. We build a sequential discrete choice model for web site out...

  3. 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.

  4. Resolving the Structure of Active Sites on Platinum Catalytic Nanoparticles

    DEFF Research Database (Denmark)

    Chang, Lan Yun; Barnard, Amanda S.; Gontard, Lionel Cervera; Dunin-Borkowski, Rafal E.

    2010-01-01

    Accurate understanding of the structure of active sites is fundamentally important in predicting catalytic properties of heterogeneous nanocatalysts. We present an accurate determination of both experimental and theoretical atomic structures of surface monatomic steps on industrial platinum...... nanoparticles. This comparison reveals that the edges of nanoparticles can significantly alter the atomic positions of monatomic steps in their proximity, which can lead to substantial deviations in the catalytic properties compared with the extended surfaces....

  5. 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.)

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

    International Nuclear Information System (INIS)

    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

  7. 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

  8. 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.

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

    International Nuclear Information System (INIS)

    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

  10. 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.

  11. 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

  12. Seismic activity parameters of the Finnish potential repository sites

    International Nuclear Information System (INIS)

    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.)

  13. 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.)

  14. 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

  15. A caspase active site probe reveals high fractional inhibition needed to block DNA fragmentation.

    Science.gov (United States)

    Méthot, Nathalie; Vaillancourt, John P; Huang, JingQi; Colucci, John; Han, Yongxin; Ménard, Stéphane; Zamboni, Robert; Toulmond, Sylvie; Nicholson, Donald W; Roy, Sophie

    2004-07-01

    Apoptotic markers consist of either caspase substrate cleavage products or phenotypic changes that manifest themselves as a consequence of caspase-mediated substrate cleavage. We have shown recently that pharmacological inhibitors of caspase activity prevent the appearance of two such apoptotic manifestations, alphaII-spectrin cleavage and DNA fragmentation, but that blockade of the latter required a significantly higher concentration of inhibitor. We investigated this phenomenon through the use of a novel radiolabeled caspase inhibitor, [(125)I]M808, which acts as a caspase active site probe. [(125)I]M808 bound to active caspases irreversibly and with high sensitivity in apoptotic cell extracts, in tissue extracts from several commonly used animal models of cellular injury, and in living cells. Moreover, [(125)I]M808 detected active caspases in septic mice when injected intravenously. Using this caspase probe, an active site occupancy assay was developed and used to measure the fractional inhibition required to block apoptosis-induced DNA fragmentation. In thymocytes, occupancy of up to 40% of caspase active sites had no effect on DNA fragmentation, whereas inhibition of half of the DNA cleaving activity required between 65 and 75% of active site occupancy. These results suggest that a high and persistent fractional inhibition will be required for successful caspase inhibition-based therapies. PMID:15067000

  16. 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...

  17. 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......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...... overpotentials and is made of precious materials. A possible solution is the use of non-noble electrocatalysts with single-metal active sites. Here, on the basis of DFT calculations of adsorbed intermediates and a thermodynamic analysis, we compare the oxygen reduction (ORR) and evolution (OER) activities of...... functionalized graphitic materials and gas-phase porphyrins with late transition metals. We find that both kinds of materials follow approximately the same activity trends, and active sites with transition metals from groups 7 to 9 may be good ORR and OER electrocatalysts. However, spin analyses show more...

  18. 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.

  19. 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

    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...... 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...

  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. 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

  4. 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

  5. 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 ...

  6. Depth and stratigraphy of regolith. Site descriptive modelling SDM-Site Laxemar

    International Nuclear Information System (INIS)

    At the Laxemar-Simpevarp site, numerical and descriptive modelling are performed both for the deep bedrock and for the surface systems. The surface geology and regolith depth are important parameters for e.g. hydrogeological and geochemical modelling and for the over all understanding of the area. Regolith refers to all the unconsolidated deposits overlying the bedrock. The regolith depth model (RDM) presented here visualizes the stratigraphical distribution of the regolith as well as the elevation of the bedrock surface. The model covers 280 km2 including both terrestrial and marine areas. In the model the stratigraphy is represented by six layers (Z1-Z6) that corresponds to different types of regolith. The model is geometric and the properties of the layers are assigned by the user according to the purpose. The GeoModel program, which is an ArcGIS extension, was used for modelling the regolith depths. A detailed topographical Digital Elevation Model (DEM) and a map of Quaternary deposits were used as input to the model. Altogether 319 boreholes and 440 other stratigraphical observations were also used. Furthermore a large number of depth data interpreted from geophysical investigations were used; refraction seismic measurements from 51 profiles, 11,000 observation points from resistivity measurements and almost 140,000 points from seismic and sediment echo sounding data. The results from the refraction seismic and resistivity measurements give information about the total regolith depths, whereas most other data also give information about the stratigraphy of the regolith. Some of the used observations did not reach the bedrock surface. They do, however, describe the minimum regolith depth at each location and were therefore used where the regolith depth would have been thinner without using the observation point. A large proportion of the modelled area has a low data density and the area was therefore divided into nine domains. These domains were defined based on

  7. 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

  8. 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

  9. 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.

  10. 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...

  11. Site specific rationale for technical impracticability of active groundwater restoration at a former manufactured gas plant site

    International Nuclear Information System (INIS)

    The National Contingency Plan (40 CFR Part 300 ) requires that remedial strategies must, at minimum, protect human health and the environment and meet applicable and relevant or appropriate requirements (ARARs). Where groundwater is impacted, maximum contaminant levels (MCLs) and maximum contaminant level goals (MCLGs) set under the Safe Drinking Water Act are often used as ARARs, whether or not the aquifer is a reasonably anticipated future source of drinking water. The US Environmental Protection Agency now recognizes the difficulty of groundwater restoration at sites where dense nonaqueous phase liquids are present, particularly in certain complex hydrogeological settings (EPA 1993). However, demonstration of impracticability generally does not occur until active remediation (e.g., pump and treat) has been shown to be ineffective. A case study of a former manufactured gas plant (MGP) is used to demonstrate how physical and chemical properties of the aquifer and coal tar, the major waste product from MGP sites, influence the feasibility of active restoration. Field characterization investigations, laboratory studies, and groundwater modeling are integrated into a demonstration following EPA guidelines. Laboratory studies included microbiological characterization and natural biodegradation and suggest that intrinsic bioremediation is occurring at this site. This work will be useful as EPA continues to develop presumptive remedies for cleanup under Superfund

  12. 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)

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

    Science.gov (United States)

    Koh-Stenta, Xiaoying; Joy, Joma; Wang, Si Fang; Kwek, Perlyn Zekui; Wee, John Liang Kuan; Wan, Kah Fei; Gayen, Shovanlal; Chen, Angela Shuyi; Kang, CongBao; Lee, May Ann; Poulsen, Anders; Vasudevan, Subhash G; Hill, Jeffrey; Nacro, Kassoum

    2015-01-01

    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. PMID:26677315

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

    Science.gov (United States)

    Koh-Stenta, Xiaoying; Joy, Joma; Wang, Si Fang; Kwek, Perlyn Zekui; Wee, John Liang Kuan; Wan, Kah Fei; Gayen, Shovanlal; Chen, Angela Shuyi; Kang, CongBao; Lee, May Ann; Poulsen, Anders; Vasudevan, Subhash G; Hill, Jeffrey; Nacro, Kassoum

    2015-01-01

    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. PMID:26677315

  15. 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

  16. 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)

  17. Active control: Wind turbine model

    DEFF Research Database (Denmark)

    Bindner, H.

    1999-01-01

    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....... The models are all formulated as linear differential equations. The models are validated throughcomparisons with measurements performed on a Vestas WD 34 400 kW wind turbine. It is shown from a control point of view simple linear models can be used to describe the dynamic behavior of a pitch...

  18. 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

  19. 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

  20. 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)

  1. 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.

  2. 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.

    2016-01-01

    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. PMID:27306204

  3. 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

  4. 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),

  5. Metal active site elasticity linked to activation of homocysteine in methionine synthases

    Energy Technology Data Exchange (ETDEWEB)

    Koutmos, Markos; Pejchal, Robert; Bomer, Theresa M.; Matthews, Rowena G.; Smith, Janet L.; Ludwig, Martha L. (Michigan)

    2008-04-02

    Enzymes possessing catalytic zinc centers perform a variety of fundamental processes in nature, including methyl transfer to thiols. Cobalamin-independent (MetE) and cobalamin-dependent (MetH) methionine synthases are two such enzyme families. Although they perform the same net reaction, transfer of a methyl group from methyltetrahydrofolate to homocysteine (Hcy) to form methionine, they display markedly different catalytic strategies, modular organization, and active site zinc centers. Here we report crystal structures of zinc-replete MetE and MetH, both in the presence and absence of Hcy. Structural investigation of the catalytic zinc sites of these two methyltransferases reveals an unexpected inversion of zinc geometry upon binding of Hcy and displacement of an endogenous ligand in both enzymes. In both cases a significant movement of the zinc relative to the protein scaffold accompanies inversion. These structures provide new information on the activation of thiols by zinc-containing enzymes and have led us to propose a paradigm for the mechanism of action of the catalytic zinc sites in these and related methyltransferases. Specifically, zinc is mobile in the active sites of MetE and MetH, and its dynamic nature helps facilitate the active site conformational changes necessary for thiol activation and methyl transfer.

  6. 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

  7. 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. PMID:26940877

  8. 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

  9. Reduction of urease activity by interaction with the flap covering the active site.

    Science.gov (United States)

    Macomber, Lee; Minkara, Mona S; Hausinger, Robert P; Merz, Kenneth M

    2015-02-23

    With the increasing appreciation for the human microbiome coupled with the global rise of antibiotic resistant organisms, it is imperative that new methods be developed to specifically target pathogens. To that end, a novel computational approach was devised to identify compounds that reduce the activity of urease, a medically important enzyme of Helicobacter pylori, Proteus mirabilis, and many other microorganisms. Urease contains a flexible loop that covers its active site; Glide was used to identify small molecules predicted to lock this loop in an open conformation. These compounds were screened against the model urease from Klebsiella aerogenes, and the natural products epigallocatechin and quercetin were shown to inhibit at low and high micromolar concentrations, respectively. These molecules exhibit a strong time-dependent inactivation of urease that was not due to their oxygen sensitivity. Rather, these compounds appear to inactivate urease by reacting with a specific Cys residue located on the flexible loop. Substitution of this cysteine by alanine in the C319A variant increased the urease resistance to both epigallocatechin and quercetin, as predicted by the computational studies. Protein dynamics are integral to the function of many enzymes; thus, identification of compounds that lock an enzyme into a single conformation presents a useful approach to define potential inhibitors. PMID:25594724

  10. Recent Experience Using Active Love Wave Techniques to Characterize Seismographic Station Sites

    Science.gov (United States)

    Martin, A. J.; Yong, A.; Salomone, L.

    2014-12-01

    Active-source Love waves recorded by the multi-channel analysis of surface wave (MASLW) technique were recently analyzed in two site characterization projects. Between 2010 and 2011, the 2009 American Recovery and Reinvestment Act (ARRA) funded GEOVision to conduct geophysical investigations at 189 seismographic stations—185 in California and 4 in the Central Eastern U.S. (CEUS). The original project plan was to utilize active and passive Rayleigh wave-based techniques to obtain shear-wave velocity (VS) profiles to a minimum depth of 30 m and the time-averaged VS of the upper 30 meters (VS30). Early in the investigation it became evident that Rayleigh wave techniques, such as multi-channel analysis of surface waves (MASRW), were not effective at characterizing all sites. Shear-wave seismic refraction and MASLW techniques were therefore applied. The MASLW technique was deployed at a total of 38 sites, in addition to other methods, and used as the primary technique to characterize 22 sites, 5 of which were also characterized using Rayleigh wave techniques. In 2012, the Electric Power Research Institute funded characterization of 33 CEUS station sites. Based on experience from the ARRA investigation, both MASRW and MASLW data were acquired by GEOVision at 24 CEUS sites—the remaining 9 sites and 2 overlapping sites were characterized by University of Texas, Austin. Of the 24 sites characterized by GEOVision, 16 were characterized using MASLW data, 4 using both MASLW and MASRW data and 4 using MASRW data. Love wave techniques were often found to perform better, or at least yield phase velocity data that could be more readily modeled using the fundamental mode assumption, at shallow rock sites, sites with steep velocity gradients, and, sites with a thin, low velocity, surficial soil layer overlying stiffer sediments. These types of velocity structure often excite dominant higher modes in Rayleigh wave data, but not in Love wave data. At such sites, it may be possible

  11. 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.

  12. Probing the putative active site of YjdL

    DEFF Research Database (Denmark)

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

    2012-01-01

    with Glu388, a preliminary orientation model of a dipeptide in the YjdL cavity is presented. Single site mutations of particularly Ala281 and Trp278 support the presented orientation. A dipeptide bound in the cavity of YjdL appears to be oriented such that the N-terminal side chain protrudes into a sub...... 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. In the...... presented orientation model, Tyr25 and Tyr58 both appear to be in proximity of the dipeptide backbone while Lys117 appears to be in proximity of the peptide C-terminus. Mutational studies of these conserved residues highlight their functional importance....

  13. Active site and laminarin binding in glycoside hydrolase family 55.

    Science.gov (United States)

    Bianchetti, Christopher M; Takasuka, Taichi E; Deutsch, Sam; Udell, Hannah S; Yik, Eric J; Bergeman, Lai F; Fox, Brian G

    2015-05-01

    The Carbohydrate Active Enzyme (CAZy) database indicates that glycoside hydrolase family 55 (GH55) contains both endo- and exo-β-1,3-glucanases. The founding structure in the GH55 is PcLam55A from the white rot fungus Phanerochaete chrysosporium (Ishida, T., Fushinobu, S., Kawai, R., Kitaoka, M., Igarashi, K., and Samejima, M. (2009) Crystal structure of glycoside hydrolase family 55 β-1,3-glucanase from the basidiomycete Phanerochaete chrysosporium. J. Biol. Chem. 284, 10100-10109). Here, we present high resolution crystal structures of bacterial SacteLam55A from the highly cellulolytic Streptomyces sp. SirexAA-E with bound substrates and product. These structures, along with mutagenesis and kinetic studies, implicate Glu-502 as the catalytic acid (as proposed earlier for Glu-663 in PcLam55A) and a proton relay network of four residues in activating water as the nucleophile. Further, a set of conserved aromatic residues that define the active site apparently enforce an exo-glucanase reactivity as demonstrated by exhaustive hydrolysis reactions with purified laminarioligosaccharides. Two additional aromatic residues that line the substrate-binding channel show substrate-dependent conformational flexibility that may promote processive reactivity of the bound oligosaccharide in the bacterial enzymes. Gene synthesis carried out on ∼30% of the GH55 family gave 34 active enzymes (19% functional coverage of the nonredundant members of GH55). These active enzymes reacted with only laminarin from a panel of 10 different soluble and insoluble polysaccharides and displayed a broad range of specific activities and optima for pH and temperature. Application of this experimental method provides a new, systematic way to annotate glycoside hydrolase phylogenetic space for functional properties. PMID:25752603

  14. 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.

  15. 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

  16. 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.; Vind, J.; Patkar, S.A.; Toxvaerd, S.; Kinnunen, P.K.J.

    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 to...

  17. Modelling of bedrock and groundwater flow for site evaluation

    International Nuclear Information System (INIS)

    Site for final disposal of spent nuclear fuel in Finland will be selected by the end of the year 2000. TVO is responsible for site selection program. In 1987 five areas were selected for preliminary site characterization. Areas comprise Finnish Precambrian crystalline rock types. Typical extent of an area under investigation is 5-8 square-km. In 1992 will be decided which 2 or 3 areas will be characterized in detail during 1993-2000. The emphasis of site investigation is put on the identification and analysis of hydraulically conductive zones and fracturing. Three-dimensional groundwater modelling has been a tool to evaluate suitability of the area for final disposal from the safety point of view. Attempts are made to increase the degree of reality in groundwater modelling. Computer code used: FEFLOW. 6 figs., 2 tabs

  18. Computational models of epileptiform activity.

    Science.gov (United States)

    Wendling, Fabrice; Benquet, Pascal; Bartolomei, Fabrice; Jirsa, Viktor

    2016-02-15

    We reviewed computer models that have been developed to reproduce and explain epileptiform activity. Unlike other already-published reviews on computer models of epilepsy, the proposed overview starts from the various types of epileptiform activity encountered during both interictal and ictal periods. Computational models proposed so far in the context of partial and generalized epilepsies are classified according to the following taxonomy: neural mass, neural field, detailed network and formal mathematical models. Insights gained about interictal epileptic spikes and high-frequency oscillations, about fast oscillations at seizure onset, about seizure initiation and propagation, about spike-wave discharges and about status epilepticus are described. This review shows the richness and complementarity of the various modeling approaches as well as the fruitful contribution of the computational neuroscience community in the field of epilepsy research. It shows that models have progressively gained acceptance and are now considered as an efficient way of integrating structural, functional and pathophysiological data about neural systems into "coherent and interpretable views". The advantages, limitations and future of modeling approaches are discussed. Perspectives in epilepsy research and clinical epileptology indicate that very promising directions are foreseen, like model-guided experiments or model-guided therapeutic strategy, among others. PMID:25843066

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

    International Nuclear Information System (INIS)

    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

  20. 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.

  1. 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.

  2. 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

  3. 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.

  4. 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

  5. Hydrologic modelling of the migration site at the Grimsel test site - the steady state

    International Nuclear Information System (INIS)

    Tracer migration experiments are in progress at the Grimsel Test Site (GTS) in order to test radionuclide transport models and to develop appropriate experimental techniques. In order to assist design and to interpret field tracer tests the knowledge of the hydrology of the site is essential. This report describes the hydraulic modelling efforts with the following objectives: 1) to interpret experimental findings, 2) to provide input, such as flowpaths and flow velocities, for transport modelling, 3) to assist in the design of the tracer experiments. The model concept is based upon the observations, that the fracture, where the migration experiments will take place, is relatively planar, has an average aperture of a few millimeters and is filled with a clayish material: The migration fracture is modelled as a two-dimensional, isotropic, heterogeneous equivalent porous medium. To allow for a sufficiently detailed model a hierarchical approach was followed where the boundaries for the 'local' model, i.e. the model in the vicinity of the migration site, were taken by first solving a larger 'regional' model with coarser discretization. Transmissivity values as extracted from single borehole tests were used for definition of the heterogeneous transmissivity field in the model calculations. Model results for hydrostatic pressures and discharge rates compare favourably with experimental data, eventhough some problems remain to be resolved. Calculations for dipole arrangements have been performed; they turned out to be useful tools for deciding on injection- and withdrawal rates to be applied in the migration experiments as well as for qualitatively estimating tracer recovery rates. (author) 20 figs., 10 tabs., 11 refs

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. Diffusion models and neural activity

    Czech Academy of Sciences Publication Activity Database

    Ricciardi, L. M.; Lánský, Petr

    London : Nature publishing group, 2003 - (Nadel, L.), s. 968-972 ISBN 0-333-79261-0 R&D Projects: GA ČR GA309/02/0168 Institutional research plan: CEZ:AV0Z5011922 Keywords : Neuronal activity, Diffusion model Subject RIV: ED - Physiology

  12. Hierarchical modeling of active materials

    International Nuclear Information System (INIS)

    Intelligent (or smart) materials are increasingly becoming key materials for use in actuators and sensors. If an intelligent material is used as a sensor, it can be embedded in a variety of structure functioning as a health monitoring system to make their life longer with high reliability. If an intelligent material is used as an active material in an actuator, it plays a key role of making dynamic movement of the actuator under a set of stimuli. This talk intends to cover two different active materials in actuators, (1) piezoelectric laminate with FGM microstructure, (2) ferromagnetic shape memory alloy (FSMA). The advantage of using the FGM piezo laminate is to enhance its fatigue life while maintaining large bending displacement, while that of use in FSMA is its fast actuation while providing a large force and stroke capability. Use of hierarchical modeling of the above active materials is a key design step in optimizing its microstructure for enhancement of their performance. I will discuss briefly hierarchical modeling of the above two active materials. For FGM piezo laminate, we will use both micromechanical model and laminate theory, while for FSMA, the modeling interfacing nano-structure, microstructure and macro-behavior is discussed. (author)

  13. 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,...

  14. 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

  15. 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

  16. 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

  17. 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...

  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. Human glutaminyl cyclase and bacterial zinc aminopeptidase share a common fold and active site

    Directory of Open Access Journals (Sweden)

    Misquitta Stephanie A

    2004-02-01

    Full Text Available Abstract Background Glutaminyl cyclase (QC forms the pyroglutamyl residue at the amino terminus of numerous secretory peptides and proteins. We previously proposed the mammalian QC has some features in common with zinc aminopeptidases. We now have generated a structural model for human QC based on the aminopeptidase fold (pdb code 1AMP and mutated the apparent active site residues to assess their role in QC catalysis. Results The structural model proposed here for human QC, deposited in the protein databank as 1MOI, is supported by a variety of fold prediction programs, by the circular dichroism spectrum, and by the presence of the disulfide. Mutagenesis of the six active site residues present in both 1AMP and QC reveal essential roles for the two histidines (140 and 330, QC numbering and the two glutamates (201 and 202, while the two aspartates (159 and 248 appear to play no catalytic role. ICP-MS analysis shows less than stoichiometric zinc (0.3:1 in the purified enzyme. Conclusions We conclude that human pituitary glutaminyl cyclase and bacterial zinc aminopeptidase share a common fold and active site residues. In contrast to the aminopeptidase, however, QC does not appear to require zinc for enzymatic activity.

  20. 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

  1. 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.

  2. The discrete-modelling approach adopted in SITE-94

    International Nuclear Information System (INIS)

    A discrete-feature approach is applied to model 3-D, site-scale groundwater flow to predict hydrological parameters for radionuclide migration in fractured crystalline rock, at the Aespoe site in Sweden. The approach is based on networks of discrete, piecewise-planar elements, which represent transmissive features on scales ranging from individual fractures in the vicinity of waste canisters, to regional fracture zones that connect to the surface environment. At each scale within the model, the formulation is explicitly in terms of the geometry of the types of features that are indicated to control groundwater flow and solute transport. The approach integrates a variety of field data in a single model, and uses simulated hydrological testing, including hydraulic interference tests and tracer tests, to test the derived descriptions of site variability. Distributions of effective parameters from a suite of variational cases indicate that variability of hydrologic properties within site-scale fracture zones is a main source of uncertainty in geologic-barrier performance, given the type of site-characterization data that were available from Aespoe. Types of data that are needed for reducing this uncertainty are discussed. (author)

  3. SITE-94. Modelling of near-field chemistry for SITE-94

    International Nuclear Information System (INIS)

    This report evaluates methods for the incorporation of site data into models simulating the long-term chemical evolution of the near field. The models are based on limiting conditions at equilibrium, or steady state, in three closed systems representing fully saturated bentonite, Feo corrosion products of the canister and spent fuel. A l kg reference mass of site groundwater is assumed to equilibrate first with bentonite and then with the canister's corrosion products. A third closed system representing spent fuel is modeled in terms of spent-fuel dissolution in 1 kg of water evolved from the canister, coupled with steady-state constraints on the rate of oxidant production by α radiolysis of H2O(l). Precipitation of secondary minerals controlling the solubilities of radioelements dissolved from spent fuel is also simulated in this model. Version 7.2 of the EQ3/6 geochemical software package and its supporting composite thermodynamic database, dataO.com.R22, are used to carry out these calculations. It is concluded that chemical models of near-field evolution combined with thermodynamic models of radionuclide speciation-solubility behavior can assist efforts to assimilate site characterization data into the performance assessment process, and to deal with uncertainties that are inherent in both site properties and in concepts of near field chemistry. It is essential, however, that expert judgement and prudence should be exercised such that model results are conservative with respect to acknowledged and documented uncertainties. Most importantly, it must be recognized that it is probably not possible to model with a high-level of accuracy the complex chemical environments and long timescales involved in disposal technologies for nuclear wastes. For performance assessment, however, only bounding values are needed, and modeling approaches such as described in this report are useful for this purpose. Technical peer review and cross-comparisons of near-field modeling

  4. 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.

  5. 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...

  6. 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.

  7. Unsaturated zone transport modeling of the Greater Confinement Disposal Site

    International Nuclear Information System (INIS)

    Unsaturated zone transport modeling is being conducted as part of the performance assessment of the Greater Confinement Disposal (GCD) facility which is located on the Nevada Test Site. This performance assessment is based on an iterative process of modeling and data collection to assess the likelihood the site will meet the US Environmental Protection Agency's containment, individual protection and groundwater protection requirements for the disposal of transuranic wastes, high-level wastes and spent fuel. The current iteration of the performance assessment evaluates the potential impact of future events on the transport system. The future events included in this analysis are subsidence, bioturbation, erosion, climate change, irrigated farming and drilling. This paper presents the unsaturated transport model, how it fits into the performance assessment and how the future events are incorporated in the model

  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. Probabilistic fracture network models for preliminary site characterization

    International Nuclear Information System (INIS)

    Ontario Power Generation's Deep Geologic Repository Technology Program has developed a geostatistical procedure for creating 3D fracture network models (FNMs) that honour the types of information typically available for preliminary site characterization: detailed information on the locations of surface lineaments from aerial photography and remote sensing; regional tectonic information on stress; geomechanical and structural geology principles; field data gathered from geologically analogous sites. This approach provides a systematic and traceable method that is flexible and that accommodates data from many different sources. The detailed, complex and realistic models of 3D fracture geometry produced by this method can serve as the basis for developing rock property models to be used in flow and transport studies. In addition to being ideally suited to preliminary site characterization, the approach also readily incorporates field data that may become available during subsequent site investigations, including ground reconnaissance, borehole programs and other subsurface studies. The FNMs from this method are probabilistic in the sense that they consist of a family of equally likely renditions of fracture geometry, each one honouring the same surface and subsurface constraints. Such probabilistic models are well suited to studying issues that involve risk assessment and quantification of uncertainty. The geostatistical procedure for simulating FNMs is described, its use in case study examples is presented, and the realism of its fracture geometries is tested using field data collected from the Laegerdorf chalk quarry in northern Germany. (author)

  10. 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.

  11. A Model Privacy Statement for Ohio Library Web Sites.

    Science.gov (United States)

    Monaco, Michael J.

    The purpose of this research was to develop a model privacy policy statement for library World Wide Web sites. First, standards of privacy protection were identified. These standards were culled from the privacy and confidentiality policies of the American Library Association, the Federal Trade Commission's online privacy reports, the guidelines…

  12. 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

  13. 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...

  14. 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.

  15. Discrete-Feature Model Implementation of SDM-Site Forsmark

    International Nuclear Information System (INIS)

    A discrete-feature model (DFM) was implemented for the Forsmark repository site based on the final site descriptive model from surface based investigations. The discrete-feature conceptual model represents deformation zones, individual fractures, and other water-conducting features around a repository as discrete conductors surrounded by a rock matrix which, in the present study, is treated as impermeable. This approximation is reasonable for sites in crystalline rock which has very low permeability, apart from that which results from macroscopic fracturing. Models are constructed based on the geological and hydrogeological description of the sites and engineering designs. Hydraulic heads and flows through the network of water-conducting features are calculated by the finite-element method, and are used in turn to simulate migration of non-reacting solute by a particle-tracking method, in order to estimate the properties of pathways by which radionuclides could be released to the biosphere. Stochastic simulation is used to evaluate portions of the model that can only be characterized in statistical terms, since many water-conducting features within the model volume cannot be characterized deterministically. Chapter 2 describes the methodology by which discrete features are derived to represent water-conducting features around the hypothetical repository at Forsmark (including both natural features and features that result from the disturbance of excavation), and then assembled to produce a discrete-feature network model for numerical simulation of flow and transport. Chapter 3 describes how site-specific data and repository design are adapted to produce the discrete-feature model. Chapter 4 presents results of the calculations. These include utilization factors for deposition tunnels based on the emplacement criteria that have been set forth by the implementers, flow distributions to the deposition holes, and calculated properties of discharge paths as well as

  16. Advertising on Social Network Sites: A Structural Equation Modelling Approach

    OpenAIRE

    Anant Saxena; Uday Khanna

    2013-01-01

    Social networking sites (SNSs) emerged as one of the most powerful media for advertising across the globe. Globally, companies are shifting a larger pie of their advertising budgets towards social networking sites for better reach and interactive platform. The companies are also looking at it as a low-cost model, which could reap results in minimum time possible for the targeted ‘Facebook generation’. These very facts motivate researchers to study the value of advertisements on social net...

  17. Recent progress in volcanism studies: Site characterization activities for the Yucca Mountain site characterization project

    International Nuclear Information System (INIS)

    Significant progress has been made on volcanism studies over the past calendar year. There are a number of major highlights from this work. Geochronology data have been obtained for the Lathrop Wells center using a range of isotopic, radiogenic, and age-calibrated methods. Initial work is encouraging but still insufficient to resolve the age of the center with confidence. Geologic mapping of the Sleeping Butte volcanic centers was completed and a report issued on the geology and chronology data. Twenty shallow trenches have been constructed in volcanic units of the Lathrop Wells volcanic center. Results of detailed studies of the trenches support a polycyclic eruptive history. New soil data from the trenches continue to support a late Pleistocene or Holocene age for many of the volcanic units at the center. Geochemical data (trace element and isotopic analysis) show that the volcanic units of the Lathrop Wells center cannot be related to one another by fractional crystallization of a single magma batch, supporting a polycyclic model of volcanism. Structural models using existing data are used to evaluate the probability of magmatic disruption of a potential repository. Several permissive models have been developed but none lead to significant differences in calculating the disruption ratio. Work was initiated on the eruptive and subsurface effects of magmatic activity on a repository. (author)

  18. 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

  19. 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

  20. 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

  1. Modeling study on geological environment at Horonobe URL site

    International Nuclear Information System (INIS)

    The Horonobe underground research project has been operated by Japan Nuclear Cycle Development Institute to study the geological environment of sedimentary rocks in deep underground. The objectives of this study are to develop a geological environment model, which incorporate the current findings and the data obtained through the geological, geophysical, and borehole investigations at Horonobe site, and to predict the hydrological and geochemical impacts caused by the URL shaft excavation to the surrounding area. A three-dimensional geological structure model was constructed, integrating a large-scale model (25km x 15km) and a high-resolution site-scale model (4km x 4km) that have been developed by JNC. The constructed model includes surface topography, geologic formations (such as Yuchi, Koetoi, Wakkanai, and Masuporo Formations), and two major faults (Ohomagari fault and N1 fault). In hydrogeological modeling, water-conductive fractures identified in Wakkanai Formation are modeled stochastically using EHCM (Equivalent Heterogeneous Continuum Model) approach, to represent hydraulic heterogeneity and anisotropy in the fractured rock mass. Numerical code EQUIV FLO (Shimo et al., 1996), which is a 3D unsaturated-saturated groundwater simulator capable of EHCM, was used to simulate the regional groundwater flow. We used the same model and the code to predict the transient hydrological changes caused by the shaft excavations. Geochemical data in the Horonobe site such as water chemistries, mineral compositions of rocks were collected and summarized into digital datasets. M3 (Multivariate, Mixing and Mass-balance) method developed by SKB (Laaksoharju et al., 1999) was used to identify waters of different origins, and to infer the mixing ratio of these end-members to reproduce each sample's chemistry. Thermodynamic code such as RHREEQC, GWB, and EQ3/6 were used to model chemical reactions that explain the present minerals and aqueous concentrations observed in the site

  2. 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

  3. 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

  4. 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

  5. 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

  6. Analysis of correlations between sites in models of protein sequences

    International Nuclear Information System (INIS)

    A criterion based on conditional probabilities, related to the concept of algorithmic distance, is used to detect correlated mutations at noncontiguous sites on sequences. We apply this criterion to the problem of analyzing correlations between sites in protein sequences; however, the analysis applies generally to networks of interacting sites with discrete states at each site. Elementary models, where explicit results can be derived easily, are introduced. The number of states per site considered ranges from 2, illustrating the relation to familiar classical spin systems, to 20 states, suitable for representing amino acids. Numerical simulations show that the criterion remains valid even when the genetic history of the data samples (e.g., protein sequences), as represented by a phylogenetic tree, introduces nonindependence between samples. Statistical fluctuations due to finite sampling are also investigated and do not invalidate the criterion. A subsidiary result is found: The more homogeneous a population, the more easily its average properties can drift from the properties of its ancestor. copyright 1998 The American Physical Society

  7. The influence of a small amount of active sites on the adsorption kinetics of nitrogen on ruthenium

    International Nuclear Information System (INIS)

    Recently, Dahl et al. [S. Dahl, A. Logadottir, R.C. Egeberg, J.H. Larsen, I. Chorkendorff, E. Toernqvist, J.K. Norskov, Phys. Rev. Lett. 83 (1999) 1814; S. Dahl, E. Toernqvist, I. Chorkendorff, J. Catal. 192 (2000) 381] have proposed very interesting hypothesis that the rate of dissociation and adsorption of nitrogen on Ru(0 0 0 1) facet is totally dominated by the presence of a small amount of step sites on Ru(0 0 0 1) terraces. Following this idea, a kinetic model, based on applying the Statistical Rate Theory approach, was developed in order to explain if such mechanism is able to explain the observed features of the system N2/Ru(0 0 0 1). As a result, it was stated that the activation barrier for adsorption on the active (step) sites is equal to 36 kJ/mol; in turn, the adsorption energy of nitrogen atoms on the active sites is 43 kJ/mol. It implies that the rate of adsorption via the active sites is much faster than direct adsorption on the three-fold hollow sites; moreover, the occupation of the active sites is always close to zero at the investigated temperatures, so they are not blocked and may act as an indirect channel for adsorption. Thus, the rate of nitrogen adsorption on Ru(0 0 0 1) surface is governed by the rate of diffusion of nitrogen atoms from the active sites into the three-fold hollow sites. The analysis of thermodesorption spectra revealed an important role of repulsive interactions between the N atoms adsorbed on the hollow sites, the associated interaction parameter between nearest neighbors was estimated to be 5 kJ/mol. The presence of small amount of gold on Ru(0 0 0 1), apart of blocking the active sites, seems to remove the repulsion between nitrogen atoms

  8. Accelerator production of tritium activities at the Savannah River Site

    International Nuclear Information System (INIS)

    The Savannah River site (SRS) has been chosen as the site to host the accelerator production of tritium (APT). This facility, which will produce tritium for national defense purposes, is a natural extension of the site's original mission. All of the tritium for U.S. weapons needs has been produced at SRS in the heavy water reactors (now shut down) that operated until 1988. Much of the tritium-handling infrastructure still exists at SRS, and the tritium recycling and purification facilities are new and fully operational. This paper summarizes the reasons for the choice of the site and describes some of the early SRS efforts to learn the new technology, to weave into it a strong operations/production ethic, and to prepare the site to host the APT

  9. Health physics and public health activities at hazardous wastes sites

    International Nuclear Information System (INIS)

    The Agency for Toxic Substances and Disease Registry (ATSDR) has worked with the U.S. Environmental Protection Agency (EPA) at several sites contaminated with radioactive materials. The Navajo Brown Vandever (B-V) uranium mine site near Bluewater, New Mexico, and the Austin Avenue Radiation Site (AAR) in Lansdowne, Pennsylvania were the subject of ATSDR health advisories. The sites were contamined with uranium or uranium byproducts but the identification of potential health effects and actions taken to prevent or reduce exposures were approached from different perspectives. At B-V contaminants included uranium and mine tailings, radium, and radon. Contaminants at the site and physical hazards were removed. At AAR, radium and radon were located in residential settings. Residents who might have had annual exposures greater than accepted standards or recommendations were relocated and contaminated building demolished

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

    Science.gov (United States)

    Hirai, Yutaka; Ishimaru, Yuhri; Saitoh, Takayuki R.; Fujii, Michiko S.; Hidaka, Jun; Kajino, Toshitaka

    2016-02-01

    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.

  12. 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

  13. 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

  14. Analysis and radiological assessment of residues containing NORM materials resulting from earlier activities including modelling of typical industrial residues. Pt. 1. Historical investigation of the radiological relevance of NORM residues and concepts for site identification

    International Nuclear Information System (INIS)

    Natural radionuclides are part of the human environment and of the raw materials used. Technical processes may cause their accumulation in residues, and the result will be so-called NORM materials (Naturally occurring radioactive material). The amended Radiation Protection Ordinance (StrlSchV 2001) specifies how the public should be protected, but there are also residues dating back before the issuing of the StrlSchV 2001, the so-called NORM residues. The project intended to assess the risks resulting from these residues. It comprises four parts. Part 1 was for clarification of the radiological relevance of NORM residues and for the development of concepts to detect them. The criterion for their radiological relevance was their activity per mass unit and the material volume accumulated through the centuries. The former was calculated from a wide bibliographic search in the relevant literature on radiation protection, while the mass volume was obtained by a detailed historical search of the consumption of materials that may leave NORM residues. These are, in particular, residues from coal and ore mining and processing. To identify concrete sites, relevant data sources were identified, and a concept for identification of concrete NORM residues was developed on this basis. (orig.)

  15. 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.

  16. 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

  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. Modelling of nuclear explosions in hard rock sites

    International Nuclear Information System (INIS)

    This study represents part of a larger effort to systematically model the effects of differing source region properties on ground motion from underground nuclear explosions at the Nevada Test Site. In previous work by the authors the primary emphasis was on alluvium and both saturated and unsaturated tuff. We have attempted to model events on Pahute Mesa, where either the working point medium, or some of the layers above the working point, or both, are hard rock. The complex layering at these sites, however, has prevented us from drawing unambiguous conclusions about modelling hard rock. In order to learn more about the response of hard rock to underground nuclear explosions, we have attempted to model the PILEDRIVER event. PILEDRIVER was fired on June 2, 1966 in the granite stock of Area 15 at the Nevada Test Site. The working point was at a depth of 462.7 m and the yield was determined to be 61 kt. Numerous surface, sub-surface and free-field measurements were made and analyzed by SRI. An attempt was made to determine the contribution of spall to the teleseismic signal, but proved unsuccessful because most of the data from below-shot-level gauges was lost. Nonetheless, there is quite a bit of good quality data from a variety of locations. We have been able to obtain relatively good agreement with the experimental PILEDRIVER waveforms. In order to do so, we had to model the granodiorite as being considerably weaker than ''good quality'' granite, and it had to undergo considerable weakening due to shock damage as well. In addition, the near-surface layers had to be modeled as being weak and compressible and as have a much lower sound speed than the material at depth. The is consistent with a fractured and jointed material at depth, and a weathered material near the surface

  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. Hydrodynamic model of Fukushima-Daiichi site flooding

    International Nuclear Information System (INIS)

    Based on conservative assumptions, this paper proposes a hydrodynamic model to describe the occurrence and spread of a tsunami. Numerical simulation has shown that a wave can reach 15 m on the Fukushima-Daiichi coastline with the reduced hydrodynamic resistance factor being 1.8. According to the developed model, the likelihood of flooding is determined not only by the site level, earthquake intensity and distance, but also by the duration of seismic impacts, conditions of energy dissipation, epicenter size and other factors

  1. Site-specific Interaction Mapping of Phosphorylated Ubiquitin to Uncover Parkin Activation.

    Science.gov (United States)

    Yamano, Koji; Queliconi, Bruno B; Koyano, Fumika; Saeki, Yasushi; Hirokawa, Takatsugu; Tanaka, Keiji; Matsuda, Noriyuki

    2015-10-16

    Damaged mitochondria are eliminated through autophagy machinery. A cytosolic E3 ubiquitin ligase Parkin, a gene product mutated in familial Parkinsonism, is essential for this pathway. Recent progress has revealed that phosphorylation of both Parkin and ubiquitin at Ser(65) by PINK1 are crucial for activation and recruitment of Parkin to the damaged mitochondria. However, the mechanism by which phosphorylated ubiquitin associates with and activates phosphorylated Parkin E3 ligase activity remains largely unknown. Here, we analyze interactions between phosphorylated forms of both Parkin and ubiquitin at a spatial resolution of the amino acid residue by site-specific photo-crosslinking. We reveal that the in-between-RING (IBR) domain along with RING1 domain of Parkin preferentially binds to ubiquitin in a phosphorylation-dependent manner. Furthermore, another approach, the Fluoppi (fluorescent-based technology detecting protein-protein interaction) assay, also showed that pathogenic mutations in these domains blocked interactions with phosphomimetic ubiquitin in mammalian cells. Molecular modeling based on the site-specific photo-crosslinking interaction map combined with mass spectrometry strongly suggests that a novel binding mechanism between Parkin and ubiquitin leads to a Parkin conformational change with subsequent activation of Parkin E3 ligase activity. PMID:26260794

  2. 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

  3. Site-scale groundwater flow modelling of Ceberg

    Energy Technology Data Exchange (ETDEWEB)

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

    1999-06-01

    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 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 fracturezones. 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 {epsilon}{sub f} 10{sup -4} and a flow-wetted surface area of a{sub r} = 0.1 m{sup 2}/(m{sup 3} rock): The median travel time is 1720 years. The median canister flux is 3.27x10{sup -5} m/year. The median F-ratio is 1.72x10{sup 6} years/m. The base case and the deterministic variant suggest that the variability of the travel times within

  4. 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

  5. On Terminal Alkynes That Can React with Active-Site Cysteine Nucleophiles in Proteases

    OpenAIRE

    Reggy Ekkebus; van Kasteren, Sander I.; Yogesh Kulathu; Arjen Scholten; Ilana Berlin; Geurink, Paul P; Annemieke de Jong; Soenita Goerdayal; Jacques Neefjes; Heck, Albert J.R.; David Komander; Huib Ovaa

    2013-01-01

    Active-site directed probes are powerful in studies of enzymatic function. We report an active-site directed probe based on a warhead so far considered unreactive. By replacing the C-terminal carboxylate of ubiquitin (Ub) with an alkyne functionality, a selective reaction with the active-site cysteine residue of de-ubiquitinating enzymes was observed. The resulting product was shown to be a quaternary vinyl thioether, as determined by X-ray crystallography. Proteomic analysis of proteins boun...

  6. 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.

  7. 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

  8. 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.

  9. Applicability of deterministic methods in seismic site effects modeling

    International Nuclear Information System (INIS)

    The up-to-date information related to local geological structure in the Bucharest urban area has been integrated in complex analyses of the seismic ground motion simulation using deterministic procedures. The data recorded for the Vrancea intermediate-depth large earthquakes are supplemented with synthetic computations all over the city area. The hybrid method with a double-couple seismic source approximation and a relatively simple regional and local structure models allows a satisfactory reproduction of the strong motion records in the frequency domain (0.05-1)Hz. The new geological information and a deterministic analytical method which combine the modal summation technique, applied to model the seismic wave propagation between the seismic source and the studied sites, with the mode coupling approach used to model the seismic wave propagation through the local sedimentary structure of the target site, allows to extend the modelling to higher frequencies of earthquake engineering interest. The results of these studies (synthetic time histories of the ground motion parameters, absolute and relative response spectra etc) for the last 3 Vrancea strong events (August 31,1986 Mw=7.1; May 30,1990 Mw = 6.9 and October 27, 2004 Mw = 6.0) can complete the strong motion database used for the microzonation purposes. Implications and integration of the deterministic results into the urban planning and disaster management strategies are also discussed. (authors)

  10. 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.

  11. Testing the FOCUS model PEARL in an Italian site

    Science.gov (United States)

    Bouraoui, F.; Bidoglio, G.

    2003-04-01

    Pesticides are integral part of the modern agricultural production system . The use of pesticide has soared during the post war period, and now the consumption of pesticide has been reducing in Europe. However, the reduction is difficult to attribute to one specific factor since the application of pesticide is highly variable and linked to climatic, out-breaks of diseases, etc. Furthermore, new molecules are being produced which are more efficient and require a lower dosage. In the EU, the placing on the market of Plant Protection Products (PPP) is regulated at the Community Level by the Council Directive (91/414/EEC). The PPP stresses the need of validated models to calculate predicted environmental concentrations. In this context, European Commission set up a FOrum for the Co-ordination of pesticide fate models and their USe (FOCUS). In a complementary effort, DG research supported the APECOP project with one major objective being the validation and improvement of existing pesticide fate models. The research presented here focuses on the validation of the PEARL model in an Italian site. The PEARL model, which is one of the FOCUS model, is actually used in the Dutch pesticide registration procedure. The test site is located near Bologna (Italy). The 35 months long experiment was conducted on a 107m by 28m plot with a loamy soil for . The experiment involved the application of KBr as a tracer and two applications of ethoprophos and three applications of Aclonifen. A sequential approach was used for the Bologna site. During this exercise only the measured soil physical parameters were used. The simulation with the PEARL model yielded negative values for both soil moisture profile and pesticide content. In a second step, the water transport module was calibrated, using measured soil moisture profile. This improved greatly the prediction of the soil water balance. Information relative to pesticide degradation and sorption where then included. This allowed a good

  12. 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

  13. 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

  14. 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

  15. Targeting mechanisms at sites of complement activation for imaging and therapy.

    Science.gov (United States)

    Holers, V Michael

    2016-06-01

    The complement system plays a key role in many acute injury states as well as chronic autoimmune and inflammatory diseases. Localized complement activation and alternative pathway-mediated amplification on diverse target surfaces promote local recruitment of pro-inflammatory cells and elaboration of other mediators. Despite a general understanding of the architecture of the system, though, many of the mechanisms that underlie site-specific complement activation and amplification in vivo are incompletely understood. In addition, there is no capability yet to measure the level of local tissue site-specific complement activation in patients without performing biopsies to detect products using immunohistochemical techniques. Herein is reviewed emerging evidence obtained through clinical research studies of human rheumatoid arthritis along with translational studies of its disease models which demonstrate that several parallel mechanisms are involved in site-specific amplification of activation of the complement system in vivo. Among these processes are de-regulation of the alternative pathway, effector pathway-catalyzed amplification of proximal complement activation, recognition of injury-associated ligands by components of the lectin pathway, and engagement of pathogenic natural antibodies that recognize a limited set of injury-associated neoepitopes. Studies suggest that each of these inter-related processes can play key roles in amplification of complement-dependent injury on self-tissues in vivo. These findings, in addition to development of an imaging strategy described herein designed to quantitatively measure local complement C3 fixation, have relevance to therapeutic and diagnostic strategies targeting the complement system. PMID:25979851

  16. 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.

  17. 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

  18. 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

  19. 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

  20. 76 FR 7226 - Commercial Wind Lease Issuance and Site Characterization Activities; Atlantic Outer Continental...

    Science.gov (United States)

    2011-02-09

    ... site characterization and assessment data the lessee may submit a construction and operations plan (COP... 30 CFR 285.620-.629. Although BOEMRE does not authorize site characterization activities (i.e... on the environmental effects of reasonably foreseeable site characterization surveys that may...

  1. The status of Yucca Mountain site characterization activities

    International Nuclear Information System (INIS)

    The U.S. Department of Energy (DOE) Office of Civilian Radioactive Waste Management is continuing its studies to determine if Yucca Mountain in Nevada can safely isolate high-level nuclear waste for the next ten thousand years. As mandated by Congress in 1987, DOE is studying the rocks, the climate, and the water table at Yucca Mountain to ensure that the site is suitable before building a repository about 305 meters (1,000 feet) below the surface. Yucca Mountain, located 161 kilometers (100 miles) northwest of Las Vegas, lies on the western edge of the Nevada Test Site. Nevada and DOE have been in litigation for almost two years over three environmental permits needed to conduct studies, but recent court decisions have allowed limited work to take place. This paper will examine progress made on the Yucca Mountain Site Characterization Project (YMP) during the past year and continuing into 1992, discuss the complex legal issues that are delaying progress, and describe new site drilling work. Title I and II design work on the underground exploratory studies facility (ESF) also will be discussed

  2. 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.

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

    International Nuclear Information System (INIS)

    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 enhance the confidence in the

  5. Application of Probabilistic Performance Assessment Modeling for Optimization of Maintenance Studies for Low-Level Radioactive Waste Disposal Sites at the Nevada Test Site

    International Nuclear Information System (INIS)

    The U.S. Department of Energy (DOE), National Nuclear Security Administration of the Nevada Operations Office (NNSA/NV) operates and maintains two active facilities on the Nevada Test Site (NTS) that dispose defense-generated low-level radioactive waste (LLW), mixed radioactive waste, and ''classified waste'' in shallow trenches and pits. The operation and maintenance of the LLW disposal sites are self-regulated by the DOE under DOE Order 435.1. This Order requires formal review of a performance assessment (PA) and composite analysis (CA; assessment of all interacting radiological sources) for each LLW disposal system followed by an active maintenance program that extends through and beyond the site closure program. The Nevada disposal facilities continue to receive NTS-generated LLW and defense-generated LLW from across the DOE complex. The PA/CAs for the sites have been conditionally approved and the facilities are now under a formal maintenance program that requires testing of conceptual models, quantifying and attempting to reduce uncertainty, and implementing confirmatory and long-term background monitoring, all leading to eventual closure of the disposal sites. To streamline and reduce the cost of the maintenance program, the NNSA/NV is converting the deterministic PA/CAs to probabilistic models using GoldSim, a probabilistic simulation computer code. The output of probabilistic models will provide expanded information supporting long-term decision objectives of the NTS disposal sites

  6. 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

  7. A Biosphere model for use in SITE-94

    International Nuclear Information System (INIS)

    A simple biosphere model has been designed for use in the SKI Project SITE-94 related to a hypothetical repository for spent nuclear fuel on the island of Aespoe. The model provides results in terms of radiation dose per 1 Bq/year, unless otherwise indicated, and results will thus have to be scaled with actual flux of radionuclides per year entering the primary biosphere recipients. The model does not include radioactive decay as there is assumed no delay in the model system, except for where explicitly mentioned. Specifically, no radioactive transitions resulting in daughter nuclides are considered. Calculated yearly individual and population committed (50 years) radiation doses to man are expressed as mSv/h, under the assumption of a flux of one Bq/year into the primary biosphere recipient. Calculated radiation doses resulting from the present biosphere model are hypothetical, and should under no circumstances be considered as real. Neither should they be used as quantitative information for decision purposes. The biosphere model is of a rough and primitive character and its precision, relative to the real biosphere in the surroundings of Aespoe is envisaged to be several orders of magnitude. 8 refs

  8. 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

  9. 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...

  10. 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.

  11. Groundwater flow modelling at the Olkiluoto site, Finland

    International Nuclear Information System (INIS)

    Preliminary site investigations for spent fuel disposal has been carried out at the Olkiluoto site, Finland. During the investigations high salt concentrations were measured in the groundwater samples deep in the bedrock. In this study, the groundwater flow is analyzed at Olkiluoto taking into account the effects of salinity. The transient simulations are performed by solving coupled and non-linear partial differential equations describing the flow and solute transport. A site-specific simulation model for flow and transport is developed on the basis of the field investigations. The simulations are carried out for a period that started when the highest hills at Olkiluoto rose above sea level. The simulation period continues until the present day. The results of the coupled simulations were strongly dependent on the poorly known initial salinity distribution in the solution domain. The DP approximation together with the EC approximation proved to be a useful complementary approach when simulating solute transport in a fractured rock mass. The simulations also confirm the assumption that the realistic simulation of groundwater flow at Olkiluoto requires taking into account the effects of salinity

  12. Human Activities in Natura 2000 Sites: A Highly Diversified Conservation Network

    OpenAIRE

    Tsiafouli, Maria A.; Apostolopoulou, Evangelia; Mazaris, Antonios D.; Kallimanis, Athanasios S; Drakou, Evangelia G.; Pantis, John D.

    2013-01-01

    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...

  13. 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 the Energy Policy Act of 1992. DATES: In our Federal Register Notice of November 24, 2010, (75...

  14. 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

  15. 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...

  16. 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.)

  17. Update of the geological models of the Gideaa study site

    International Nuclear Information System (INIS)

    During the period 1981-83, SKB performed surface and borehole investigations at the Gideaa site, as part of a site selection program for the purpose of assessing their suitability for a repository of spent nuclear fuel. This study presents a review and an update of the structural and lithological models. In a three dimensional model of the lithology, it is demonstrated that the host rock, paragneiss, is intermingled by elongated bodies of orthogneiss, with a variable thickness of up to 25 m. Lithological sequence does not change within repository depth, whereas the hydraulic conductivity of 25 m packer tests show higher magnitudes between ground level and 200 m depth than at repository depth (500 m). The fracture frequency of orthogneiss and paragneiss is similar. The gneiss complex is intersected by steeply dipping dolerites trending E-W, and a few steep N-S trending orogenic pegmatites. The dolerite dykes often show jointing forming pillars of solid rock, where the joints are infilled by calcite, and are interpreted to be less conductive than other rock types. Twelve fracture zones have been identified in the area, many of which are highly conductive. The fracture zones intersect all rock types in the area, and do not follow rock boundaries, but may be influenced by the penetrative orientation of the foliation. The fracture system is predominantly steep and is trending N-S and E-W and is locally influenced by the NE-SW trending zones. 16 refs., 35 figs., 11 tabs

  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. 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

  20. The active site of hen egg-white lysozyme: flexibility and chemical bonding

    International Nuclear Information System (INIS)

    Chemical bonding at the active site of lysozyme is analyzed on the basis of a multipole model employing transferable multipole parameters from a database. Large B factors at low temperatures reflect frozen-in disorder, but therefore prevent a meaningful free refinement of multipole parameters. Chemical bonding at the active site of hen egg-white lysozyme (HEWL) is analyzed on the basis of Bader’s quantum theory of atoms in molecules [QTAIM; Bader (1994 ▶), Atoms in Molecules: A Quantum Theory. Oxford University Press] applied to electron-density maps derived from a multipole model. The observation is made that the atomic displacement parameters (ADPs) of HEWL at a temperature of 100 K are larger than ADPs in crystals of small biological molecules at 298 K. This feature shows that the ADPs in the cold crystals of HEWL reflect frozen-in disorder rather than thermal vibrations of the atoms. Directly generalizing the results of multipole studies on small-molecule crystals, the important consequence for electron-density analysis of protein crystals is that multipole parameters cannot be independently varied in a meaningful way in structure refinements. Instead, a multipole model for HEWL has been developed by refinement of atomic coordinates and ADPs against the X-ray diffraction data of Wang and coworkers [Wang et al. (2007), Acta Cryst. D63, 1254–1268], while multipole parameters were fixed to the values for transferable multipole parameters from the ELMAM2 database [Domagala et al. (2012), Acta Cryst. A68, 337–351] . Static and dynamic electron densities based on this multipole model are presented. Analysis of their topological properties according to the QTAIM shows that the covalent bonds possess similar properties to the covalent bonds of small molecules. Hydrogen bonds of intermediate strength are identified for the Glu35 and Asp52 residues, which are considered to be essential parts of the active site of HEWL. Furthermore, a series of weak C

  1. Isolation of active site and antibody-binding fragments of human erythrocyte transglutaminase

    International Nuclear Information System (INIS)

    Catalytically active human erythrocyte transglutaminase (TGase) was purified using an immunoaffinity column prepared from a monoclonal antibody to guinea pig liver TGase. The enzyme activity was completely inhibited by incorporation of iodo[14C]acetamide to the level of 1 mole per 1 mole of TGase. The 14C-labeled TGase was digested with cyanogen bromide, subjected to HPLC, and four pure peptides were isolated with molecular weights ranging from 3-22 KDa. Only one of the peptides was radiolabeled and characterized as an active site peptide of 10 KDa. Another peptide of 18 KDa was identified as a monoclonal antibody-binding domain of TGase. Although the active site and the antibody-binding domain were present on different cyanogen bromide fragments, the mouse anti-TGase inhibited 100% of TGase activity. The results suggest that the antibody-binding site is not located on the enzyme active site sequence, but that the three dimensional space configuration of the antigen-antibody complex hinders substrate binding to the active site. The radiolabeled active site cysteine residue was not found in the N-terminal 21 amino acids of the 10 KDa peptide. Additional fragments of the active site peptide are currently being analyzed

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

    International Nuclear Information System (INIS)

    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 the bedrock

  3. 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

  4. Modelling of unconfined aquifer at Kalpakkam Plant site

    International Nuclear Information System (INIS)

    The rainwater is the main source of recharge to the shallow unconfined groundwater system at Kalpakkam plant site. Both single layer and double layer models were conceptualized by employing available geohydrological data in the study area. First considering the sandy formation as a single homogeneous unit layer, the model was constructed and calibrated in two stages viz., steady state flow and transient state flow conditions. During the model calibration, field values of hydraulic conductivity Kx=38.8 m|d, Ky=38.8 m|d, Kz=3.88 m|d for sandy formation and Kx=17.11 m|d, Ky=17.11 m|d, Kz=17.11 m|d for weathered rock, were employed. Similarly the values of (Ss) specific storage 0.0381, 0.000313 were assigned for sandy and weathered rock respectively. The April 2006 water table data were taken as the initial head condition. The constant head boundary was assigned along north, east and west direction. The single layer model was run and calibrated for steady state flow and further developed for transient condition by inputting the successive eight months water table data (May 2006 to December 2006). From the actual lithology of the study area, the model was then developed for double layer system of sand and weathered rock. Since, the water table fluctuations were observed the above two layers per some of the bore wells. The hydraulic conductivity and specific storage of the sandy formation were retained and the appropriate aquifer parameters for weathered zone were also suitably included. The results of single and double layer model were compared with respect to regression coefficients and it was observed that applicability of single or double layer modeling depended on the water column fluctuation at a given bore well location. (author)

  5. 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

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. 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...

  11. 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

  12. 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.

  13. 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

  14. 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

  15. 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.

  16. Assessment of activation products in the Savannah River Site environment

    International Nuclear Information System (INIS)

    This document assesses the impact of radioactive activation products released from SRS facilities since the first reactor became operational late in 1953. The isotopes reported here are those whose release resulted in the highest dose to people living near SRS: 32P, 51Cr, 60C, and 65Zn. Release pathways, emission control features, and annual releases to the aqueous and atmospheric environments are discussed. No single incident has resulted in a major acute release of activation products to the environment. The releases were the result of normal operations of the reactors and separations facilities. Releases declined over the years as better controls were established and production was reduced. The overall radiological impact of SRS activation product atmospheric releases from 1954 through 1994 on the offsite maximally exposed individual can be characterized by a total dose of 0.76 mrem. During the same period, such an individual received a total dose of 14,400 mrem from non-SRS sources of ionizing radiation present in the environment. SRS activation product aqueous releases between 1954 and 1994 resulted in a total dose of 54 mrem to the offsite maximally exposed individual. The impact of SRS activation product releases on offsite populations also has been evaluated

  17. Assessment of activation products in the Savannah River Site environment

    Energy Technology Data Exchange (ETDEWEB)

    Carlton, W.H.; Denham, M.

    1996-07-01

    This document assesses the impact of radioactive activation products released from SRS facilities since the first reactor became operational late in 1953. The isotopes reported here are those whose release resulted in the highest dose to people living near SRS: {sup 32}P, {sup 51}Cr, {sup 60}C, and {sup 65}Zn. Release pathways, emission control features, and annual releases to the aqueous and atmospheric environments are discussed. No single incident has resulted in a major acute release of activation products to the environment. The releases were the result of normal operations of the reactors and separations facilities. Releases declined over the years as better controls were established and production was reduced. The overall radiological impact of SRS activation product atmospheric releases from 1954 through 1994 on the offsite maximally exposed individual can be characterized by a total dose of 0.76 mrem. During the same period, such an individual received a total dose of 14,400 mrem from non-SRS sources of ionizing radiation present in the environment. SRS activation product aqueous releases between 1954 and 1994 resulted in a total dose of 54 mrem to the offsite maximally exposed individual. The impact of SRS activation product releases on offsite populations also has been evaluated.

  18. Grimsel Test Site: modelling radionuclide migration field experiments

    International Nuclear Information System (INIS)

    In the migration field experiments at Nagra's Grimsel Test Site, the processes of nuclide transport through a well defined fractured shear-zone in crystalline rock are being investigated. For these experiments, model calculations have been performed to obtain indications on validity and limitation of the model applied and the data deduced under field conditions. The model consists of a hydrological part, where the dipole flow fields of the experiments are determined, and a nuclide transport part, where the flow field driven nuclide propagation through the shear-zone is calculated. In addition to the description of the model, analytical expressions are given to guide the interpretation of experimental results. From the analysis of experimental breakthrough curves for conservative uranine, weakly sorbing sodium and more stronger sorbing strontium tracers, the following main results can be derived: i) The model is able to represent the breakthrough curves of the migration field experiments to a high degree of accuracy, ii) The process of matrix diffusion is manifest through the tails of the breakthrough curves decreasing with time as t-3/2 and through the special shape of the tail ends, both confirmed by the experiments, iii) For nuclide sorbing rapidly, not too strongly, linearly, and exhibiting a reversible cation exchange process on fault gouge, the laboratory sorption coefficient can reasonably well be extrapolated to field conditions. Adequate care in selecting and preparing the rock samples is, of course, a necessary requirement. Using the parameters determined in the previous analysis, predictions are made for experiments in a smaller an faster flow field. For conservative uranine and weakly sorbing sodium, the agreement of predicted and measured breakthrough curves is good, for the more stronger sorbing strontium reasonable, confirming that the model describes the main nuclide transport processes adequately. (author) figs., tabs., 29 refs

  19. 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...

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

    OpenAIRE

    Anca IONCE

    2009-01-01

    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...

  1. A model for intrusion dose calculations for radioactive waste disposal sites

    International Nuclear Information System (INIS)

    Safe management and disposal of radioactive waste is one of the main problems for nuclear energy, both for fission or fusion sources. High-level waste from nuclear reactors will have to be disposed of in deep underground repositories. The main purpose of this disposal, from the safety viewpoint, is to avoid the return of the radioactive waste into the biosphere, with possible interaction with the public. Intrusion is a way by which this could occur, that is, public inadvertent intrusion into a repository site, taking place after the site has lost its institutional control. The authors describe the assessment of a model for intrusion into a radioactive waste disposal site. An example of application to a fusion-specific repository, developed as part of the Safety and Environmental Assessment of Fusion Power (SEAFP)-2 activities, will be given, up to the evaluation of doses to the inadvertent intruder

  2. 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.

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

    International Nuclear Information System (INIS)

    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

  4. 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...

  5. 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

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

    Energy Technology Data Exchange (ETDEWEB)

    Holt, V.L.; Baron, L.A.

    1994-05-01

    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&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&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&SI. Together, the general HASP for the WAG 2 RI&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&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.

  7. Off-site medical activities, Nevada Test Site and the medical liaison officer network: a historical review

    International Nuclear Information System (INIS)

    The ''off-site'' was originally defined as ''that area surrounding the Nevada Test Site (NTS) for a radius of about 300 miles.'' Prior to 1954, the off-site radiological safety activities were conducted by the Atomic Energy Commission. In 1954, the Public Health Service was given the responsibility for off-site monitoring, and, in addition, a physician was also on temporary assignment. This physician, in addition to functioning as a monitor, also functioned part time as a physical liaison in regard to possible or alleged radiation injury. Medical concern was based upon two crude guidelines: possible radiation ''overexposure'' based upon extrapolation from surface and air radiological monitoring; and determination of actual radiation injury based upon signs and symptoms among people alleging radiation injury. The area of concern expanded to 13 areas surrounding the Nevada Test Site, and in 1956, the first Medical Liaison Officer Network (MLON) was initiated. Over the years, MLON increased to a point where there was a representative from every state in the Union; the area of concern expanded to include the entire United States, parts of the South Pacific, Hawaii, and Alaska; and sophisticated methods of evaluation were added--urine sampling, thyroid scanning, blood counts, and whole-body counting. Epidemiological studies were initiated on body burdens of radionuclides and certain disease clusters

  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. 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)

  10. D Surveying and Modeling of Archaeological Sites - Some Critical Issues -

    Science.gov (United States)

    Gonizzi Barsanti, S.; Remondino, F.; Visintini, D.

    2013-07-01

    The goal of the reported project is to test and evaluate 3D surveying and modelling methods to document the remaining ancient byzantine city walls of the archaeological site of Aquileia in Friuli Venezia Giulia, Italy. The objectives are threefold: (1) to use 3D data to create maps, façades and sections that provide information useful for archaeological purposes such as the investigation of architectural construction techniques or construction phases, (2) to evaluate and compare photogrammetric and laser scanner data in order to identify the advantages and disadvantages of the two 3D surveying techniques for archaeological applications and needs and (3) to draw broader conclusions about the applicability of photogrammetry and laser scanning for documenting and analysing ancient walls within a particular set of environmental circumstances. The paper presents the employed 3D surveying techniques, the obtained 3D results and 2D products and some critical comments.

  11. Activation of brown adipose tissue mitochondrial GDP binding sites

    International Nuclear Information System (INIS)

    The primary function of brown adipose tissue (BAT) is heat production. This ability is attributed to the existence of a unique inner mitochondrial membrane protein termed the uncoupling protein or thermogenin. This protein is permeable to H+ and thus allows respiration (and therefore thermogenesis) to proceed at a rapid rate, independent of ADP phosphorylation. Proton conductance can be inhibited by the binding of purine nucleotides to the uncoupling protein. The binding of [3H]-GDP to BAT mitochondria is frequently used as a measure of BAT thermogenic activity. Rats fed a diet that was low but adequate in protein exhibited a decrease in feed efficiency. In addition, BAT thermogenesis was activated as indicated by an elevation in the level of GDP binding to BAT mitochondria. This phenomena occurred in older rats and persisted over time

  12. Activation of brown adipose tissue mitochondrial GDP binding sites

    Energy Technology Data Exchange (ETDEWEB)

    Swick, A.G.

    1987-01-01

    The primary function of brown adipose tissue (BAT) is heat production. This ability is attributed to the existence of a unique inner mitochondrial membrane protein termed the uncoupling protein or thermogenin. This protein is permeable to H+ and thus allows respiration (and therefore thermogenesis) to proceed at a rapid rate, independent of ADP phosphorylation. Proton conductance can be inhibited by the binding of purine nucleotides to the uncoupling protein. The binding of (/sup 3/H)-GDP to BAT mitochondria is frequently used as a measure of BAT thermogenic activity. Rats fed a diet that was low but adequate in protein exhibited a decrease in feed efficiency. In addition, BAT thermogenesis was activated as indicated by an elevation in the level of GDP binding to BAT mitochondria. This phenomena occurred in older rats and persisted over time.

  13. 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

  14. 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

  15. 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

  16. Activation of Mitogen-Activated Protein Kinase Is Required for Migration and Invasion of Placental Site Trophoblastic Tumor

    OpenAIRE

    Köbel, Martin; Pohl, Gudrun; Schmitt, Wolfgang D.; Hauptmann, Steffen; Wang, Tian-Li; Shih, Ie-Ming

    2005-01-01

    Placental site trophoblastic tumor (PSTT) is a gestational neoplasm derived from the extravillous (intermediate) trophoblast of the implantation site. PSTT is characterized by a highly invasive phenotype, but the molecular mechanisms are poorly understood. In this report, we demonstrate that PSTTs expressed the activated (phosphorylated) form of mitogen-activated protein kinase (MAPK) in 84% of cases, whereas the normal extravillous trophoblastic cells did not. To characterize the role of MAP...

  17. Experience in decommissioning activities at the BR3 site

    Energy Technology Data Exchange (ETDEWEB)

    Klein, Michel E-mail: mklein@sckcen.be; Dadoumont, Jerome; Demeulemeester, Yves; Massaut, Vincent

    2001-04-01

    We give an overview of the experience, SCK-CEN acquired during 11 years of decommissioning activities of a PWR fission reactor. Experience has been gained in decontamination and dismantling technologies and in waste management. Dismantling an old PWR is quite different from the dismantling of the future fusion reactor. However, we can try to find out some common generic features and draw some lessons. Our experience shows that it is important to take the decommissioning aspects into account as soon as possible.

  18. Lipolytic activity from bacteria prospected in polluted portuary sites

    Directory of Open Access Journals (Sweden)

    Kaori Levy Fonseca

    2014-06-01

    This study demonstrates that these TBT resistant isolates have, at the same time, the capacity to produce enzymes with a large biotechnological potential but, nevertheless, their relationship is not well understood, representing a novel approach. It is expected for these organisms to produce highly biotechnological relevant biocatalysts, due to their severe adaptations (Suehiro et al., 2007. The fully characterization of these lipases, mostly for F3 with elevated lipolytic activity exhibited, presents also a future challenge.

  19. 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

  20. 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

  1. Modeling the hydrothermal circulation and the hydrogen production at the Rainbow site with Cast3M

    Science.gov (United States)

    Perez, F.; Mügler, C.; Charlou, J.; Jean-baptiste, P.

    2012-12-01

    On the Mid-Atlantic Ridge, the Rainbow venting site is described as an ultramafic-hosted active hydrothermal site and releases high fluxes of methane and hydrogen [1, 2]. This behavior has first been interpreted as the result of serpentinization processes. But geochemical reactions involving olivine and plagioclase assemblages, and leading to chlorite, tremolite, talc and magnetite assemblages, could contribute to the observed characteristics of the exiting fluid [2]. The predominance of one of these geochemical reactions or their coexistence strongly depend on the hydrothermal fluid circulation. We developed and validated a 2D/3D numerical model using a Finite Volume method to simulate heat driven fluid flows in the framework of the Cast3M code [3, 4]. We also developed a numerical model for hydrogen production and transport that is based on experimental studies of the serpentinization processes [5-6]. This geochemical model takes into account the exothermic and water-consuming behavior of the serpentinization reaction and it can be coupled to our thermo-hydrogeological model. Our simulations provide temperatures, mass fluxes and venting surface areas very close to those estimated in-situ [7]. We showed that a single-path model [8] was necessary to simulate high values such as the in-situ measured temperatures and estimated water mass fluxes of the Rainbow site [7]. This single-path model will be used to model the production and transport of hydrogen at the Rainbow hydrothermal site. References [1]Charlou et al. (2010) AGU Monograph series. [2]Seyfried et al. (2011) Geochim. Cosmochim. Acta 75, 1574-1593. [3]http://www-cast3m.cea.fr. [4]Martin & Fyfe (1970) Chem. Geol. 6, 185-202. [5] Marcaillou et al. (2011) Earth and Planet. Sci. Lett. 303, 281-290. [6]Malvoisin et al. (2012) JGR, 117, B01104. [7]Perez et al. (2012) submited to Computational Geosciences. [8]Lowell & Germanovich (2004) AGU, Washington DC, USA.

  2. Current disposal planning for dry active wastes at Rokkasho Site

    Energy Technology Data Exchange (ETDEWEB)

    Takeuchi, Mitsuo [Japan Nuclear Fuel Ltd., Aomori (Japan)

    1997-02-01

    In nuclear power stations, two kinds of low level radioactive wastes are generated: `uniform solidified waste` in which waste liquid, spent resin and so on are uniformly solidified and `solid waste` in which metals, lagging materials, plastics and others are solidified. In Rokkasho Low Level Radioactive Waste Burying Center, the burying facility for the first period for the uniform solidified waste started the operation in December, 1992, and this time as the second period plan, it has been planned to increase No. 2 waste burying facility for the solid waste. The kinds of the radioactive waste solidified in containers to be buried are the solid state radioactive waste generated by the operation of nuclear power stations and that generated accompanying the operation of this facility. The wastes are classified, cut, pressed and melted as occasion demands so that cement filling material is easily filled in containers, and solidified in the containers. As for the waste to be buried, at the time of its acceptance, 6 months or longer have elapsed since its generation in nuclear power stations, and the surface dose equivalent rate does not exceed 10 mSv/h. The acceptance plan and the expected number of burying, the total radioactivity of buried waste, and the location, geological and hydraulic features, the structure and facilities of waste burying facilities, the method of burying, the management of waste burying site and the evaluation of dose equivalent are reported. (K.I.)

  3. Current disposal planning for dry active wastes at Rokkasho Site

    International Nuclear Information System (INIS)

    In nuclear power stations, two kinds of low level radioactive wastes are generated: 'uniform solidified waste' in which waste liquid, spent resin and so on are uniformly solidified and 'solid waste' in which metals, lagging materials, plastics and others are solidified. In Rokkasho Low Level Radioactive Waste Burying Center, the burying facility for the first period for the uniform solidified waste started the operation in December, 1992, and this time as the second period plan, it has been planned to increase No. 2 waste burying facility for the solid waste. The kinds of the radioactive waste solidified in containers to be buried are the solid state radioactive waste generated by the operation of nuclear power stations and that generated accompanying the operation of this facility. The wastes are classified, cut, pressed and melted as occasion demands so that cement filling material is easily filled in containers, and solidified in the containers. As for the waste to be buried, at the time of its acceptance, 6 months or longer have elapsed since its generation in nuclear power stations, and the surface dose equivalent rate does not exceed 10 mSv/h. The acceptance plan and the expected number of burying, the total radioactivity of buried waste, and the location, geological and hydraulic features, the structure and facilities of waste burying facilities, the method of burying, the management of waste burying site and the evaluation of dose equivalent are reported. (K.I.)

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

    International Nuclear Information System (INIS)

    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

  5. 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.

  6. Death-Associated Protein Kinase Activity Is Regulated by Coupled Calcium/Calmodulin Binding to Two Distinct Sites.

    Science.gov (United States)

    Simon, Bertrand; Huart, Anne-Sophie; Temmerman, Koen; Vahokoski, Juha; Mertens, Haydyn D T; Komadina, Dana; Hoffmann, Jan-Erik; Yumerefendi, Hayretin; Svergun, Dmitri I; Kursula, Petri; Schultz, Carsten; McCarthy, Andrew A; Hart, Darren J; Wilmanns, Matthias

    2016-06-01

    The regulation of many protein kinases by binding to calcium/calmodulin connects two principal mechanisms in signaling processes: protein phosphorylation and responses to dose- and time-dependent calcium signals. We used the calcium/calmodulin-dependent members of the death-associated protein kinase (DAPK) family to investigate the role of a basic DAPK signature loop near the kinase active site. In DAPK2, this loop comprises a novel dimerization-regulated calcium/calmodulin-binding site, in addition to a well-established calcium/calmodulin site in the C-terminal autoregulatory domain. Unexpectedly, impairment of the basic loop interaction site completely abolishes calcium/calmodulin binding and DAPK2 activity is reduced to a residual level, indicative of coupled binding to the two sites. This contrasts with the generally accepted view that kinase calcium/calmodulin interactions are autonomous of the kinase catalytic domain. Our data establish an intricate model of multi-step kinase activation and expand our understanding of how calcium binding connects with other mechanisms involved in kinase activity regulation. PMID:27133022

  7. 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.

  8. 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)

  9. 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

  10. 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 ...

  11. 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.

  12. 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

  13. 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

  14. Site descriptive modelling and use of the rock visualisation system tool

    International Nuclear Information System (INIS)

    The Swedish Nuclear Fuel and Waste Management Co. (SKB) has started site investigations for a deep repository for spent nuclear fuel at two different sites in Sweden. To support the site investigations, data need to be interpreted and assessed into Site Descriptive Models. The models should be multidisciplinary interpretations of geology, rock mechanics, hydrogeology, hydro-geochemistry, transport properties and ecosystems using site investigation data from deep bore holes and the surface. The modelling comprises identification of data, evaluation of primary data, three dimensional modelling and overall confidence evaluation. In the current presentation, the methodology is exemplified for geological modelling. (author)

  15. Quantifying and modeling soil erosion and sediment export from construction sites in southern California

    Science.gov (United States)

    Wernet, A. K.; Beighley, R. E.

    2006-12-01

    Soil erosion is a power process that continuously alters the Earth's landscape. Human activities, such as construction and agricultural practices, and natural events, such as forest fires and landslides, disturb the landscape and intensify erosion processes leading to sudden increases in runoff sediment concentrations and degraded stream water quality. Understanding soil erosion and sediment transport processes is of great importance to researchers and practicing engineers, who routinely use models to predict soil erosion and sediment movement for varied land use and climate change scenarios. However, existing erosion models are limited in their applicability to constructions sites which have highly variable soil conditions (density, moisture, surface roughness, and best management practices) that change often in both space and time. The goal of this research is to improve the understanding, predictive capabilities and integration of treatment methodologies for controlling soil erosion and sediment export from construction sites. This research combines modeling with field monitoring and laboratory experiments to quantify: (a) spatial and temporal distribution of soil conditions on construction sites, (b) soil erosion due to event rainfall, and (c) potential offsite discharge of sediment with and without treatment practices. Field sites in southern California were selected to monitor the effects of common construction activities (ex., cut/fill, grading, foundations, roads) on soil conditions and sediment discharge. Laboratory experiments were performed in the Soil Erosion Research Laboratory (SERL), part of the Civil and Environmental Engineering department at San Diego State University, to quantify the impact of individual factors leading to sediment export. SERL experiments utilize a 3-m by 10-m tilting soil bed with soil depths up to 1 m, slopes ranging from 0 to 50 percent, and rainfall rates up to 150 mm/hr (6 in/hr). Preliminary modeling, field and laboratory

  16. 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

  17. 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

  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. Multi-site validation of a soil organic matter model based on generally available input data

    Science.gov (United States)

    Franko, Uwe; Kolbe, Hartmut; Thiel, Enrico; Ließ, Ekkehard

    2010-05-01

    Regionalization of soil organic matter (SOM) dynamics by means of modelling is often restricted by the availability of model inputs on the used scale. Taking this into account the approach of the CANDY model (Franko et al., 1995) has been strongly simplified with a remarkable reduction of input requirements. This simplified model called Candy Carbon balance (CCB) was validated against a large number of long term datasets from arable field experiments mainly situated in Germany but also from some places in Europe altogether containing 41 sites with 65 experiments and a total number of 598 different treatments. The required input data are: - soil: clay content, soil classification - climate: rainfall and air temperature as long term averages - management: crop rotation with yields and organic amendments - SOM: at least one initial value; more observations for validation purpose During the calculation process the model makes use of some other soil parameters like silt content, bulk density, pore volume, field capacity and permanent wilting point. These data may be delivered by the user or if absent they will be calculated from pedotransfer functions. If the initial information includes not only organic Carbon (Corg) but also total Nitrogen (Nt) the SOM dynamics will be modelled for both elements. The CCB model follows the CANDY concept distributing SOM in a long term stabilized and a decomposable fraction. The long term stabilized part is calculated comparable to the CIPS model (Kuka,2005) taking the SOM in soil micro pores as highly stabilized so that its turnover can be neglected for this model application and hence will show no dynamics during simulation. Soil texture, rainfall, irrigation amount and air temperature are used to estimate the site specific biologic activity for SOM turnover in terms of Biological Active Time (BAT). Annual yield data are transformed to the amounts of organic matter input due to cropping that together with organic amendments are the

  20. 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.

  1. 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...

  2. 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... published a final rule under 10 CFR Part 765 in the Federal Register on May 23, 1994, (59 FR 26714) to...

  3. Three-dimensional groundwater flow modelling for a potential repository site

    International Nuclear Information System (INIS)

    In Finland site investigations are carried out at five places in order to find a suitable site in the Finnish bedrock for a repository for spent nuclear fuel. The aim is to model the bedrock and the ground water flow to facilitate comparison of the sites. In this work we describe the geohydrological model as well as the finite element models for one of the sites and present some preliminary estimates for flow rates and path lines based upon the computed head field

  4. 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

  5. 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.

  6. 1993 annual report of hazardous waste activities for the Oak Ridge K-25 site

    International Nuclear Information System (INIS)

    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

  7. 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

  8. 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...

  9. 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 ...

  10. Molecular dynamics explorations of active site structure in designed and evolved enzymes

    OpenAIRE

    Osuna Oliveras, Sílvia; Jiménez-Osés, Gonzalo; Noey, Elizabeth L.; Houk, Kendall N.

    2015-01-01

    This Account describes the use of molecular dynamics (MD) simulations to reveal how mutations alter the structure and organization of enzyme active sites. As proposed by Pauling about 70 years ago and elaborated by many others since then, biocatalysis is efficient when functional groups in the active site of an enzyme are in optimal positions for transition state stabilization. Changes in mechanism and covalent interactions are often critical parts of enzyme catalysis. We describe our explora...

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

    International Nuclear Information System (INIS)

    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

  12. 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

  13. 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.

  14. Modeling of active beam units with Modelica

    DEFF Research Database (Denmark)

    Maccarini, Alessandro; Hultmark, Göran; Vorre, Anders; Afshari, Alireza; Bergsøe, Niels Christian

    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...

  15. 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…

  16. Threat Modelling for Active Directory

    OpenAIRE

    Chadwick, David W

    2004-01-01

    This paper analyses the security threats that can arise against an Active Directory server when it is included in a Web application. The approach is based on the STRIDE classification methodology. The paper also provides outline descriptions of countermeasures that can be deployed to protect against the different threats and vulnerabilities identified here.

  17. 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

  18. 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.

  19. 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....

  20. 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

  1. 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

  2. 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

  3. 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...

  4. 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.

  5. 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…

  6. 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…

  7. 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.

  8. Mathematical Modelling of Leachate Production from Waste Contained Site

    Directory of Open Access Journals (Sweden)

    Ojolo S. Joshua

    2012-07-01

    Full Text Available In this work, mathematical models of leachate production from Waste Contained Site (WCS was developed and validated using the existing experimental data with aid of MATLAB, 2007a. When the leachate generation potentials (Lo were 100m3, 80m3 and 50m3, the maximum amount of leachate generated were about 2920m3, 2338m3 and 1461m3 for about 130 days respectively. It was noted that as the leachate percolates through a selected distance, the concentration keeps decreasing for one-dimensional flow in all the cases considered. Decreasing in concentration continues until a point was reached when the concentration was almost zero and later constant. The effects of diffusivity, amount of organic content present within the waste and gravity, as cases, were also considered in various occasions during the percolation. Comparison of their effects was also taken into account. In case of gravity at constant diffusivity, decrease in concentration was not rapid but gradually while much organic content in the waste caused the rate of leachate production to be rapid; hence, giving rise to a sharp sloped curve. It can be concluded that gravity influences the rate of change in the concentration of the leachate generation as the leachate percolate downward to the underground water. When the diffusivity and gravity are put into consideration, the concentration of the leachate decreases gradually and slowly.

  9. Near-field modeling in Frenchman Flat, Nevada Test Site

    International Nuclear Information System (INIS)

    The US Department of Energy (DOE) is investigating the effects of nuclear testing in underground test areas (the UGTA program) at the Nevada Test Site. The principal focus of the UGTA program is to better understand and define subsurface radionuclide migration. The study described in this report focuses on the development of tools for generating maps of hydrogeologic characteristics of subsurface Tertiary volcanic units at the Frenchman Flat corrective Action Unit (CAU). The process includes three steps. The first step involves generation of three-dimensional maps of the geologic structure of subsurface volcanic units using geophysical logs to distinguish between two classes: densely welded tuff and nonwelded tuff. The second step generates three-dimensional maps of hydraulic conductivity utilizing the spatial distribution of the two geologic classes obtained in the first step. Each class is described by a correlation structure based on existing data on hydraulic conductivity, and conditioned on the generated spatial location of each class. The final step demonstrates the use of the maps of hydraulic conductivity for modeling groundwater flow and radionuclide transport in volcanic tuffs from an underground nuclear test at the Frenchman Flat CAU. The results indicate that the majority of groundwater flow through the volcanic section occurs through zones of densely welded tuff where connected fractures provide the transport pathway. Migration rates range between near zero to approximately four m/yr, with a mean rate of 0.68 m/yr. This report presents the results of work under the FY96 Near-Field Modeling task of the UGTA program

  10. 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

  11. Functional characterization of autophosphorylation sites of the activated insulin receptor-tyrosine kinase

    International Nuclear Information System (INIS)

    Insulin receptor, solubilized from 3T3-L1 cellular membranes and then purified, was autophosphorylated with [γ-32P]ATP in the absence or presence of insulin. Specific phosphopeptides generated by trypsin digestion of the 32P-labeled β-subunit were identified and separated by reverse phase HPLC. In the absence of insulin, radioactivity of the phosphopeptides is evenly distributed among four major peaks designated as sites I, II, III and IV, according to their order of elution. This pattern is maintained for at least the first 30 min of autophosphorylation. When the reaction is carried out in the presence of insulin, > 50% of the total 32P radioactivity is found in site I and the rate of 32P incorporation into this site is markedly higher than into sites II, III and IV. Maximal activation of tyrosine kinase activity, as estimated by substrate phosphorylation, is coincident with the nearly complete phosphorylation of site I. Delayed activation of previously autophosphorylated receptor by insulin, but not by EGF or IGF-I, produced a similar pattern where phosphorylated site I predominates. These observations indicate that one major insulin-regulated autophosphorylation site in the β-subunit is responsible for activation of the insulin receptor tyrosine kinase. The isolation of this phosphopeptide on a preparative scale and its characterization are now in progress

  12. Functional characterization of autophosphorylation sites of the activated insulin receptor-tyrosine kinase

    Energy Technology Data Exchange (ETDEWEB)

    Flores-Riveros, J.R.; Lane, M.D.

    1987-05-01

    Insulin receptor, solubilized from 3T3-L1 cellular membranes and then purified, was autophosphorylated with (..gamma..-/sup 32/P)ATP in the absence or presence of insulin. Specific phosphopeptides generated by trypsin digestion of the /sup 32/P-labeled ..beta..-subunit were identified and separated by reverse phase HPLC. In the absence of insulin, radioactivity of the phosphopeptides is evenly distributed among four major peaks designated as sites I, II, III and IV, according to their order of elution. This pattern is maintained for at least the first 30 min of autophosphorylation. When the reaction is carried out in the presence of insulin, > 50% of the total /sup 32/P radioactivity is found in site I and the rate of /sup 32/P incorporation into this site is markedly higher than into sites II, III and IV. Maximal activation of tyrosine kinase activity, as estimated by substrate phosphorylation, is coincident with the nearly complete phosphorylation of site I. Delayed activation of previously autophosphorylated receptor by insulin, but not by EGF or IGF-I, produced a similar pattern where phosphorylated site I predominates. These observations indicate that one major insulin-regulated autophosphorylation site in the ..beta..-subunit is responsible for activation of the insulin receptor tyrosine kinase. The isolation of this phosphopeptide on a preparative scale and its characterization are now in progress.

  13. 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.

  14. Site-specific targeting of antibody activity in vivo mediated by disease-associated proteases

    OpenAIRE

    Erster, Oran; Thomas, Jerry M; Hamzah, Juliana; Jabaiah, Abeer M.; Getz, Jennifer A.; Schoep, Tobias; Hall, Sejal S.; Ruoslahti, Erkki; Daugherty, Patrick S.

    2012-01-01

    As a general strategy to selectively target antibody activity in vivo, a molecular architecture was designed to render binding activity dependent upon proteases in disease tissues. A protease-activated antibody (pro-antibody) targeting vascular cell adhesion molecule 1 (VCAM-1), a marker of atherosclerotic plaques, was constructed by tethering a binding site-masking peptide to the antibody via a matrix metalloprotease (MMP) susceptible linker. Pro-antibody activation in vitro by MMP-1 yielded...

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. Active Learning for Player Modeling

    DEFF Research Database (Denmark)

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

    2015-01-01

    the full dataset) is necessary for the construction of accu- rate models that are as accurate as those constructed from the full dataset. This indicates the potential of the method and its benefits in cases when obtaining the data is expensive or time, storage or effort consuming. The results also...... indicate that the method can be used online during the content generation process where the mod- els can improve and better content can be presented as the game is being played....

  1. Homology modeling and SAR analysis of Schistosoma japonicum cathepsin D (SjCD) with statin inhibitors identify a unique active site steric barrier with potential for the design of specific inhibitors

    Czech Academy of Sciences Publication Activity Database

    Caffrey, C. R.; Plachá, L.; Bařinka, Cyril; Hradilek, Martin; Dostál, Jiří; Sajid, M.; McKerrow, J. H.; Majer, P.; Konvalinka, Jan; Vondrášek, Jiří

    2005-01-01

    Roč. 386, č. 4 (2005), 339-349. ISSN 1431-6730 R&D Projects: GA MŠk(CZ) LC512; GA ČR(CZ) GP203/02/P095; GA AV ČR(CZ) IAA400550510 Grant ostatní: SFSF(US) AI 53247; NATO(XE) CLG 974914 Institutional research plan: CEZ:AV0Z4055905 Keywords : schistotoma * proteases of parasites * modelling Subject RIV: CE - Biochemistry Impact factor: 2.577, year: 2005

  2. Pharmacophore model of the quercetin binding site of the SIRT6 protein.

    Science.gov (United States)

    Ravichandran, S; Singh, N; Donnelly, D; Migliore, M; Johnson, P; Fishwick, C; Luke, B T; Martin, B; Maudsley, S; Fugmann, S D; Moaddel, R

    2014-04-01

    SIRT6 is a histone deacetylase that has been proposed as a potential therapeutic target for metabolic disorders and the prevention of age-associated diseases. We have previously reported on the identification of quercetin and vitexin as SIRT6 inhibitors, and studied structurally related flavonoids including luteolin, kaempferol, apigenin and naringenin. It was determined that the SIRT6 protein remained active after immobilization and that a single frontal displacement could correctly predict the functional activity of the immobilized enzyme. The previous study generated a preliminary pharmacophore for the quercetin binding site on SIRT6, containing 3 hydrogen bond donors and one hydrogen bond acceptor. In this study, we have generated a refined pharmacophore with an additional twelve quercetin analogs. The resulting model had a positive linear behavior between the experimental elution time verses the fit values obtained from the model with a correlation coefficient of 0.8456. PMID:24491483

  3. 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...

  4. 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

  5. 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.

  6. 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)

  7. 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...

  8. Computational Models for Analysis of Illicit Activities

    DEFF Research Database (Denmark)

    Nizamani, Sarwat

    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....... These models include a model for analyzing evolution of terrorist networks; a text classification model for detecting suspicious text and identification of suspected authors of anonymous emails; and a semantic analysis model for news reports, which may help analyze the illicit activities in certain area...... with location and temporal information. For the network evolution, the hierarchical agglomerative clustering approach has been applied to terrorist networks as case studies. The networks' evolutions show that how individual actors who are initially isolated from each other are converted in small groups, which...

  9. High-Pressure Phase Diagram in the Manganites: a Two-site Model Study

    OpenAIRE

    Sacchetti, A.; Postorino, P.; Capone, M.

    2004-01-01

    The pressure dependence of the Curie temperature $T_C$ in manganites, recently studied over a wide pressure range, is not quantitatively accounted for by the quenching of Jahn-Teller distortions, and suggests the occurrence of a new pressure-activated localizing processes. We present a theoretical calculation of $T_C$ based on a two-site double-exchange model with electron-phonon coupling interaction and direct superexchange between the $% t_{2g}$ core spins. We calculate the pressure depende...

  10. 77 FR 39508 - Commercial Wind Lease Issuance and Site Assessment Activities on the Atlantic Outer Continental...

    Science.gov (United States)

    2012-07-03

    ... specific project proposals on those leases) in an identified Wind Energy Area (WEA) on the OCS offshore... Activities on the Atlantic OCS Offshore RI and MA'' to: Program Manager, Office of Renewable Energy Programs... Bureau of Ocean Energy Management Commercial Wind Lease Issuance and Site Assessment Activities on...

  11. 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)

  12. Site-specific dissociation dynamics of H2/D2 on Ag(111) and Co(0001) and the validity of the site-averaging model

    International Nuclear Information System (INIS)

    Dissociative chemisorption of polyatomic molecules on metal surfaces involves high-dimensional dynamics, of which quantum mechanical treatments are computationally challenging. A promising reduced-dimensional approach approximates the full-dimensional dynamics by a weighted average of fixed-site results. To examine the performance of this site-averaging model, we investigate two distinct reactions, namely, hydrogen dissociation on Co(0001) and Ag(111), using accurate first principles potential energy surfaces (PESs). The former has a very low barrier of ∼0.05 eV while the latter is highly activated with a barrier of ∼1.15 eV. These two systems allow the investigation of not only site-specific dynamical behaviors but also the validity of the site-averaging model. It is found that the reactivity is not only controlled by the barrier height but also by the topography of the PES. Moreover, the agreement between the site-averaged and full-dimensional results is much better on Ag(111), though quantitative in neither system. Further quasi-classical trajectory calculations showed that the deviations can be attributed to dynamical steering effects, which are present in both reactions at all energies

  13. 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.)

  14. 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.

  15. Cyanide does more to inhibit heme enzymes, than merely serving as an active-site ligand

    International Nuclear Information System (INIS)

    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

  16. Modeling site productivity of anatolian black pine stands in response to site factors in buldan district, turkey

    International Nuclear Information System (INIS)

    This study was performed to determine modeling height growth of Anatolian black pine (Pinusnigra Arn. ssp. pallasiana (Lamb.) Holmboe) stands according to the site factors in the Buldan forest district. Site index and environmental data obtained from 19 sample plots in the district were fitted by Stepwise Multiple Regression Analysis (SMRA) and Regression Tree (RT) using SPSS 17.0 and DTREG softwares. Schist structured quartzites, slope position and clay percent of B horizon (R2 =0,67) were determined as the most significant variables for the model obtained from SMRA. Two different models were determined by RT statistics. The first one was represented by slope position and altitude (R2 =0,67), while slope position and surface stoniness were the most important variables in the second model and prediction values of site index were separately calculated by all these models. Consequently, R2 =0,84 was the most significance level when the average of these prediction values correlated with the actual site index values. (author)

  17. 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.

  18. 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

  19. 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

  20. 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.

  1. 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.

  2. Substrate Shuttling Between Active Sites of Uroporphyrinogen Decarboxylase in Not Required to Generate Coproporphyrinogen

    Energy Technology Data Exchange (ETDEWEB)

    Phillips, J.; Warby, C; Whitby, F; Kushner, J; Hill, C

    2009-01-01

    Uroporphyrinogen decarboxylase (URO-D; EC 4.1.1.37), the fifth enzyme of the heme biosynthetic pathway, is required for the production of heme, vitamin B12, siroheme, and chlorophyll precursors. URO-D catalyzes the sequential decarboxylation of four acetate side chains in the pyrrole groups of uroporphyrinogen to produce coproporphyrinogen. URO-D is a stable homodimer, with the active-site clefts of the two subunits adjacent to each other. It has been hypothesized that the two catalytic centers interact functionally, perhaps by shuttling of reaction intermediates between subunits. We tested this hypothesis by construction of a single-chain protein (single-chain URO-D) in which the two subunits were connected by a flexible linker. The crystal structure of this protein was shown to be superimposable with wild-type activity and to have comparable catalytic activity. Mutations that impaired one or the other of the two active sites of single-chain URO-D resulted in approximately half of wild-type activity. The distributions of reaction intermediates were the same for mutant and wild-type sequences and were unaltered in a competition experiment using I and III isomer substrates. These observations indicate that communication between active sites is not required for enzyme function and suggest that the dimeric structure of URO-D is required to achieve conformational stability and to create a large active-site cleft.

  3. Atmospheric considerations for CTA site search using global models

    CERN Document Server

    Louedec, K

    2012-01-01

    The Cherenkov Telescope Array (CTA) will be the next high-energy gamma-ray observatory. Selection of the sites, one in each hemisphere, is not obvious since several factors have to be taken into account. Among them, and probably the most crucial, are the atmospheric conditions. Indeed, CTA will use the atmosphere as a giant calorimeter, i.e. as part of the detector. The Southern Hemisphere presents mainly four candidate sites: one in Namibia, one in Chile and two in Argentina. Using atmospheric tools already validated in other air shower experiments, the purpose of this work is to complete studies aiming to choose the site with the best quality for the atmosphere. Three strong requirements are checked: the cloud cover and the frequency of clear skies, the wind speed and the backward trajectories of air masses travelling above the sites and directly linked to the aerosol concentrations. It was found, that the Namibian site is favoured, and one site in Argentina is clearly not suited. Atmospheric measurements a...

  4. Structure analysis reveals the flexibility of the ADAMTS-5 active site

    Energy Technology Data Exchange (ETDEWEB)

    Shieh, Huey-Sheng; Tomasselli, Alfredo G.; Mathis, Karl J.; Schnute, Mark E.; Woodard, Scott S.; Caspers, Nicole; Williams, Jennifer M.; Kiefer, James R.; Munie, Grace; Wittwer, Arthur; Malfait, Anne-Marie; Tortorella, Micky D. (Pfizer)

    2012-03-02

    A ((1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl) succinamide derivative (here referred to as Compound 12) shows significant activity toward many matrix metalloproteinases (MMPs), including MMP-2, MMP-8, MMP-9, and MMP-13. Modeling studies had predicted that this compound would not bind to ADAMTS-5 (a disintegrin and metalloproteinase with thrombospondin motifs-5) due to its shallow S1' pocket. However, inhibition analysis revealed it to be a nanomolar inhibitor of both ADAMTS-4 and -5. The observed inconsistency was explained by analysis of crystallographic structures, which showed that Compound 12 in complex with the catalytic domain of ADAMTS-5 (cataTS5) exhibits an unusual conformation in the S1' pocket of the protein. This first demonstration that cataTS5 can undergo an induced conformational change in its active site pocket by a molecule like Compound 12 should enable the design of new aggrecanase inhibitors with better potency and selectivity profiles.

  5. Nuclear waste: Issues concerning DOE's postponement of second repository siting activities

    International Nuclear Information System (INIS)

    In May 1986 the Department of Energy announced it was postponing site-specific work for a second nuclear waste repository because of progress made in siting the first repository and the uncertainty about when a second repository might be needed. A DOE draft report, which tentatively identified potential sites in seven different states, received considerable comment and objections by concerned states, Indian tribes, and individuals. Following the postponement decision, DOE initiated actions to redirect and restructure the second repository program, concentrating on technical issues rather than site-specific work. This reduction includes a phase-down of siting activities and the formulation of a Technology Development Program with an emphasis on cooperative efforts in international research

  6. 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

  7. 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...

  8. 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.

  9. 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

  10. Counting Active Sites on Titanium Oxide-Silica Catalysts for Hydrogen Peroxide Activation through In Situ Poisoning with Phenylphosphonic Acid

    Energy Technology Data Exchange (ETDEWEB)

    Eaton, Todd R.; Boston, Andrew M.; Thompson, Anthony B.; Gray, Kimberly A.; Notestein, Justin M. [NWU

    2015-06-04

    Quantifying specific active sites in supported catalysts improves our understanding and assists in rational design. Supported oxides can undergo significant structural changes as surface densities increase from site-isolated cations to monolayers and crystallites, which changes the number of kinetically relevant sites. Herein, TiOx domains are titrated on TiOx–SiO2 selectively with phenylphosphonic acid (PPA). An ex situ method quantifies all fluid-accessible TiOx, whereas an in situ titration during cis-cyclooctene epoxidation provides previously unavailable values for the number of tetrahedral Ti sites on which H2O2 activation occurs. We use this method to determine the active site densities of 22 different catalysts with different synthesis methods, loadings, and characteristic spectra and find a single intrinsic turnover frequency for cis-cyclooctene epoxidation of (40±7) h-1. This simple method gives molecular-level insight into catalyst structure that is otherwise hidden when bulk techniques are used.

  11. 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

  12. 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

  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. 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

  17. Framework for Evaluating the Version Management Capabilities of a Class of UML Modeling Tools from the Viewpoint of Multi-site, Multi-partner Product Line Organizations

    OpenAIRE

    Koivulahti-Ojala, Mervi; Käkölä, Timo

    2009-01-01

    UML models are widely used in software product line engineering for activities such as modeling the software product line reference architecture, detailed design, and automation of software code generation and testing. But in high-tech companies, modeling activities are typically distributed across multiple sites and involve multiple partners in different countries, thus complicating model management. Today’s UML modeling tools support sophisticated version management ...

  18. 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

  19. 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

  20. Learning models of activities involving interacting objects

    DEFF Research Database (Denmark)

    Manfredotti, Cristina; Pedersen, Kim Steenstrup; Hamilton, Howard J.; Zilles, Sandra

    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...

  1. 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...

  2. 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

  3. 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.

  4. 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.

  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. 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.

  7. Transient Thermal-Hydraulic Modelling of ETRR-2 for Off-Site Power Loss

    International Nuclear Information System (INIS)

    A transient thermal-hydraulic model entitled ETRR-2 Transient Analysis (ETRR2TA) has been developed to simulate the steady state operation and transient behaviour of ETRR-2 core after loss of off-site power. The model consists of five interactively coupled sub-models for (a) coolant; (b) clad; (c) fuel; (d) chimney; and (e) natural circulation flow. The model divides the active core into specified axial regions and the fuel plate into specified radial zones, then a nodal calculation is performed for both average and hot channels with a chopped cosine shaped heat generation flux. The model also predicts the onset of nucleate boiling, onset of flow instability and critical heat flux phenomena. The model is verified by PARET code for the ETRR-2 core with upward flow direction. It is also validated by a benchmark problem for a 10 MW generic reactor with downward flow direction. The comparisons show good agreement. The model results for ETRR-2 is analysed and discussed. (author)

  8. Thermodynamic modeling of donor splice site recognition in pre-mRNA

    Science.gov (United States)

    Garland, Jeffrey A.; Aalberts, Daniel P.

    2004-04-01

    When eukaryotic genes are edited by the spliceosome, the first step in intron recognition is the binding of a U1 small nuclear RNA with the donor ( 5' ) splice site. We model this interaction thermodynamically to identify splice sites. Applied to a set of 65 annotated genes, our “finding with binding” method achieves a significant separation between real and false sites. Analyzing binding patterns allows us to discard a large number of decoy sites. Our results improve statistics-based methods for donor site recognition, demonstrating the promise of physical modeling to find functional elements in the genome.

  9. 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.

  10. 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

  11. 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.

  12. 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

  13. Greater confinement disposal of high activity and special case wastes at the Nevada Test Site: A unified migration assessment approach

    International Nuclear Information System (INIS)

    The Department of Energy's Nevada Field Office has disposed of a small quantity of high activity and special case wastes using Greater Confinement Disposal facilities in Area 5 of the Nevada Test Site. Because some of these wastes are transuranic radioactive wastes, the Environmental Protection Agency standards for their disposal under 40 CFR Part 191 which requires a compliance assessment. In conducting the 40 CFR Part 191 compliance assessment, review of the Greater Confinement Disposal inventory revealed potentially land disposal restricted hazardous wastes. The regulatory options for disposing of land disposal restricted wastes consist of (1) treatment and monitoring, or (2) developing a no-migration petition. Given that the waste is already buried without treatment, a no-migration petition becomes the primary option. Based on a desire to minimize costs associated with site characterization and performance assessment, a single approach has been developed for assessing compliance with 40 CFR Part 191, DOE Order 5820.2A (which regulates low-level radioactive wastes contained in Greater Confinement Disposal facilities) and developing a no-migration petition. The approach consists of common points of compliance, common time frame for analysis, and common treatment of uncertainty. The procedure calls for conservative bias of modeling assumptions, including model input parameter distributions and adverse processes and events that can occur over the regulatory time frame, coupled with a quantitative treatment of data and parameter uncertainty. This approach provides a basis for a defensible regulatory decision. In addition, the process is iterative between modeling and site characterization activities, where the need for site characterization activities is based on a quantitative definition of the most important and uncertain parameters or assumptions

  14. 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.

  15. 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. PMID:23571828

  16. 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

  17. 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.

  18. Exploring the active site structure of photoreceptor proteins by Raman optical activity

    Science.gov (United States)

    Unno, Masashi

    2015-03-01

    Understanding protein function at the atomic level is a major challenge in a field of biophysics and requires the combined efforts of structural and functional methods. We use photoreceptor proteins as a model system to understand in atomic detail how a chromophore and a protein interact to sense light and send a biological signal. A potential technique for investigating molecular structures is Raman optical activity (ROA), which is a spectroscopic method with a high sensitivity to the structural details of chiral molecules. However, its application to photoreceptor proteins has not been reported. Thus we have constructed ROA spectrometer using near-infrared (NIR) laser excitation at 785 nm. The NIR excitation enables us to measure ROA spectra for a variety of biological samples, including photoreceptor proteins, without fluorescence from the samples. In the present study, we have applied the NIR-ROA to bacteriorhodopsin (BR) and photoactive yellow protein (PYP). BR is a light-driven proton pump and contains a protonated Schiff base of retinal as a chromophore. PYP is a blue light receptor, and this protein has the 4-hydroxycinnamyl chromophore, which is covalently linked to Cys69 through a thiolester bond. We have successfully obtained the ROA spectra of the chromophore within a protein environment. Furthermore, calculations of the ROA spectra utilizing density functional theory provide detailed structural information, such as data on out-of-plane distortions of the chromophore. The structural information obtained from the ROA spectra includes the positions of hydrogen atoms, which are usually not detected in the crystal structures of biological samples.

  19. 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

  20. 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

  1. Critical properties of the Ziff, Gulari, and Barshad (ZGB) model with inert sites.

    Science.gov (United States)

    Hoenicke, G L; de Andrade, M F; Figueiredo, W

    2014-08-21

    We study the model proposed by Ziff, Gulari, and Barshad to mimic the oxidation of carbon monoxide (CO) in the presence of fixed impurities distributed over the catalytic surface. Our focus is on the continuous phase transition between the active phase, where occurs the production of carbon dioxide (CO2), and the inactive phase, where all the non inert sites become filled with oxygen molecules. We employ Monte Carlo simulations to calculate the different ratios between moments of the order parameter at the critical point, as well as, we determine the critical exponents β and ν⊥ as a function of the concentration of impurities. We show that the presence of impurities over the catalytic surface changes the critical behavior of the system. The critical exponents depend on the concentration of impurities and the model does not belong to the directed percolation universality class. PMID:25149808

  2. An analytic model for ionization distributions produced in nanometer sites by protons

    International Nuclear Information System (INIS)

    The initial spatial pattern of energy deposition by ionizing radiation plays a significant role in the subsequent evolution of biologically active chemical species. The study of track structure includes both theoretical and experimental investigation of the spatial pattern of energy deposition. The modeling of stochastic processes in the transfer of energy in macromolecular systems focused on understanding anisotropic radical yields observed in neutron irradiation of oriented deoxyribonucleic acid (DNA) fibers. Extensive computer simulations of proton tracks have been made for protons of energy E, passing through spherical sites of diameter d, off center by a distance b, which we call eccentricity. Computed ionization distributions for 0.3 d/2 were obtained. The log normal function, f(j) = EXP(- (ln(j)-μ)2 / 2 σ2) / σ j (2π) is used to represent these distributions phenomenologically. A concise computer code system written in FORTRAN is under development to evaluate the model of the stochastics of ionization. For high-velocity charged particles and sufficiently small sites it is quite possible for the particle to pass through the site without depositing any energy or without ionization. This situation indicates a breakdown in the proportionality between fluence and dose, and it is therefore desirable to know how frequently this happens and, ideally, to be able to quantify the frequency. From the computer simulations it was discovered that in sites smaller than 1000 nm in diameter, the frequency for zero ionization is simply related to the cross sections for ionization, f(j-O) = EXP [-d(1-b2)1/2/λj(E)p] where j is the ionization number and λj is the mean free path for the interaction

  3. Identification of two catalytic residues in RAG1 that define a single active site within the RAG1/RAG2 protein complex.

    Science.gov (United States)

    Fugmann, S D; Villey, I J; Ptaszek, L M; Schatz, D G

    2000-01-01

    During V(D)J recombination, the RAG1 and RAG2 proteins cooperate to catalyze a series of DNA bond breakage and strand transfer reactions. The structure, location, and number of active sites involved in RAG-mediated catalysis have as yet not been determined. Using protein secondary structure prediction algorithms, we have identified a region of RAG1 with possible structural similarities to the active site regions of transposases and retroviral integrases. Based on this information, we have identified two aspartic acid residues in RAG1 (D600 and D708) that function specifically in catalysis. The results support a model in which RAG1 contains a single, divalent metal ion binding active site structurally related to the active sites of transposases/integrases and responsible for all catalytic functions of the RAG protein complex. PMID:10678172

  4. 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

    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...... specificity and acting as an allosteric site. Although SBSs share many roles with CBMs they may not simply be an alternative to CBMs, but rather complementary as SBSs and CBMs frequently co-occur in enzymes. Despite a relatively long history, it is only in recent years that SBSs have been studied in great...

  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. 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

  7. Site investigation SFR. Hydrogeological modelling of SFR. Model version 0.2

    International Nuclear Information System (INIS)

    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

  8. Bedrock Hydrogeology-Groundwater flow modelling. Site investigation SFR

    International Nuclear Information System (INIS)

    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

  9. 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 a