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Sample records for active surface site

  1. Growth exponents in surface models with non-active sites

    NASA Astrophysics Data System (ADS)

    Santos, M.; Figueiredo, W.; Aarão Reis, F. D. A.

    2006-11-01

    In this work, we studied the role played by the inactive sites present on the substrate of a growing surface. In our model, one particle sticks at the surface if the site where it falls is an active site. However, we allow the deposited particle to diffuse along the surface in accordance with some mechanism previously defined. Using Monte Carlo simulations, and some analytical results, we have investigated the model in (1+1) and (2+1) dimensions considering different relaxation mechanisms. We show that the consideration of non-active sites is a crucial point in the model. In fact, we have seen that the saturation regime is not observed for any value of the density of inactive sites. Besides, the growth exponent β turns to be one, at long times, whatever the mechanism of diffusion we consider in one and two dimensions.

  2. Mimicking enzymatic active sites on surfaces for energy conversion chemistry.

    PubMed

    Gutzler, Rico; Stepanow, Sebastian; Grumelli, Doris; Lingenfelder, Magalí; Kern, Klaus

    2015-07-21

    Metal-organic supramolecular chemistry on surfaces has matured to a point where its underlying growth mechanisms are well understood and structures of defined coordination environments of metal atoms can be synthesized in a controlled and reproducible procedure. With surface-confined molecular self-assembly, scientists have a tool box at hand which can be used to prepare structures with desired properties, as for example a defined oxidation number and spin state of the transition metal atoms within the organic matrix. From a structural point of view, these coordination sites in the supramolecular structure resemble the catalytically active sites of metallo-enzymes, both characterized by metal centers coordinated to organic ligands. Several chemical reactions take place at these embedded metal ions in enzymes and the question arises whether these reactions also take place using metal-organic networks as catalysts. Mimicking the active site of metal atoms and organic ligands of enzymes in artificial systems is the key to understanding the selectivity and efficiency of enzymatic reactions. Their catalytic activity depends on various parameters including the charge and spin configuration in the metal ion, but also on the organic environment, which can stabilize intermediate reaction products, inhibits catalytic deactivation, and serves mostly as a transport channel for the reactants and products and therefore ensures the selectivity of the enzyme. Charge and spin on the transition metal in enzymes depend on the one hand on the specific metal element, and on the other hand on its organic coordination environment. These two parameters can carefully be adjusted in surface confined metal-organic networks, which can be synthesized by virtue of combinatorial mixing of building synthons. Different organic ligands with varying functional groups can be combined with several transition metals and spontaneously assemble into ordered networks. The catalytically active metal

  3. A proposed definition of the 'activity' of surface sites on lactose carriers for dry powder inhalation.

    PubMed

    Grasmeijer, Floris; Frijlink, Henderik W; de Boer, Anne H

    2014-06-01

    A new definition of the activity of surface sites on lactose carriers for dry powder inhalation is proposed which relates to drug detachment during dispersion. The new definition is expected to improve the understanding of 'carrier surface site activity', which stimulates the unambiguous communication about this subject and may aid in the rational design and interpretation of future formulation studies. In contrast to the currently prevailing view on carrier surface site activity, it follows from the newly proposed definition that carrier surface site activity depends on more variables than just the physicochemical properties of the carrier surface. Because the term 'active sites' is ambiguous, it is recommended to use the term 'highly active sites' instead to denote carrier surface sites with a relatively high activity. PMID:24613490

  4. Evolution of anatase surface active sites probed by in situ sum-frequency phonon spectroscopy

    PubMed Central

    Cao, Yue; Chen, Shiyou; Li, Yadong; Gao, Yi; Yang, Deheng; Shen, Yuen Ron; Liu, Wei-Tao

    2016-01-01

    Surface active sites of crystals often govern their relevant surface chemistry, yet to monitor them in situ in real atmosphere remains a challenge. Using surface-specific sum-frequency spectroscopy, we identified the surface phonon mode associated with the active sites of undercoordinated titanium ions and conjoint oxygen vacancies, and used it to monitor them on anatase (TiO2) (101) under ambient conditions. In conjunction with theory, we determined related surface structure around the active sites and tracked the evolution of oxygen vacancies under ultraviolet irradiation. We further found that unlike in vacuum, the surface oxygen vacancies, which dominate the surface reactivity, are strongly regulated by ambient gas molecules, including methanol and water, as well as weakly associated species, such as nitrogen and hydrogen. The result revealed a rich interplay between prevailing ambient species and surface reactivity, which can be omnipresent in environmental and catalytic applications of titanium dioxides. PMID:27704049

  5. The calculation of surface orbital energies for specific types of active sites on dispersed metal catalysts

    SciTech Connect

    Augustine, R.L.; Lahanas, K.M.; Cole, F.

    1992-11-01

    An angular overlap calculation has been used to determine the s, p, and d orbital energy levels of the different types of surface sites present on dispersed metal catalysts. These data can permit a Frontier Molecular Orbital treatment of specific site activities as long as the surface orbital availability for overlap with adsorbed substrates is considered along with its energy value and symmetry.

  6. The calculation of surface orbital energies for specific types of active sites on dispersed metal catalysts

    SciTech Connect

    Augustine, R.L.; Lahanas, K.M.; Cole, F.

    1992-01-01

    An angular overlap calculation has been used to determine the s, p, and d orbital energy levels of the different types of surface sites present on dispersed metal catalysts. These data can permit a Frontier Molecular Orbital treatment of specific site activities as long as the surface orbital availability for overlap with adsorbed substrates is considered along with its energy value and symmetry.

  7. Extending the Diffuse Layer Model of Surface Acidity Behavior: III. Estimating Bound Site Activity Coefficients

    EPA Science Inventory

    Although detailed thermodynamic analyses of the 2-pK diffuse layer surface complexation model generally specify bound site activity coefficients for the purpose of accounting for those non-ideal excess free energies contributing to bound site electrochemical potentials, in applic...

  8. Evidence for surface Ag + complexes as the SERS-active sites on Ag electrodes

    NASA Astrophysics Data System (ADS)

    Watanabe, T.; Kawanami, O.; Honda, K.; Pettinger, B.

    1983-12-01

    Evidence is given that SERS-active sites at Ag electrodes are associated with Ag + ions, forming sparingly soluble surface complexes with ligands such as pyridine molecules and halide ions. Such surface Ag + complexes contribute a factor of >800 to the overall (10 7-fold) enhancement, possibly via a resonance Raman effect.

  9. From single crystal surfaces to single atoms: investigating active sites in electrocatalysis.

    PubMed

    O'Mullane, Anthony P

    2014-04-21

    Electrocatalytic processes will undoubtedly be at the heart of energising future transportation and technology with the added importance of being able to create the necessary fuels required to do so in an environmentally friendly and cost effective manner. For this to be successful two almost mutually exclusive surface properties need to be reconciled, namely producing highly active/reactive surface sites that exhibit long term stability. This article reviews the various approaches which have been undertaken to study the elusive nature of these active sites on metal surfaces which are considered as adatoms or clusters of adatoms with low coordination number. This includes the pioneering studies at extended well defined stepped single crystal surfaces using cyclic voltammetry up to the highly sophisticated in situ electrochemical imaging techniques used to study chemically synthesised nanomaterials. By combining the information attained from single crystal surfaces, individual nanoparticles of defined size and shape, density functional theory calculations and new concepts such as mesoporous multimetallic thin films and single atom electrocatalysts new insights into the design and fabrication of materials with highly active but stable active sites can be achieved. The area of electrocatalysis is therefore not only a fascinating and exciting field in terms of realistic technological and economical benefits but also from the fundamental understanding that can be acquired by studying such an array of interesting materials. PMID:24599277

  10. Enthalpic Breakdown of Water Structure on Protein Active-Site Surfaces.

    PubMed

    Haider, Kamran; Wickstrom, Lauren; Ramsey, Steven; Gilson, Michael K; Kurtzman, Tom

    2016-09-01

    The principles underlying water reorganization around simple nonpolar solutes are well understood and provide the framework for the classical hydrophobic effect, whereby water molecules structure themselves around solutes so that they maintain favorable energetic contacts with both the solute and the other water molecules. However, for certain solute surface topographies, water molecules, due to their geometry and size, are unable to simultaneously maintain favorable energetic contacts with both the surface and neighboring water molecules. In this study, we analyze the solvation of ligand-binding sites for six structurally diverse proteins using hydration site analysis and measures of local water structure, in order to identify surfaces at which water molecules are unable to structure themselves in a way that maintains favorable enthalpy relative to bulk water. These surfaces are characterized by a high degree of enclosure, weak solute-water interactions, and surface constraints that induce unfavorable pair interactions between neighboring water molecules. Additionally, we find that the solvation of charged side chains in an active site generally results in favorable enthalpy but can also lead to pair interactions between neighboring water molecules that are significantly unfavorable relative to bulk water. We find that frustrated local structure can occur not only in apolar and weakly polar pockets, where overall enthalpy tends to be unfavorable, but also in charged pockets, where overall water enthalpy tends to be favorable. The characterization of local water structure in these terms may prove useful for evaluating the displacement of water from diverse protein active-site environments.

  11. Active-site titration analysis of surface influence on immobilized Candida antarctica Lipase B activity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Matrix morphology and surface polarity effects were investigated for Candida antarctica lipase B immobilization. Measurements of the amount of lipase immobilized (bicinchoninic acid method) and the catalyst’s tributyrin hydrolysis activity, coupled with a determination of the lipase’s functional fr...

  12. Testing the applicability of rapid on-site enzymatic activity detection for surface water monitoring

    NASA Astrophysics Data System (ADS)

    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

    bacteria. Therefore the applicability of on-site enzymatic activity determination as a direct surrogate or proxy parameter for microbiological standard assays and quantification of fecal indicator bacteria (FIB) concentration could not be approved and further research in this field is necessary. Presently we conclude that rapid on-site detection of enzymatic activity is applicable for surface water monitoring and that it constitutes a complementary on-site monitoring parameter with high potential. Selection of the type of measured enzymatic activities has to be done on a catchment-specific basis and further work is needed to learn more about its detailed information characteristics in different habitats. The accomplishment of this method detecting continuous data of enzymatic activity in high temporal resolution caused by a target bacterial member is on the way of becoming a powerful tool for water quality monitoring, health related water quality- and early warning requirements.

  13. A facile reflux procedure to increase active surface sites form highly active and durable supported palladium@platinum bimetallic nanodendrites

    NASA Astrophysics Data System (ADS)

    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.

  14. Analysis of structural changes in active site of luciferase adsorbed on nanofabricated hydrophilic Si surface by molecular-dynamics simulations

    SciTech Connect

    Nishiyama, Katsuhiko; Hoshino, Tadatsugu

    2007-05-21

    Interactions between luciferase and a nanofabricated hydrophilic Si surface were explored by molecular-dynamics simulations. The structural changes in the active-site residues, the residues affecting the luciferin binding, and the residues affecting the bioluminescence color were smaller on the nanofabricated hydrophilic Si surface than on both a hydrophobic Si surface and a hydrophilic Si surface. The nanofabrication and wet-treatment techniques are expected to prevent the decrease in activity of luciferase on the Si surface.

  15. Limitations of the potentiometric titration technique in determining the proton active site density of goethite surfaces

    NASA Astrophysics Data System (ADS)

    Lützenkirchen, Johannes; Boily, Jean-François; Lövgren, Lars; Sjöberg, Staffan

    2002-10-01

    Density of proton active surface sites at mineral surfaces is a property of fundamental importance in equilibrium modeling of surface complexation reactions. In this article, methods for an experimental determination of these sites at the surface of α-FeOOH (goethite) are explored. It is shown that previously obtained saturation data of goethite with respect to protons do not yield a site density that can be considered as an intrinsic sorbent property: the results are below crystallographically expected values and values for different ionic media in terms of composition and concentration yield different numbers - for example, chloride would yield higher values than nitrate at the same concentration, and higher electrolyte concentration would favor higher apparent maxima. Although site saturation might be explained by electrostatic repulsion, which is more efficient at high electrolyte concentration or for certain ions, further independent experimental results show that no saturation occurs on goethite down to ph ≡ -log[H +] = 2.2 and possibly to ph = 1.0 in 0.6 M NaCl. For those very low pH values, the experimental charging curve was obtained by coulometric back titration (using the Gran plot) or titrations with tris (hydroxymethyl)-aminomethane of the supernatant of acidified goethite suspension. These experimental data are to our knowledge the first high quality data at such low pHs. However, small errors in the determination of proton concentrations (1%) are shown to strongly affect the shape of the charging curve for ph < 2. Furthermore, goethite dissolution (proton consumption and iron reduction in coulometric titrations) and liquid junction effects interfere at low ph, hampering the straightforward application of coulometric Gran titrations over the whole pH range. From these experiments, it can nonetheless be ascertained that a minimum of 2.5 protons/nm 2 can be adsorbed at the goethite surface from the point of zero charge (ph 9.4) to pH 0.9. Although

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

    PubMed

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

    2012-12-19

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

  17. Detection analysis of surface hydroxyl active sites and simulation calculation of the surface dissociation constants of aqueous diatomite suspensions

    NASA Astrophysics Data System (ADS)

    Ma, Shu-Cui; Wang, Zhi-Gang; Zhang, Ji-Lin; Sun, De-Hui; Liu, Gui-Xia

    2015-02-01

    The surface properties of the diatomite were investigated using nitrogen adsorption/deadsorption isotherms, TG-DSC, FTIR, and XPS, and surface protonation-deprotonation behavior was determined by continuous acid-base potentiometric titration technique. The diatomite sample with porous honeycomb structure has a BET specific surface area of 10.21 m2/g and large numbers of surface hydroxyl functional groups (i.e. tbnd Si-OH, tbnd Fe-OH, and tbnd Al-OH). These surface hydroxyls can be protonated or deprotonated depending on the pH of the suspension. The experimental potentiometric data in two different ionic strength solutions (0.1 and 0.05 mol/L NaCl) were fitted using ProtoFit GUI V2.1 program by applying diffuse double layer model (DLM) with three amphoteric sites and minimizing the sum of squares between a dataset derivative function and a model derivative function. The optimized surface parameters (i.e. surface dissociation constants (log K1, log K2) and surface site concentrations (log C)) of the sample were obtained. Based on the optimized surface parameters, the surface species distribution was calculated using Program-free PHREEQC 3.1.2. Thus, this work reveals considerable new information about surface protonation-deprotonation processes and surface adsorptive behaviors of the diatomite, which helps us to effectively use the cheap and cheerful diatomite clay adsorbent.

  18. Active Sites on the Surface of Nano-Sized SiO2-TiO2 Composites

    NASA Astrophysics Data System (ADS)

    Valova, M. S.; Koryakova, O. V.; Maksimovskikh, A. I.; Fedorova, O. V.; Murashkevich, A. N.; Alisienok, O. A.

    2014-07-01

    The nature and amount of active sites on the surface of nano-sized SiO2-TiO2 oxides were studied by FTIR spectroscopy and back-titration methods. Increasing the TiO2 content in the SiO2-TiO2 composites increased the amount of activated surface H2O and adsorbed CO2. This increased the amount of active basic centers on the oxide surface and caused the first of two observed mechanisms for benzaldehyde adsorption (with and without its activation) to begin to prevail.

  19. Immobilization of alkaline phosphatase on solid surface through self-assembled monolayer and by active-site protection.

    PubMed

    Gao, En-Feng; Kang, Kyung Lhi; Kim, Jeong Hee

    2014-06-01

    Retaining biological activity of a protein after immobilization is an important issue and many studies reported to enhance the activity of proteins after immobilization. We recently developed a new immobilization method of enzyme using active-site protection and minimization of the cross-links between enzyme and surface with a DNA polymerase as a model system. In this study, we extended the new method to an enzyme with a small mono-substrate using alkaline phosphatase (AP) as another model system. A condition to apply the new method is that masking agents, in this case its own substrate needs to stay at the active-site of the enzyme to be immobilized in order to protect the active-site during the harsh immobilization process. This could be achieved by removal of essential divalent ion, Zn2+ that is required for full enzyme activity of AP from the masking solution while active-site of AP was protected with p-nitrophenyl phosphate (pNPP). Approximately 40% of the solution-phase activity was acquired with active-site protected immobilized AP. In addition to protection active-site of AP, the number of immobilization links was kinetically controlled. When the mole fraction of the activated carboxyl group of the linker molecule in self-assembled monolayer (SAM) of 12-mercaptododecanoic acid and 6-mercapto-1-ethanol was varied, 10% of 12-mercaptododecanoic acid gave the maximum enzyme activity. Approximately 51% increase in enzyme activity of the active-site protected AP was observed compared to that of the unprotected group. It was shown that the concept of active-site protection and kinetic control of the number of covalent immobilization bonds can be extended to enzymes with small mono-substrates. It opens the possibility of further extension of the new methods of active-site protection and kinetic control of immobilization bond to important enzymes used in research and industrial fields. PMID:24738440

  20. Use of Temperature and Surface Gas Flux as Novel Measures of Microbial Activity at a Crude Oil Spill Site

    NASA Astrophysics Data System (ADS)

    Bekins, B. A.; Warren, E.; Sihota, N. J.; Hostettler, F. D.

    2012-12-01

    Degradation of crude oil in the subsurface has been studied for over 30 years at a spill site located near Bemidji, Minnesota, USA. The well-characterized site is being used to experiment with the use of surface gas flux and temperature measurements as novel methods for quantifying microbial activity. In the largest subsurface oil body, a 2-m-thick smear zone spans the water table 6-8 m below the surface. Methane produced from degradation of the oil diffuses upward and mixes with oxygen from the surface supporting aerobic methanotrophy at 2-4 m depth. The methane oxidation produces CO2 and heat at rates which are hypothetically proportional to other measures of subsurface microbial activity. To test this hypothesis, vertical profiles of temperature and microbial populations, surface CO2 flux, and oil degradation state were measured at three sites in the oil body and one background site. Temperature increases in the oil zone near the water table were 1-4°C above the background site. The site with the highest temperature increase at the water table also had the highest concentrations of gene copy numbers for methanogens (mcrA) and methanotrophs (pmoA) along with the most degraded oil. Surface CO2 flux over the oil sites averaged more than twice that at the background site but was not consistently highest over the site with the highest activity by other measures. One possible explanation for this discrepancy is variation in the effective diffusion coefficient of the vadose zone between the methanotrophic zone and the surface. At the level of the methanotrophic zone, temperatures were elevated 2-6°C over the background values but again the site with greatest average annual temperature increase was not at the most active site. This may be due to enhanced recharge at the most active site, which lies at the center of a local topographic depression where focused recharge occurs. Overall, the temperature and flux data showed significant increases at the oil sites compared

  1. The Role of OOH Binding Site and Pt Surface Structure on ORR Activities

    PubMed Central

    Jia, Qingying; Caldwell, Keegan; Ziegelbauer, Joseph M.; Kongkanand, Anusorn; Wagner, Frederick T.; Mukerjee, Sanjeev; Ramaker, David E.

    2015-01-01

    We present experimentally observed molecular adsorbate coverages (e.g., O(H), OOH and HOOH) on real operating dealloyed bimetallic PtMx (M = Ni or Co) catalysts under oxygen reduction reaction (ORR) conditions obtained using X-ray absorption near edge spectroscopy (XANES). The results reveal a complex Sabatier catalysis behavior and indicate the active ORR mechanism changes with Pt–O bond weakening from the O2 dissociative mechanism, to the peroxyl mechanism, and finally to the hydrogen peroxide mechanism. An important rearrangement of the OOH binding site, an intermediate in the ORR, enables facile H addition to OOH and faster O–O bond breaking on 111 faces at optimal Pt–O bonding strength, such as that occurring in dealloyed PtM core-shell nanoparticles. This rearrangement is identified by previous DFT calculations and confirmed from in situ measured OOH adsorption coverages during the ORR. The importance of surface structural effects and 111 ordered faces is confirmed by the higher specific ORR rates on solid core vs porous multi-core nanoparticles. PMID:26190857

  2. Activity of radon (222Rn) in the lower atmospheric surface layer of a typical rural site in south India

    NASA Astrophysics Data System (ADS)

    Kumar, K. Charan; Prasad, T. Rajendra; Ratnam, M. Venkat; Nagaraja, Kamsali

    2016-09-01

    Analysis of one year measurements of in situ radon (222Rn) and its progenies along with surface air temperature, relative humidity and pressure near to the Earth's surface has been carried out for the first time at the National Atmospheric Research Laboratory (NARL, 13.5∘N and 79.2∘E) located in a rural site in Gadanki, south India. The dataset was analysed to understand the behaviour of radon in relation to the surface air temperature and relative humidity at a rural site. It was observed that over a period of the 24 hours in a day, the activity of radon and its progenies reaches a peak in the morning hours followed by a remarkable decrease in the afternoon hours. Relatively, a higher concentration of radon was observed at NARL during fair weather days, and this can be attributed to the presence of rocky hills and dense vegetation surrounding the site. The high negative correlation between surface air temperature and activity of radon (R = - 0.70, on an annual scale) suggests that dynamical removal of radon due to increased vertical mixing is one of the most important controlling processes of the radon accumulation in the atmospheric surface layer. The annual averaged activity of radon was found to be 12.01±0.66 Bq m-3 and 4.25±0.18 Bq m-3 for its progenies, in the study period.

  3. Switching on the Metathesis Activity of Re Oxo Alkylidene Surface Sites through a Tailor-Made Silica-Alumina Support.

    PubMed

    Valla, Maxence; Stadler, David; Mougel, Victor; Copéret, Christophe

    2016-01-18

    Re oxo alkylidene surface species are putative active sites in classical heterogeneous Re-based alkene-metathesis catalysts. However, the lack of evidence for such species questions their existence and/or relevance as reaction intermediates. Using Re(O)(=CH-CH=CPh2)(OtBuF6)3(THF), the corresponding well-defined Re oxo alkylidene surface species can be generated on both silica and silica-alumina supports. While inactive on the silica support, it displays very good activity, even for functionalized olefins, on the silica-alumina support. PMID:26756446

  4. Endocrine disrupting activities of surface water associated with a West Virginia oil and gas industry wastewater disposal site.

    PubMed

    Kassotis, Christopher D; Iwanowicz, Luke R; Akob, Denise M; Cozzarelli, Isabelle M; Mumford, Adam C; Orem, William H; Nagel, Susan C

    2016-07-01

    Currently, >95% of end disposal of hydraulic fracturing wastewater from unconventional oil and gas operations in the US occurs via injection wells. Key data gaps exist in understanding the potential impact of underground injection on surface water quality and environmental health. The goal of this study was to assess endocrine disrupting activity in surface water at a West Virginia injection well disposal site. Water samples were collected from a background site in the area and upstream, on, and downstream of the disposal facility. Samples were solid-phase extracted, and extracts assessed for agonist and antagonist hormonal activities for five hormone receptors in mammalian and yeast reporter gene assays. Compared to reference water extracts upstream and distal to the disposal well, samples collected adjacent and downstream exhibited considerably higher antagonist activity for the estrogen, androgen, progesterone, glucocorticoid and thyroid hormone receptors. In contrast, low levels of agonist activity were measured in upstream/distal sites, and were inhibited or absent at downstream sites with significant antagonism. Concurrent analyses by partner laboratories (published separately) describe the analytical and geochemical profiling of the water; elevated conductivity as well as high sodium, chloride, strontium, and barium concentrations indicate impacts due to handling of unconventional oil and gas wastewater. Notably, antagonist activities in downstream samples were at equivalent authentic standard concentrations known to disrupt reproduction and/or development in aquatic animals. Given the widespread use of injection wells for end-disposal of hydraulic fracturing wastewater, these data raise concerns for human and animal health nearby. PMID:27073166

  5. Endocrine disrupting activities of surface water associated with a West Virginia oil and gas industry wastewater disposal site

    USGS Publications Warehouse

    Kassotis, Christopher D.; Iwanowicz, Luke; Akob, Denise M.; Cozzarelli, Isabelle M.; Mumford, Adam; Orem, William H.; Nagel, Susan C.

    2016-01-01

    Currently, >95% of end disposal of hydraulic fracturing wastewater from unconventional oil and gas operations in the US occurs via injection wells. Key data gaps exist in understanding the potential impact of underground injection on surface water quality and environmental health. The goal of this study was to assess endocrine disrupting activity in surface water at a West Virginia injection well disposal site. Water samples were collected from a background site in the area and upstream, on, and downstream of the disposal facility. Samples were solid-phase extracted, and extracts assessed for agonist and antagonist hormonal activities for five hormone receptors in mammalian and yeast reporter gene assays. Compared to reference water extracts upstream and distal to the disposal well, samples collected adjacent and downstream exhibited considerably higher antagonist activity for the estrogen, androgen, progesterone, glucocorticoid and thyroid hormone receptors. In contrast, low levels of agonist activity were measured in upstream/distal sites, and were inhibited or absent at downstream sites with significant antagonism. Concurrent analyses by partner laboratories (published separately) describe the analytical and geochemical profiling of the water; elevated conductivity as well as high sodium, chloride, strontium, and barium concentrations indicate impacts due to handling of unconventional oil and gas wastewater. Notably, antagonist activities in downstream samples were at equivalent authentic standard concentrations known to disrupt reproduction and/or development in aquatic animals. Given the widespread use of injection wells for end-disposal of hydraulic fracturing wastewater, these data raise concerns for human and animal health nearby.

  6. Adsorption of cadmium ions on oxygen surface sites in activated carbon

    SciTech Connect

    Jia, Y.F.; Thomas, K.M.

    2000-02-08

    Various types of oxygen functional groups were introduced onto the surface of coconut shell derived activated carbon by oxidation using nitric acid. Fourier-transform infrared spectroscopy (FTIR), temperature-programmed desorption (TPD), and selective neutralization were used to characterize the surface oxygen functional groups. The oxidized carbons were also heat treated to provide a suite of carbons where the oxygen functional groups of various thermal stabilities were varied progressively. The adsorption of cadmium ions was enhanced dramatically by oxidation of the carbon. The ratio of released protons to adsorbed cadmium ions on oxidized carbon was approximately 2, indicating cation exchange was involved in the process of adsorption. Na{sup +} exchange studies with the oxidized carbon gave a similar ratio. After heat treatment of the oxidized carbons to remove oxygen functional groups, the ratio of H{sup +} released to Cd{sup 2+} adsorbed and the adsorption capacity decreased significantly. Both reversible and irreversible processes were involved in cadmium ion adsorption with reversible adsorption having higher enthalpy. The irreversible adsorption resulted from cation exchange with carboxylic acid groups, whereas the reversible adsorption probably involved physisorption of the partially hydrated cadmium ion.

  7. A Conserved Surface Loop in Type I Dehydroquinate Dehydratases Positions an Active Site Arginine and Functions in Substrate Binding

    SciTech Connect

    Light, Samuel H.; Minasov, George; Shuvalova, Ludmilla; Peterson, Scott N.; Caffrey, Michael; Anderson, Wayne F.; Lavie, Arnon

    2012-04-18

    Dehydroquinate dehydratase (DHQD) catalyzes the third step in the biosynthetic shikimate pathway. We present three crystal structures of the Salmonella enterica type I DHQD that address the functionality of a surface loop that is observed to close over the active site following substrate binding. Two wild-type structures with differing loop conformations and kinetic and structural studies of a mutant provide evidence of both direct and indirect mechanisms of involvement of the loop in substrate binding. In addition to allowing amino acid side chains to establish a direct interaction with the substrate, closure of the loop necessitates a conformational change of a key active site arginine, which in turn positions the substrate productively. The absence of DHQD in humans and its essentiality in many pathogenic bacteria make the enzyme a target for the development of nontoxic antimicrobials. The structures and ligand binding insights presented here may inform the design of novel type I DHQD inhibiting molecules.

  8. Can we define an asymptotic value for the ice active surface site density for heterogeneous ice nucleation?

    NASA Astrophysics Data System (ADS)

    Niedermeier, Dennis; Augustin-Bauditz, Stefanie; Hartmann, Susan; Wex, Heike; Ignatius, Karoliina; Stratmann, Frank

    2015-05-01

    The immersion freezing behavior of droplets containing size-segregated, monodisperse feldspar particles was investigated. For all particle sizes investigated, a leveling off of the frozen droplet fraction was observed reaching a plateau within the heterogeneous freezing temperature regime (T >- 38°C). The frozen fraction in the plateau region was proportional to the particle surface area. Based on these findings, an asymptotic value for ice active surface site density ns, which we named ns⋆, could be determined for the investigated feldspar sample. The comparison of these results with those of other studies not only elucidates the general feasibility of determining such an asymptotic value but also shows that the value of ns⋆ strongly depends on the method of the particle surface area determination. However, such an asymptotic value might be an important input parameter for atmospheric modeling applications. At least it shows that care should be taken when ns is extrapolated to lower or higher temperature.

  9. Experimental and computational investigation of acetic acid deoxygenation over oxophilic molybdenum carbide: Surface chemistry and active site identity

    DOE PAGES

    Schaidle, Joshua A.; Blackburn, Jeffrey; Farberow, Carrie A.; Nash, Connor; Steirer, K. Xerxes; Clark, Jared; Robichaud, David J.; Ruddy, Daniel A.

    2016-01-21

    Ex situ catalytic fast pyrolysis (CFP) is a promising route for producing fungible biofuels; however, this process requires bifunctional catalysts that favor C–O bond cleavage, activate hydrogen at near atmospheric pressure and high temperature (350–500 °C), and are stable under high-steam, low hydrogen-to-carbon environments. Recently, early transition-metal carbides have been reported to selectively cleave C–O bonds of alcohols, aldehydes, and oxygenated aromatics, yet there is limited understanding of the metal carbide surface chemistry under reaction conditions and the identity of the active sites for deoxygenation. In this study, we evaluated molybdenum carbide (Mo2C) for the deoxygenation of acetic acid, anmore » abundant component of biomass pyrolysis vapors, under ex situ CFP conditions, and we probed the Mo2C surface chemistry, identity of the active sites, and deoxygenation pathways using in situ diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), X-ray photoelectron spectroscopy (XPS), and density functional theory (DFT) calculations.« less

  10. Recent characterization activities of Midway Valley as a potential repository surface facility site

    SciTech Connect

    Gibson, J.D.; Wesling, J.R.; Swan, F.H.; Bullard, T.F.

    1992-01-31

    Midway Valley, located at the eastern base of Yucca Mountain, Nye County, Nevada, has been identified as a possible location for the surface facilities of a potential high-level nuclear-waste repository. This structural and topographic valley is bounded by two north- trending, down-to-the-west normal faults: the Paintbrush Canyon fault on the east and the Bow Ridge fault on the west. Surface and near-surface geological data have been acquired from Midway Valley during the past three years with particular emphasis on evaluating the existence of Quaternary faults. A detailed (1:6000) surficial geological map has been prepared based on interpretation of new and existing aerial photographs, field mapping, soil pits, and trenches. No evidence was found that would indicate displacement of these surficial deposits along previously unrecognized faults. However, given the low rates of Quaternary faulting and the extensive areas that are covered by late Pleistocene to Holocene deposits south of Sever Wash, Quaternary faulting between known faults cannot be precluded based on surface evidence alone. Middle to late Pleistocene alluvial fan deposits (Unit Q3) exist at or near the surface throughout Midway Valley. Confidence is increased that the potential for surface fault rupture in Midway Valley can be assessed by excavations that expose the deposits and soils associated with Unit Q3 or older units (middle Pleistocene or earlier).

  11. Effects of Al(3+) Ions on Formation of Silica Framework and Surface Active Sites for SO4(2-) Ions.

    PubMed

    Sasahara, Shigeo; Ozeki, Sumio

    2016-07-19

    Al(3+) ions were introduced into silica framework at 318 K in order to make active Al sites for SO4(2-) by the addition of aqueous sodium silicate solution to aqueous sulfuric acid solution of Al2(SO4)3. The (27)Al and (29)Si NMR spectra of aluminosilicates were measured at 278 K with reaction time. (29)Si NMR spectra were analyzed by the multivariate curve resolution. The addition of Al(3+) ions to aqueous silicate solution promoted gel formation. Small amounts of Al(3+) ions were incorporated as a four-coordinated complex at early stage of polymerization reaction of silicates and during subsequent reaction six-coordinated Al complex increased, suggesting reversible conversion between 4- and 6-coordinated complexes. SO4(2-) ions interact with positive surfaces of aluminosilicates and are specifically adsorbed on the surface sites of 6-coordinated Al(3+) species, which may be stabilized on silicate surfaces as [Al(H2O)5SO4](+). PMID:27352046

  12. Effects of Al(3+) Ions on Formation of Silica Framework and Surface Active Sites for SO4(2-) Ions.

    PubMed

    Sasahara, Shigeo; Ozeki, Sumio

    2016-07-19

    Al(3+) ions were introduced into silica framework at 318 K in order to make active Al sites for SO4(2-) by the addition of aqueous sodium silicate solution to aqueous sulfuric acid solution of Al2(SO4)3. The (27)Al and (29)Si NMR spectra of aluminosilicates were measured at 278 K with reaction time. (29)Si NMR spectra were analyzed by the multivariate curve resolution. The addition of Al(3+) ions to aqueous silicate solution promoted gel formation. Small amounts of Al(3+) ions were incorporated as a four-coordinated complex at early stage of polymerization reaction of silicates and during subsequent reaction six-coordinated Al complex increased, suggesting reversible conversion between 4- and 6-coordinated complexes. SO4(2-) ions interact with positive surfaces of aluminosilicates and are specifically adsorbed on the surface sites of 6-coordinated Al(3+) species, which may be stabilized on silicate surfaces as [Al(H2O)5SO4](+).

  13. Mg2+ binds to the surface of thymidylate synthase and affects hydride transfer at the interior active site

    PubMed Central

    Wang, Zhen; Sapienza, Paul J.; Abeysinghe, Thelma; Luzum, Calvin; Lee, Andrew L.; Finer-Moore, Janet S.; Stroud, Robert M.; Kohen, Amnon

    2013-01-01

    Thymidylate synthase (TSase) produces the sole intracellular de novo source of thymidine (i.e. the DNA base T) and thus is a common target for antibiotic and anticancer drugs. Mg2+ has been reported to affect TSase activity, but the mechanism of this interaction has not been investigated. Here we show that Mg2+ binds to the surface of Escherichia coli TSase and affects the kinetics of hydride transfer at the interior active site (16 Å away). Examination of the crystal structures identifies a Mg2+ near the glutamyl moiety of the folate cofactor, providing the first structural evidence for Mg2+ binding to TSase. The kinetics and NMR relaxation experiments suggest that the weak binding of Mg2+ to the protein surface stabilizes the closed conformation of the ternary enzyme complex and reduces the entropy of activation on the hydride transfer step. Mg2+ accelerates the hydride transfer by ca. 7-fold but does not affect the magnitude or temperature-dependence of the intrinsic kinetic isotope effect. These results suggest that Mg2+ facilitates the protein motions that bring the hydride donor and acceptor together, but it does not change the tunneling ready state of the hydride transfer. These findings highlight how variations in cellular Mg2+ concentration can modulate enzyme activity through long-range interactions in the protein, rather than binding at the active site. The interaction of Mg2+ with the glutamyl-tail of the folate cofactor and nonconserved residues of bacterial TSase may assist in designing antifolates with poly-glutamyl substitutes as species-specific antibiotic drugs. PMID:23611499

  14. Mg2+ binds to the surface of thymidylate synthase and affects hydride transfer at the interior active site.

    PubMed

    Wang, Zhen; Sapienza, Paul J; Abeysinghe, Thelma; Luzum, Calvin; Lee, Andrew L; Finer-Moore, Janet S; Stroud, Robert M; Kohen, Amnon

    2013-05-22

    Thymidylate synthase (TSase) produces the sole intracellular de novo source of thymidine (i.e., the DNA base T) and thus is a common target for antibiotic and anticancer drugs. Mg(2+) has been reported to affect TSase activity, but the mechanism of this interaction has not been investigated. Here we show that Mg(2+) binds to the surface of Escherichia coli TSase and affects the kinetics of hydride transfer at the interior active site (16 Å away). Examination of the crystal structures identifies a Mg(2+) near the glutamyl moiety of the folate cofactor, providing the first structural evidence for Mg(2+) binding to TSase. The kinetics and NMR relaxation experiments suggest that the weak binding of Mg(2+) to the protein surface stabilizes the closed conformation of the ternary enzyme complex and reduces the entropy of activation on the hydride transfer step. Mg(2+) accelerates the hydride transfer by ~7-fold but does not affect the magnitude or temperature dependence of the intrinsic kinetic isotope effect. These results suggest that Mg(2+) facilitates the protein motions that bring the hydride donor and acceptor together, but it does not change the tunneling ready state of the hydride transfer. These findings highlight how variations in cellular Mg(2+) concentration can modulate enzyme activity through long-range interactions in the protein, rather than binding at the active site. The interaction of Mg(2+) with the glutamyl tail of the folate cofactor and nonconserved residues of bacterial TSase may assist in designing antifolates with polyglutamyl substitutes as species-specific antibiotic drugs.

  15. Surface carbon transformations at a site of active continental serpentinization: the Tablelands, Newfoundland, Canada

    NASA Astrophysics Data System (ADS)

    Rietze, A.; Szponar, N.; Lang, S. Q.; Kohl, L.; Morrill, P. L.

    2013-12-01

    The Tablelands in Newfoundland, Canada contain terrestrial peridotite-hosted groundwater springs associated with serpentinization. These springs act as windows into subsurface systems and provide insight into their biogeochemistry. However, at sites where ultra-basic water pools and mixes with overland flow the reactions in the pools must be considered when trying to source organic compounds. We will present data from a pool (WHC2) located in the Tablelands to determine the biogeochemical carbon transformations at this mixing site. The ultra-basic, reducing groundwater springs had higher concentrations of alkanes (C1-C4) and organic acids (acetate and formate) than the overland flow, suggesting that these organics originated from the groundwater source. A two component mixing model was developed to predict what the concentrations of alkanes and organic acids would be in the WHC2 pool based on physical mixing of groundwater and overland flow. Acetate and C2-C4 alkane concentrations were fairly well predicted by the mixing model, suggesting little consumption or production of this organic acid and these alkanes in the pool. However, methane concentrations were under predicted by the model at two sampling points in the pool, suggesting production of methane at these sites. At the same two sampling locations formate concentrations were over predicted by the model, suggesting that formate was being consumed in the pool. The water at these sampling times was highly reducing; therefore oxidation of formate was not likely responsible for the consumption of formate. Organic acid fermentation using formate is one possible sink for formate and source for methane. However, the genomic data from the site has shown little evidence for microbial methanogenesis (1). Geochemical measurements of the carbon in the pool can help elucidate the most dominant source of methane. On a Bernard plot (C1/C2+ vs. δ13CCH4 (‰)) the alkanes measured at the springs plot in the thermogenic

  16. Applicability of rapid and on-site measured enzyme activity for surface water quality monitoring in an agricultural catchment

    NASA Astrophysics Data System (ADS)

    Stadler, Philipp; Farnleitner, Andreas H.; Sommer, Regina; Kumpan, Monika; Zessner, Matthias

    2014-05-01

    For the near real time and on-site detection of microbiological fecal pollution of water, the measurement of beta-D- Glucuronidase (GLUC) enzymatic activity has been suggested as a surrogate parameter and has been already successfully operated for water quality monitoring of ground water resources (Ryzinska-Paier et al. 2014). Due to possible short measure intervals of three hours, this method has high potential as a water quality monitoring tool. While cultivation based standard determination takes more than one working day (Cabral 2010) the potential advantage of detecting the GLUC activity is the high temporal measuring resolution. Yet, there is still a big gap of knowledge on the fecal indication capacity of GLUC (specificity, sensitivity, persistence, etc.) in relation to potential pollution sources and catchment conditions (Cabral 2010, Ryzinska-Paier et al. 2014). Furthermore surface waters are a big challenge for automated detection devices in a technical point of view due to the high sediment load during event conditions. This presentation shows results gained form two years of monitoring in an experimental catchment (HOAL) dominated by agricultural land use. Two enzymatic measurement devices are operated parallel at the catchment outlet to test the reproducibility and precision of the method. Data from continuous GLUC monitoring under both base flow and event conditions is compared with reference samples analyzed by standardized laboratory methods for fecal pollution detection (e.g. ISO 16649-1, Colilert18). It is shown that rapid enzymatic on-site GLUC determination can successfully be operated from a technical point of view for surface water quality monitoring under the observed catchment conditions. The comparison of enzyme activity with microbiological standard analytics reveals distinct differences in the dynamic of the signals during event conditions. Cabral J. P. S. (2010) "Water Microbiology. Bacterial Pathogens and Water" International Journal of

  17. Can we define an asymptotic value for the ice active surface site density for heterogeneous ice nucleation?

    NASA Astrophysics Data System (ADS)

    Niedermeier, Dennis; Augustin-Bauditz, Stefanie; Hartmann, Susan; Wex, Heike; Ignatius, Karoliina; Stratmann, Frank

    2015-04-01

    The formation of ice in atmospheric clouds has a substantial influence on the radiative properties of clouds as well as on the formation of precipitation. Therefore much effort has been made to understand and quantify the major ice formation processes in clouds. Immersion freezing has been suggested to be a dominant primary ice formation process in low and mid-level clouds (mixed-phase cloud conditions). It also has been shown that mineral dust particles are the most abundant ice nucleating particles in the atmosphere and thus may play an important role for atmospheric ice nucleation (Murray et al., 2012). Additionally, biological particles like bacteria and pollen are suggested to be potentially involved in atmospheric ice formation, at least on a regional scale (Murray et al., 2012). In recent studies for biological particles (SNOMAX and birch pollen), it has been demonstrated that freezing is induced by ice nucleating macromolecules and that an asymptotic value for the mass density of these ice nucleating macromolecules can be determined (Hartmann et al., 2013; Augustin et al., 2013, Wex et al., 2014). The question arises whether such an asymptotic value can also be determined for the ice active surface site density ns, a parameter which is commonly used to describe the ice nucleation activity of e.g., mineral dust. Such an asymptotic value for ns could be an important input parameter for atmospheric modeling applications. In the presented study, we therefore investigated the immersion freezing behavior of droplets containing size-segregated, monodisperse feldspar particles utilizing the Leipzig Aerosol Cloud Interaction Simulator (LACIS). For all particle sizes considered in the experiments, we observed a leveling off of the frozen droplet fraction reaching a plateau within the heterogeneous freezing temperature regime (T > -38°C) which was proportional to the particle surface area. Based on these findings, we could determine an asymptotic value for the ice

  18. ROLE OF C AND P SITES ON THE CHEMICAL ACTIVITY OF METAL CARBIDE AND PHOSPHIDES: FROM CLUSTERS TO SINGLE-CRYSTAL SURFACES

    SciTech Connect

    RODRIGUEZ,J.A.; VINES, F.; LIU, P.; ILLAS, F.

    2007-07-01

    Transition metal carbides and phosphides have shown tremendous potential as highly active catalysts. At a microscopic level, it is not well understood how these new catalysts work. Their high activity is usually attributed to ligand or/and ensemble effects. Here, we review recent studies that examine the chemical activity of metal carbide and phosphides as a function of size, from clusters to extended surfaces, and metal/carbon or metal/phosphorous ratio. These studies reveal that the C and P sites in these compounds cannot be considered as simple spectators. They moderate the reactivity of the metal centers and provide bonding sites for adsorbates.

  19. Redox-active on-surface polymerization of single-site divalent cations from pure metals by a ketone-functionalized phenanthroline

    SciTech Connect

    Skomski, Daniel; Tempas, Christopher D.; Bukowski, Gregory S.; Smith, Kevin A.; Tait, Steven L.

    2015-03-14

    Metallic iron, chromium, or platinum mixing with a ketone-functionalized phenanthroline ligand on a single crystal gold surface demonstrates redox activity to a well-defined oxidation state and assembly into thermally stable, one dimensional, polymeric chains. The diverging ligand geometry incorporates redox-active sub-units and bi-dentate binding sites. The gold surface provides a stable adsorption environment and directs growth of the polymeric chains, but is inert with regard to the redox chemistry. These systems are characterized by scanning tunnelling microscopy, non-contact atomic force microscopy, and X-ray photoelectron spectroscopy under ultra-high vacuum conditions. The relative propensity of the metals to interact with the ketone group is examined, and it is found that Fe and Cr more readily complex the ligand than Pt. The formation and stabilization of well-defined transition metal single-sites at surfaces may open new routes to achieve higher selectivity in heterogeneous catalysts.

  20. Examination of metals from aerospace-related activity in surface water samples from sites surrounding the Kennedy Space Center (KSC), Florida.

    PubMed

    Bowden, John A; Cantu, Theresa M; Scheidt, Douglas M; Lowers, Russell H; Nocito, Brian A; Young, Vaneica Y; Guillette, Louis J

    2014-05-01

    Metal contamination from Space Shuttle launch activity was examined using inductively coupled plasma-atomic emission spectroscopy in a two-tier study sampling surface water collected from several sites at the Kennedy Space Center (KSC) and associated Merritt Island National Wildlife Refuge in east central Florida. The primary study examined both temporal changes in baseline metal concentrations (19 metals) in surface water (1996 to 2009, 11 sites) samples collected at specific long-term monitoring sites and metal deposition directly associated with Space Shuttle launch activity at two Launch Complexes (LC39A and LC39B). A secondary study examined metal concentrations at additional sites and increased the amount of elements measured to 48 elements. Our examination places a heavy focus on those metals commonly associated with launch operations (e.g., Al, Fe, Mn, and Zn), but a brief discussion of other metals (As, Cu, Mo, Ni, and Pb) is also included. While no observable accumulation of metals occurred during the time period of the study, the data obtained postlaunch demonstrated a dramatic increase for Al, Fe, Mn, and Zn. Comparing overall trends between the primary and secondary baseline surface water concentrations, elevated concentrations were generally observed at sampling stations located near the launch complexes and from sites isolated from major water systems. While there could be several natural and anthropogenic sources for metal deposition at KSC, the data in this report indicate that shuttle launch events are a significant source.

  1. Examination of metals from aerospace-related activity in surface water samples from sites surrounding the Kennedy Space Center (KSC), Florida.

    PubMed

    Bowden, John A; Cantu, Theresa M; Scheidt, Douglas M; Lowers, Russell H; Nocito, Brian A; Young, Vaneica Y; Guillette, Louis J

    2014-05-01

    Metal contamination from Space Shuttle launch activity was examined using inductively coupled plasma-atomic emission spectroscopy in a two-tier study sampling surface water collected from several sites at the Kennedy Space Center (KSC) and associated Merritt Island National Wildlife Refuge in east central Florida. The primary study examined both temporal changes in baseline metal concentrations (19 metals) in surface water (1996 to 2009, 11 sites) samples collected at specific long-term monitoring sites and metal deposition directly associated with Space Shuttle launch activity at two Launch Complexes (LC39A and LC39B). A secondary study examined metal concentrations at additional sites and increased the amount of elements measured to 48 elements. Our examination places a heavy focus on those metals commonly associated with launch operations (e.g., Al, Fe, Mn, and Zn), but a brief discussion of other metals (As, Cu, Mo, Ni, and Pb) is also included. While no observable accumulation of metals occurred during the time period of the study, the data obtained postlaunch demonstrated a dramatic increase for Al, Fe, Mn, and Zn. Comparing overall trends between the primary and secondary baseline surface water concentrations, elevated concentrations were generally observed at sampling stations located near the launch complexes and from sites isolated from major water systems. While there could be several natural and anthropogenic sources for metal deposition at KSC, the data in this report indicate that shuttle launch events are a significant source. PMID:24738662

  2. F+ tunable laser activity and interaction of atomic halogens (F, Cl and Br) at the low coordinated surface sites of SrOAb initio and DFT calculations.

    PubMed

    Shalabi, Ahmed S

    2002-10-01

    The twofold potential of F+ color centers at the low coordinated surfaces of SrO for providing tunable laser activity and adsorption properties for atomic halogens (F, Cl and Br) has been investigated using ab initio electronic structure calculations. SrO clusters of variable sizes were embedded in simulated Coulomb fields that closely approximate the Madelung fields of the host surfaces and the nearest neighbor ions to F+ were allowed to relax to equilibrium. Based on Stokes shifted optical transition bands and horizontal shifts along the configuration coordinate diagrams, the F+ laser activity was found to decrease as the coordination number of the surface ions decreases from 5 (flat) to 4 (edge) to 3 (corner). An attempt has been made to explain this result in terms of Madelung potentials and optical-optical conversion efficiencies. All relaxed excited states are deep below the conduction bands of the perfect ground states, implying that F+ is a laser-suitable defect. The most laser active flat surface is the least probable for relaxed excited state orientational destruction of F+. The excited state at the edge has the highest energy, implying exciton (energy) transfer to the flat and edge sites. F+ relaxation and defect-formation energies increase with increasing surface coordination number. The Glasner-Tompkins relation between the fundamental optical absorption of F+ in solids and the fundamental absorption of the host crystals can be generalized to include the low coordinated surfaces of SrO. The F+ color center changes the nature of halogen-surface interaction (adsorption energies) from physical adsorption to chemical adsorption. The halogen-surface interactions increase with increasing electronegativity of the halogen. The calculated adsorption energies can be explained in terms of surface electrostatic potentials, and the covalent spin pairing mechanism plays a dominant role in determining adsorbate-substrate interactions.

  3. Identical Location Transmission Electron Microscopy Imaging of Site-Selective Pt Nanocatalysts: Electrochemical Activation and Surface Disordering.

    PubMed

    Arán-Ais, Rosa M; Yu, Yingchao; Hovden, Robert; Solla-Gullón, Jose; Herrero, Enrique; Feliu, Juan M; Abruña, Héctor D

    2015-12-01

    We have employed identical location transmission electron microscopy (IL-TEM) to study changes in the shape and morphology of faceted Pt nanoparticles as a result of electrochemical cycling; a procedure typically employed for activating platinum surfaces. We find that the shape and morphology of the as-prepared hexagonal nanoparticles are rapidly degraded as a result of potential cycling up to +1.3 V. As few as 25 potential cycles are sufficient to cause significant degradation, and after about 500-1000 cycles the particles are dramatically degraded. We also see clear evidence of particle migration during potential cycling. These finding suggest that great care must be exercised in the use and study of shaped Pt nanoparticles (and related systems) as electrocatlysts, especially for the oxygen reduction reaction where high positive potentials are typically employed. PMID:26524187

  4. Conformation analysis of a surface loop that controls active site access in the GH11 xylanase A from Bacillus subtilis.

    PubMed

    Vieira, Davi Serradella; Ward, Richard John

    2012-04-01

    Xylanases (EC 3.2.1.8 endo-1,4-glycosyl hydrolase) catalyze the hydrolysis of xylan, an abundant hemicellulose of plant cell walls. Access to the catalytic site of GH11 xylanases is regulated by movement of a short β-hairpin, the so-called thumb region, which can adopt open or closed conformations. A crystallographic study has shown that the D11F/R122D mutant of the GH11 xylanase A from Bacillus subtilis (BsXA) displays a stable "open" conformation, and here we report a molecular dynamics simulation study comparing this mutant with the native enzyme over a range of temperatures. The mutant open conformation was stable at 300 and 328 K, however it showed a transition to the closed state at 338 K. Analysis of dihedral angles identified thumb region residues Y113 and T123 as key hinge points which determine the open-closed transition at 338 K. Although the D11F/R122D mutations result in a reduction in local inter-intramolecular hydrogen bonding, the global energies of the open and closed conformations in the native enzyme are equivalent, suggesting that the two conformations are equally accessible. These results indicate that the thumb region shows a broader degree of energetically permissible conformations which regulate the access to the active site region. The R122D mutation contributes to the stability of the open conformation, but is not essential for thumb dynamics, i.e., the wild type enzyme can also adapt to the open conformation.

  5. Characterization of active phosphorus surface sites at synthetic carbonate-free fluorapatite using single-pulse 1H, 31P, and 31P CP MAS NMR.

    PubMed

    Jarlbring, Mathias; Sandström, Dan E; Antzutkin, Oleg N; Forsling, Willis

    2006-05-01

    The chemically active phosphorus surface sites defined as PO(x), PO(x)H, and PO(x)H2, where x = 1, 2, or 3, and the bulk phosphorus groups of PO4(3-) at synthetic carbonate-free fluorapatite (Ca5(PO4)3F) have been studied by means of single-pulse 1H,31P, and 31P CP MAS NMR. The changes in composition and relative amounts of each surface species are evaluated as a function of pH. By combining spectra from single-pulse 1H and 31P MAS NMR and data from 31P CP MAS NMR experiments at varying contact times in the range 0.2-3.0 ms, it has been possible to distinguish between resonance lines in the NMR spectra originating from active surface sites and bulk phosphorus groups and also to assign the peaks in the NMR spectra to the specific phosphorus species. In the 31P CP MAS NMR experiments, the spinning frequency was set to 4.2 kHz; in the single-pulse 1H MAS NMR experiments, the spinning frequency was 10 kHz. The 31P CP MAS NMR spectrum of fluorapatite at pH 5.9 showed one dominating resonance line at 2.9 ppm assigned to originate from PO4(3-) groups and two weaker shoulder peaks at 5.4 and 0.8 ppm which were assigned to the unprotonated PO(x) (PO, PO2-, and PO3(2-)) and protonated PO(x)H (PO2H and PO3H-) surface sites. At pH 12.7, the intensity of the peak representing unprotonated PO(x) surface sites has increased 1.7% relative to the bulk peak, while the intensity of the peaks of the protonated species PO(x)H have decreased 1.4% relative to the bulk peak. At pH 3.5, a resonance peak at -4.5 ppm has appeared in the 31P CP MAS NMR spectrum assigned to the surface species PO(x)H2 (PO3H2). The results from the 1H MAS and 31P CP MAS NMR measurements indicated that H+, OH-, and physisorbed H2O at the surface were released during the drying process at 200 degrees C.

  6. Surface barrier research at the Hanford Site

    SciTech Connect

    Gee, G.W.; Ward, A.L.; Fayer, M.J.

    1997-12-31

    At the DOE Hanford Site, a field-scale prototype surface barrier was constructed in 1994 over an existing waste site as a part of a CERCLA treatability test. The above-grade barrier consists of a fine-soil layer overlying coarse layers of sands, gravels, basalt rock (riprap), and a low permeability asphalt layer. Two sideslope configurations, clean-fill gravel on a 10:1 slope and basalt riprap on a 2:1 slope, were built and are being tested. Design considerations included: constructability; drainage and water balance monitoring, wind and water erosion control and monitoring; surface revegetation and biotic intrusion; subsidence and sideslope stability, and durability of the asphalt layer. The barrier is currently in the final year of a three-year test designed to answer specific questions related to stability and long-term performance. One half of the barrier is irrigated such that the total water applied, including precipitation, is 480 mm/yr (three times the long-term annual average). Each year for the past two years, an extreme precipitation event (71 mm in 8 hr) representing a 1,000-yr return storm was applied in late March, when soil water storage was at a maximum. While the protective sideslopes have drained significant amounts of water, the soil cover (2-m of silt-loam soil overlying coarse sand and rock) has never drained. During the past year there was no measurable surface runoff or wind erosion. This is attributed to extensive revegetation of the surface. In addition, the barrier elevation has shown a small increase of 2 to 3 cm that is attributed to a combination of root proliferation and freeze/thaw activity. Testing will continue through September 1997. Performance data from the prototype barrier will be used by DOE in site-closure decisions at Hanford.

  7. The role of surface/interfacial Cu{sup 2+} sites in the photocatalytic activity of coupled CuO-TiO{sub 2} nanocomposites.

    SciTech Connect

    Li, G.; Dimitrijevic, N. M.; Chen, L.; Rajh, T.; Gray, K. A.; Northwestern Univ.

    2008-01-01

    Coupled CuO-TiO{sub 2} nanocomposite photocatalysts were prepared by a deposition precipitation method and were characterized with a variety of techniques. Electron paramagnetic resonance (EPR) spectroscopy was employed to study the local structures of surface/interfacial Cu{sup 2+}+ sites using Cu{sup 2+} as a sensitive paramagnetic probe. The addition of bulk CuO to TiO{sub 2} led to decreased photocatalytic efficiency in the degradation of methylene blue. However, doping with a very small amount of CuO (0.1 wt % copper loading) significantly enhanced the photocatalytic activity of TiO{sub 2}. EPR study of the TiO{sub 2} surface revealed the presence of both highly dispersed CuO clusters and substitutional Cu{sup 2+} sites (Ti-O-Cu linkages) at 0.1 wt % copper loading. The data suggest that the Ti-O-Cu linkages contributed to the improved photooxidative activity of the 0.1% CuO-TiO{sub 2} nanocomposite. In contrast, at higher loadings the bulk form of CuO created charge recombination centers lowering the photoactivity of the composites.

  8. Active surface faulting or landsliding in the Lower Tagus Valley (Portugal)? A solved controversy concerning the Vila Chã de Ourique site

    NASA Astrophysics Data System (ADS)

    Cabral, João Manuel; Marques, Fernando; Figueiredo, Paula; Matias, Luís

    2011-04-01

    The Lower Tagus Valley has experienced significant (M 6-7) historical seismicity, evidencing the presence of seismogenic faults. These are still deficiently known due to the low strain rates and the recent alluvial sedimentation of the Tagus River that buries most of the structures, though Paleoseismic evidence was allegedly found by a research team in the Tagus valley, at a site 60 km N of Lisbon, near Vila Chã de Ourique (VCO). According to this team, trenching at the VCO site exposed an active thrust fault, evidencing the surface rupture of a large earthquake that occurred in 1531. Our studies performed at this site, comprising field observations with a reappraisal of the trench outcrops previously excavated, borehole drilling, soil mechanics laboratory testing, and seismic reflection acquisition, pointed to the alternative interpretation that the outcropping structures are gravitational and not of tectonic origin. The interpretation of new outcrops crosscutting the structures exposed at the trenches, as well as newly acquired high-resolution seismic reflection data, definitely exclude the active thrust fault explanation and support a gravitational slip model for all the observed structures. Gravitational slip in the river bank slope was promoted by low shear strength clays and high pore water pressure coupled with slope toe river erosion. Gravitational slides must have occurred prior to development of the present sedimentation level of the Tagus alluvial plain, which was attained in the last few thousand years as indicated by borehole data and estimations of sedimentation rates.

  9. Oxygen plasma functionalization of parylene C coating for implants surface: nanotopography and active sites for drug anchoring.

    PubMed

    Gołda, M; Brzychczy-Włoch, M; Faryna, M; Engvall, K; Kotarba, A

    2013-10-01

    The effect of oxygen plasma treatment (t=0.1-60 min, pO2=0.2 mbar, P=50 W) of parylene C implant surface coating was investigated in order to check its influence on morphology (SEM, AFM observations), chemical composition (XPS analysis), hydrophilicity (contact angle measurements) and biocompatibility (MG-63 cell line and Staphylococcus aureus 24167 DSM adhesion screening). The modification procedure leads to oxygen insertion (up to 20 at.%) into the polymer matrix and together with surface topography changes has a dramatic impact on wettability (change of contact angle from θ=78±2 to θ=33±1.9 for unmodified and 60 min treated sample, respectively). As a result, the hydrophilic surface of modified parylene C promotes MG-63 cells growth and at the same time does not influence S. aureus adhesion. The obtained results clearly show that the plasma treatment of parylene C surface provides suitable polar groups (C=O, C-O, O-C=O, C-O-O and O-C(O)-O) for further development of the coating functionality.

  10. Five-fold twinned Pd2NiAg nanocrystals with increased surface Ni site availability to improve oxygen reduction activity.

    PubMed

    Liu, Suli; Zhang, Qinghua; Li, Yafei; Han, Min; Gu, Lin; Nan, Cewen; Bao, Jianchun; Dai, Zhihui

    2015-03-01

    The synthesis of highly active oxygen reduction reaction (ORR) catalysts with good durability and low cost is highly desirable but still remains a significant challenge. In this work, we present the synthesis of five-fold twinned Pd2NiAg nanocrystals (NCs) with a Ni-terminal surface which exhibit excellent electrocatalytic performance for ORR in alkaline media, even better than the performance of the commercial Pt/C catalyst. Using high-angle annular-dark-field imaging together with density functional theory calculations, it is found that the surfaces of the five-fold twinned Pd2NiAg NCs exhibit an unusual valence electron density. The maximum catalytic activity originates from the increased availability of surface Ni sites in five-fold twinned Pd2NiAg NCs and the features of twinned structural defects. This study provides an explanation of the enhanced ORR from the special structure of this novel material, which opens up new avenues for the design of novel classes of electrocatalysts for fuel cells and metal-air batteries. PMID:25626352

  11. Improving surface coal refuse disposal site inspections

    SciTech Connect

    Meister, R.A.; Hoffman, R.L.

    1980-06-01

    The study on improving surface coal refuse disposal site inspections included surface inspections of 15 refuse disposal sites. Monthly aerial photos were taken of the sites and computer methods were used to determine elevation changes. Photogrammetric techniques that were used are described in detail. A comparison of the results of each of these inspection techniques is included. A detailed evaluation of the photogrammetric techniques was made and conclusions were drawn concerning the advantages and disadvantages of using aerial photography and photogrammetry as part of the inspection procedure. Operators' opinions of the aerial photography methods are included.

  12. Site-directed immobilization of antibody using EDC-NHS-activated protein A on a bimetallic-based surface plasmon resonance chip

    NASA Astrophysics Data System (ADS)

    Sohn, Young-Soo; Lee, Yeon Kyung

    2014-05-01

    The characteristics of a waveguide-coupled bimetallic surface plasmon resonance (WcBiM SPR) sensor using (3-dimethylaminopropyl)-3-ethylcarbodiimide(EDC)-N-hydroxysuccinimide(NHS)-activated protein A was investigated, and the detection of IgG using the EDC-NHS-activated protein A was studied in comparison with protein A and a self-assembled monolayer (SAM). The WcBiM sensor, which has a narrower full width at half maximum (FWHM) and a steeper slope, was selected since it leads to a larger change in the reflectance in the intensity detection mode. A preparation of the EDC-NHS-activated protein A for site-directed immobilization of antibodies was relative easily compared to the engineered protein G and A. In antigen-antibody interactions, the response to IgG at the concentrations of 50, 100, and 150 ng/ml was investigated. The results showed that the sensitivity of the WcBiM sensor using the EDC-NHS-activated protein A, protein A, and SAM was 0.0185 [%/(ng/ml)], 0.0065 [%/(ng/ml)], and 0.0101 [%/(ng/ml)], respectively. The lowest detectable concentrations of IgG with the EDC-NHS-activated protein A, protein A, and SAM were 4.27, 12.83, and 8.24 ng/ml, respectively. Therefore, the increased sensitivity and lower detection capability of the WcBiM SPR chip with the EDC-NHS-activated protein A suggests that it could be used in early diagnosis where the trace level concentrations of biomolecules should be detected.

  13. Active frequency selective surfaces

    NASA Astrophysics Data System (ADS)

    Buchwald, Walter R.; Hendrickson, Joshua; Cleary, Justin W.; Guo, Junpeng

    2013-05-01

    Split ring resonator arrays are investigated for use as active elements for the realization of voltage controllable frequency selective surfaces. Finite difference time domain simulations suggest the absorptive and reflective properties of such surfaces can be externally controlled through modifications of the split ring resonator gap impedance. In this work, such voltage-controlled resonance tuning is obtained through the addition of an appropriately designed high electron mobility transistor positioned across the split ring resonator gap. It is shown that a 0.5μm gate length high electron mobility transistor allows voltage controllable switching between the two resonant conditions associated with a split ring resonator and that of a closed loop geometry when the surface is illuminated with THz radiation. Partial switching between these two resonant conditions is observed at larger gate lengths. Such active frequency selective surfaces are proposed, for example, for use as modulators in THz detection schemes and as RF filters in radar applications when scaled to operate at GHz frequencies.

  14. Salt site performance assessment activities

    SciTech Connect

    Kircher, J.F.; Gupta, S.K.

    1983-01-01

    During this year the first selection of the tools (codes) for performance assessments of potential salt sites have been tentatively selected and documented; the emphasis has shifted from code development to applications. During this period prior to detailed characterization of a salt site, the focus is on bounding calculations, sensitivity and with the data available. The development and application of improved methods for sensitivity and uncertainty analysis is a focus for the coming years activities and the subject of a following paper in these proceedings. Although the assessments to date are preliminary and based on admittedly scant data, the results indicate that suitable salt sites can be identified and repository subsystems designed which will meet the established criteria for protecting the health and safety of the public. 36 references, 5 figures, 2 tables.

  15. Microstructure of surface cerium hydride growth sites

    SciTech Connect

    Brierley, Martin; Knowles, John; Montgomery, Neil; Preuss, Michael

    2014-05-15

    Samples of cerium were exposed to hydrogen under controlled conditions causing cerium hydride sites to nucleate and grow on the surface. The hydriding rate was measured in situ, and the hydrides were characterised using secondary ion mass spectrometry, scanning electron microscopy, and optical microscopy. The results show that the hydriding rate proceeded more quickly than earlier studies. Characterisation confirmed that the hydrogen is confined to the sites. The morphology of the hydrides was confirmed to be oblate, and stressed material was observed surrounding the hydride, in a number of cases lathlike features were observed surrounding the hydride sites laterally with cracking in the surface oxide above them. It is proposed that during growth the increased lattice parameter of the CeH{sub 2} induces a lateral compressive stress around the hydride, which relieves by the ca. 16% volume collapse of the γ-Ce to α-Ce pressure induced phase transition. Cracking of the surface oxide above the laths reduces the diffusion barrier to hydrogen reaching the metal/oxide interface surrounding the hydride site and contributes to the anisotropic growth of the hydrides.

  16. Repository surface design site layout analysis

    SciTech Connect

    Montalvo, H.R.

    1998-02-27

    The purpose of this analysis is to establish the arrangement of the Yucca Mountain Repository surface facilities and features near the North Portal. The analysis updates and expands the North Portal area site layout concept presented in the ACD, including changes to reflect the resizing of the Waste Handling Building (WHB), Waste Treatment Building (WTB), Carrier Preparation Building (CPB), and site parking areas; the addition of the Carrier Washdown Buildings (CWBs); the elimination of the Cask Maintenance Facility (CMF); and the development of a concept for site grading and flood control. The analysis also establishes the layout of the surface features (e.g., roads and utilities) that connect all the repository surface areas (North Portal Operations Area, South Portal Development Operations Area, Emplacement Shaft Surface Operations Area, and Development Shaft Surface Operations Area) and locates an area for a potential lag storage facility. Details of South Portal and shaft layouts will be covered in separate design analyses. The objective of this analysis is to provide a suitable level of design for the Viability Assessment (VA). The analysis was revised to incorporate additional material developed since the issuance of Revision 01. This material includes safeguards and security input, utility system input (size and location of fire water tanks and pump houses, potable water and sanitary sewage rates, size of wastewater evaporation pond, size and location of the utility building, size of the bulk fuel storage tank, and size and location of other exterior process equipment), main electrical substation information, redundancy of water supply and storage for the fire support system, and additional information on the storm water retention pond.

  17. Surface Sites in Cu-Nanoparticles: Chemical Reactivity or Microscopy?

    PubMed

    Larmier, Kim; Tada, Shohei; Comas-Vives, Aleix; Copéret, Christophe

    2016-08-18

    Copper nanoparticles are widely used in catalysis and electrocatalysis, and the fundamental understanding of their activity requires reliable methods to assess the number of potentially reactive atoms exposed on the surface. Herein, we provide a molecular understanding of the difference observed in addressing surface site titration using prototypical methods: transmission electron micrscopy (TEM), H2 chemisorption, and N2O titration by a combination of experimental and theoretical study. We show in particular that microscopy does not allow assessing the amount of reactive surface sites, while H2 and N2O chemisorptions can, albeit with slightly different stoichiometries (1 O/2CuS and 1 H2/2.2CuS), which can be rationalized by density functional theory calculations. High-resolution TEM shows that the origin of the observed difference between microscopy and titration methods is due to the strong metal support interaction experienced by small copper nanoparticles with the silica surface. PMID:27490121

  18. Effects of surface hydrophobicity on the catalytic iron ion retention in the active site of two catechol 1,2-dioxygenase isoenzymes.

    PubMed

    Di Nardo, Giovanna; Pessione, Enrica; Cavaletto, Maria; Anfossi, Laura; Vanni, Adriano; Briganti, Fabrizio; Giunta, Carlo

    2004-12-01

    The different behaviour of two isozymes (IsoA and IsoB) of catechol 1,2-dioxygenase (C 1,20) from Acinetobacter radioresistens S13 on a hydrophobic interaction, Phenyl-Sepharose chromatographic column, prompted us to investigate the role of superficial hydrophobicity on structural-functional aspects for such class of enzymes. The interaction of 8-anilino-1-naphtalenesulphonate (ANS), a fluorescent probe known to bind to hydrophobic sites in proteins, revealed that the two isoenzymes have a markedly different hydrophobicity degree although a similar number of hydrophobic superficial sites were estimated (2.65 for IsoA and 2.18 for IsoB). ANS is easily displaced by adding the substrates catechol or 3-methylcatechol to the adduct, suggesting that the binding sites are in the near surroundings of the catalytic clefts. The analysis of the hydropathy profiles and the possible superficial cavities allowed to recognize the most feasible region for ANS binding. The lower hydrophobicity detected in the near surroundings of the catalytic pocket of IsoB supports its peculiarity to lose the catalytic metal ions more easily than IsoA. As previously suggested for other metalloenzymes, the presence of more hydrophilic and/or smaller residues near to the active site of IsoB is expected to increase the metal ligands mobility thus increasing the metal ion dissociation rate constants, estimated to be 0.078 h(-1) and 0.670 h(-1) for IsoA and IsoB respectively.

  19. Processes Impacting Atmosphere-Surface Exchanges at Arctic Terrestrial Sites

    NASA Astrophysics Data System (ADS)

    Persson, Ola; Grachev, Andrey; Konopleva, Elena; Cox, Chris; Stone, Robert; Crepinsek, Sara; Shupe, Matthew; Uttal, Taneil

    2015-04-01

    Surface energy fluxes are key to the annual cycle of near-surface and soil temperature and biologic activity in the Arctic. While these energy fluxes are undoubtedly changing to produce the changes observed in the Arctic ecosystem over the last few decades, measurements have generally not been available to quantify what processes are regulating these fluxes and what is determining the characteristics of these annual cycles. The U.S. National Oceanic and Atmospheric Administration has established, or contributed to the establishment of, several terrestrial "supersites" around the perimeter of the Arctic Ocean at which detailed measurements of atmospheric structure, surface fluxes, and soil thermal properties are being made. These sites include Barrow, Alaska; Eureka and Alert, Canada; and Tiksi, Russia. Atmospheric structure measurements vary, but include radiosoundings at all sites and remote sensing of clouds at two sites. Additionally, fluxes of sensible heat and momentum are made at all of the sites, while fluxes of moisture and CO2 are made at two of the sites. Soil temperatures are also measured in the upper 120 cm at all sites, which is deep enough to define the soil active layer. The sites have been operating between 3 years (Tiksi) and 24 years (Barrow). While all sites are located north of 71° N, the summer vegetation range from lush tundra grasses to rocky soils with little vegetation. This presentation will illustrate some of the atmospheric processes that are key for determining the annual energy and temperature cycles at these sites, and some of the key characteristics that lead to differences in, for instance, the length of the summer soil active layer between the sites. Atmospheric features and processes such as cloud characteristics, snowfall, downslope wind events, and sea-breezes have impacts on the annual energy cycle. The presence of a "zero curtain" period, when autumn surface temperature remains approximately constant at the freezing point

  20. Site Characterization of Marine Clay Deposits in South Seberang Prai, Penang using Combined Active and Passive Multichannel Analysis of Surface Wave (MASW)

    NASA Astrophysics Data System (ADS)

    Ariffin, J.; Ismail, M. A. M.; Tan, C. G.; Murtadza, N. M.

    2016-07-01

    The multichannel analysis of surface wave (MASW) has drawn considerable interest in subsoil investigation and characterization. This method has been studied and improved in the last few decades, thereby leading to several combinations of existing active and passive methods. This study aims to identify the presence of marine clay layer using combined active and passive MASW methods. The shear wave velocity profile obtained interpreting clay layer within the range of 70-150 m/s and sand layer within the range of 100-300 m/s. Results suggest that the combined MASW method significantly improves shear wave velocity profiling in shallow and deep soil layers and the results are validated using the cone resistance and shear wave velocity estimated from cone penetration test.Introduction

  1. ColiSense, today's sample today: A rapid on-site detection of β-D-Glucuronidase activity in surface water as a surrogate for E. coli.

    PubMed

    Heery, Brendan; Briciu-Burghina, Ciprian; Zhang, Dian; Duffy, Gillian; Brabazon, Dermot; O'Connor, Noel; Regan, Fiona

    2016-01-01

    A sensitive field-portable fluorimeter with incubating capability and triplicate sample chambers was designed and built. The system was optimised for the on-site analysis of E. coli in recreational waters using fluorescent based enzyme assays. The target analyte was β-D-Glucuronidase (GUS) which hydrolyses a synthetic substrate 6-Chloro-4-Methyl-Umbelliferyl-β-D-Glucuronide (6-CMUG) to release the fluorescent molecule 6-Chloro-4-Methyl-Umbelliferyl (6-CMU). The system was calibrated with 6-CMU standards. A LOD of 5 nM and a resolution of less than 1 nM was determined while enzyme kinetic tests showed detection of activities below 1 pmol min(-1) mL(-1) of sample. A field portable sample preparation, enzyme extraction protocol and continuous assay were applied with the system to analyse freshwater and marine samples. Results from a one day field trial are shown which demonstrated the ability of the system to deliver results on-site within a 75 min period.

  2. ColiSense, today's sample today: A rapid on-site detection of β-D-Glucuronidase activity in surface water as a surrogate for E. coli.

    PubMed

    Heery, Brendan; Briciu-Burghina, Ciprian; Zhang, Dian; Duffy, Gillian; Brabazon, Dermot; O'Connor, Noel; Regan, Fiona

    2016-01-01

    A sensitive field-portable fluorimeter with incubating capability and triplicate sample chambers was designed and built. The system was optimised for the on-site analysis of E. coli in recreational waters using fluorescent based enzyme assays. The target analyte was β-D-Glucuronidase (GUS) which hydrolyses a synthetic substrate 6-Chloro-4-Methyl-Umbelliferyl-β-D-Glucuronide (6-CMUG) to release the fluorescent molecule 6-Chloro-4-Methyl-Umbelliferyl (6-CMU). The system was calibrated with 6-CMU standards. A LOD of 5 nM and a resolution of less than 1 nM was determined while enzyme kinetic tests showed detection of activities below 1 pmol min(-1) mL(-1) of sample. A field portable sample preparation, enzyme extraction protocol and continuous assay were applied with the system to analyse freshwater and marine samples. Results from a one day field trial are shown which demonstrated the ability of the system to deliver results on-site within a 75 min period. PMID:26653426

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

    PubMed Central

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

    2015-01-01

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

  4. Europa's Active Surface

    NASA Technical Reports Server (NTRS)

    1996-01-01

    A newly discovered impact crater can be seen just right of the center of this image of Jupiter's moon Europa returned by NASA's Galileo spacecraft camera. The crater is about 30 kilometers (18.5 miles) in diameter. The impact excavated into Europa's icy crust, throwing debris (seen as whitish material) across the surrounding terrain. Also visible is a dark band, named Belus Linea, extending east-west across the image. This type of feature, which scientists call a 'triple band,' is characterized by a bright stripe down the middle. The outer margins of this and other triple bands are diffuse, suggesting that the dark material was put there as a result of possible geyser-like activity which shot gas and rocky debris from Europa's interior. The curving 'X' pattern seen in the lower left corner of the image appears to represent fracturing of the icy crust and infilling by slush which froze in place. The crater is centered at about 2 degrees north latitude by 239 degrees west longitude. The image was taken from a distance of 156,000 kilometers (about 96,300 miles) on June 27, 1996, during Galileo's first orbit around Jupiter. The area shown is 860 by 700 kilometers (530 by 430 miles), or about the size of Oregon and Washington combined. The Galileo mission is managed by NASA's Jet Propulsion Laboratory.

  5. Surface materials of the Viking landing sites

    NASA Technical Reports Server (NTRS)

    Moore, H. J.; Hutton, R. E.; Scott, R. F.; Spitzer, C. R.; Shorthill, R. W.

    1977-01-01

    In the present paper, the soil characteristics at the Viking sites are discussed in terms of bulk density, particle size, angle of internal friction, cohesion, and moisture content. At the Viking Lander-1 site, there is a relatively weak drift material, along with more cohesive materials of a rocky area, and rocks. A variety of materials are present also at the Lander-2 site. Moisture content is low as compared to terrestrial soils. Current estimates of some of the physical properties are tabulated and discussed.

  6. A non-active-site SET domain surface crucial for the interaction of MLL1 and the RbBP5/Ash2L heterodimer within MLL family core complexes.

    PubMed

    Shinsky, Stephen A; Hu, Michael; Vought, Valarie E; Ng, Sarah B; Bamshad, Michael J; Shendure, Jay; Cosgrove, Michael S

    2014-06-12

    The mixed lineage leukemia-1 (MLL1) enzyme is a histone H3 lysine 4 (H3K4) monomethyltransferase and has served as a paradigm for understanding the mechanism of action of the human SET1 family of enzymes that include MLL1-MLL4 and SETd1a,b. Dimethylation of H3K4 requires a sub-complex including WRAD (WDR5, RbBP5, Ash2L, and DPY-30), which binds to each SET1 family member forming a minimal core complex that is required for multiple lysine methylation. We recently demonstrated that WRAD is a novel histone methyltransferase that preferentially catalyzes H3K4 dimethylation in a manner that is dependent on an unknown non-active-site surface from the MLL1 SET domain. Recent genome sequencing studies have identified a number of human disease-associated missense mutations that localize to the SET domains of several MLL family members. In this investigation, we mapped many of these mutations onto the three-dimensional structure of the SET domain and noticed that a subset of MLL2 (KMT2D, ALR, MLL4)-associated Kabuki syndrome missense mutations map to a common solvent-exposed surface that is not expected to alter enzymatic activity. We introduced these mutations into the MLL1 SET domain and observed that all are defective for H3K4 dimethylation by the MLL1 core complex, which is associated with a loss of the ability of MLL1 to interact with WRAD or with the RbBP5/Ash2L heterodimer. Our results suggest that amino acids from this surface, which we term the Kabuki interaction surface or KIS, are required for formation of a second active site within SET1 family core complexes. PMID:24680668

  7. Human Mars Landing Site and Impacts on Mars Surface Operations

    NASA Technical Reports Server (NTRS)

    Bussey, Ben; Hoffman, Stephen J.

    2016-01-01

    NASA has begun a process to identify and discuss candidate locations where humans could land, live and work on the Martian surface. These locations are referred to as Exploration Zones (EZs). Given current mission concepts, an EZ is a collection of Regions of Interest (ROIs) that are located within approximately 100 kilometers of a centralized landing site. ROIs are areas that are relevant for scientific investigation and/or development/maturation of capabilities and resources necessary for a sustainable human presence. The EZ also contains a landing site and a habitation site that will be used by multiple human crews during missions to explore and utilize the ROIs within the EZ. These candidate EZs will be used by NASA as part of a multi-year process of determining where and how humans could explore Mars. In the near term this process includes: (a) identifying locations that would maximize the potential science return from future human exploration missions, (b) identifying locations with the potential for resources required to support humans, (c) developing concepts and engineering systems needed by future human crews to conduct operations within an EZ, and (d) identifying key characteristics of the proposed candidate EZs that cannot be evaluated using existing data sets, thus helping to define precursor measurements needed in advance of human missions. Existing and future robotic spacecraft will be tasked to gather data from specific Mars surface sites within the representative EZs to support these NASA activities. The proposed paper will describe NASA's initial steps for identifying and evaluating candidate EZs and ROIs. This includes plans for the "First Landing Site/Exploration Zone Workshop for Human Missions to the Surface of Mars" to be held in October 2015 at which proposals for EZs and ROIs will be presented and discussed. It will also include a discussion of how these considerations are (or will be) taken into account as future robotic Mars missions are

  8. Catalysis: Elusive active site in focus

    NASA Astrophysics Data System (ADS)

    Labinger, Jay A.

    2016-08-01

    The identification of the active site of an iron-containing catalyst raises hopes of designing practically useful catalysts for the room-temperature conversion of methane to methanol, a potential fuel for vehicles. See Letter p.317

  9. Patterning surface by site selective capture of biopolymer hydrogel beads.

    PubMed

    Guyomard-Lack, Aurélie; Moreau, Céline; Delorme, Nicolas; Marquis, Mélanie; Fang, Aiping; Bardeau, Jean-François; Cathala, Bernard

    2012-06-01

    This communication describes the fabrication of microstructured biopolymer surfaces by the site-selective capture of pectin hydrogel beads. A positively charged surface consisting of poly-L-lysine (PLL) was subjected to site-selective enzymatic degradation using patterned polydimethylsiloxane (PDMS) stamps covalently modified with trypsin, according to the recently described method. The patterned surface was used to capture ionically cross-linked pectin beads. The desired patterning of the hydrogel surfaces was generated by site-selective immobilization of these pectin beads. The ability of the hydrogels to be dried and swollen in water was assessed.

  10. Patterning surface by site selective capture of biopolymer hydrogel beads.

    PubMed

    Guyomard-Lack, Aurélie; Moreau, Céline; Delorme, Nicolas; Marquis, Mélanie; Fang, Aiping; Bardeau, Jean-François; Cathala, Bernard

    2012-06-01

    This communication describes the fabrication of microstructured biopolymer surfaces by the site-selective capture of pectin hydrogel beads. A positively charged surface consisting of poly-L-lysine (PLL) was subjected to site-selective enzymatic degradation using patterned polydimethylsiloxane (PDMS) stamps covalently modified with trypsin, according to the recently described method. The patterned surface was used to capture ionically cross-linked pectin beads. The desired patterning of the hydrogel surfaces was generated by site-selective immobilization of these pectin beads. The ability of the hydrogels to be dried and swollen in water was assessed. PMID:22326339

  11. Activation of Inhibitors by Sortase Triggers Irreversible Modification of the Active Site*S

    PubMed Central

    Maresso, Anthony W.; Wu, Ruiying; Kern, Justin W.; Zhang, Rongguang; Janik, Dorota; Missiakas, Dominique M.; Duban, Mark-Eugene; Joachimiak, Andrzej; Schneewind, Olaf

    2011-01-01

    Sortases anchor surface proteins to the cell wall of Gram-positive pathogens through recognition of specific motif sequences. Loss of sortase leads to large reductions in virulence, which identifies sortase as a target for the development of antibacterials. By screening 135,625 small molecules for inhibition, we report here that aryl (β-amino)ethyl ketones inhibit sortase enzymes from staphylococci and bacilli. Inhibition of sortases occurs through an irreversible, covalent modification of their active site cysteine. Sortases specifically activate this class of molecules via β-elimination, generating a reactive olefin intermediate that covalently modifies the cysteine thiol. Analysis of the three-dimensional structure of Bacillus anthracis sortase B with and without inhibitor provides insights into the mechanism of inhibition and reveals binding pockets that can be exploited for drug discovery. PMID:17545669

  12. The Exploration of Mars: Crew Surface Activities

    NASA Astrophysics Data System (ADS)

    Bhosri, Wisuwat; Cojanis, Philip; Gupta, Madhu; Khopkar, Manasi; Kiely, Aaron; Myers, Michael; Oxnevad, Knut; Sengupta, Anita; Sexton, Adam; Shaw, Don

    1999-01-01

    Surface activities of the first Mars mission crew, as suggested in phase I of the NASA HEDS reference mission, are discussed in this paper. The HEDS reference mission calls for a two phased approach. In phase I, humans supported by robotic systems will explore the Martian surface, collect and analyze geologic, geophysical, and meteorological data, search for potential permanent base sites, and conduct technology verification experiments. In phase II, a Mars base site will be selected, and the building of a permanent human base will be initiated. In this report two complementary architectures are portrayed. First, a permanent base for 3-6 people consisting of an ISRU unit, two nuclear power systems, a green house, and inflatable habitats and laboratories, built inside adobe structures. Second, a reusable, and resupplyable methane propelled very long range type traverse vehicle capable of collecting and analyzing data, and repairing and deploying scientific payloads during its planned 150 days 4800 km traverse. The very long range traverse vehicle will carry smaller rovers, crawlers, blimps, and an air drill capable of quickly reaching depths beyond 100m. The report presents a global vision of human activities on the surface of Mars at a programmatic level. It consists of several vignettes called "concept architectures" We speculate that these activities will facilitate a phase I Mars exploration architecture.

  13. Low dielectric response in enzyme active site

    PubMed Central

    Mertz, Edward L.; Krishtalik, Lev I.

    2000-01-01

    The kinetics of charge transfer depend crucially on the dielectric reorganization of the medium. In enzymatic reactions that involve charge transfer, atomic dielectric response of the active site and of its surroundings determines the efficiency of the protein as a catalyst. We report direct spectroscopic measurements of the reorganization energy associated with the dielectric response in the active site of α-chymotrypsin. A chromophoric inhibitor of the enzyme is used as a spectroscopic probe. We find that water strongly affects the dielectric reorganization in the active site of the enzyme in solution. The reorganization energy of the protein matrix in the vicinity of the active site is similar to that of low-polarity solvents. Surprisingly, water exhibits an anomalously high dielectric response that cannot be described in terms of the dielectric continuum theory. As a result, sequestering the active site from the aqueous environment inside low-dielectric enzyme body dramatically reduces the dielectric reorganization. This reduction is particularly important for controlling the rate of enzymatic reactions. PMID:10681440

  14. GIS Surface Effects Map Archive, Nevada Test Site, Nevada

    SciTech Connect

    Grasso, Dennis N.

    2003-08-28

    The GIS Surface Effects Map Archive contains a comprehensive collection of maps showing the surface effects produced by underground nuclear testing at the Nevada Test Site. From 1951 to 1992, scientists with the U.S. Geological Survey and agencies of the U.S. Department of Energy used field and aerial-photo mapping techniques to painstakingly map such surface effects as collapse sinks, craters, cracks, fractures, faults, and pressure ridges. Shortly after each test, a complex surface effects map was produced. Of the more than 920 underground detonations conducted at the Nevada Test Site, 688 were mapped for surface effects. This archive preserves these original maps in digital format. A Geographic Information System (GIS) was used to digitally reproduce each original, hand-drawn surface effects map and to assemble these maps into the digital data sets of this archive. The archive was designed to allow easy access to the maps, while preserving the original maps for perpetuity. Users can query the detonation sites database; prepare, view, and print individual or composite maps; and perform various types of scientific analysis and management tasks. Spatial analyses and queries can be performed on detonation sites and related surface effects in conjunction with other chronological, geographical, geological, or hydrological information via links to external maps and databases. This browser interface provides information about the archive, the history of surface effects mapping at the Nevada Test Site, the methods used to produce the digital surface effects maps, and links to published reports, data tables, and maps. Location maps show testing areas, operational areas, and detonation sites. Demonstration maps illustrate the methods used to produce the digital surface effects maps and exhibit some of the characteristics and uses for these data. Use the links below to view and print individual surface effects maps, retrieve information about the detonations and types of

  15. Benzene derivatives adsorbed to the Ag(111) surface: Binding sites and electronic structure

    SciTech Connect

    Miller, Daniel P.; Tymińska, Nina; Zurek, Eva; Simpson, Scott

    2015-03-14

    Dispersion corrected Density Functional Theory calculations were employed to study the adsorption of benzenes derivatized with functional groups encompassing a large region of the activated/deactivated spectrum to the Ag(111) surface. Benzenes substituted with weak activating or deactivating groups, such as methyl and fluoro, do not have a strong preference for adsorbing to a particular site on the substrate, with the corrugations in the potential energy surface being similar to those of benzene. Strong activating (N(CH{sub 3}){sub 2}) and deactivating (NO{sub 2}) groups, on the other hand, possess a distinct site preference. The nitrogen in the former prefers to lie above a silver atom (top site), but in the latter a hollow hexagonal-closed-packed (H{sub hcp}) site of the Ag(111) surface is favored instead. Benzenes derivatized with classic activating groups donate electron density from their highest occupied molecular orbital to the surface, and those functionalized with deactivating groups withdraw electron density from the surface into orbitals that are unoccupied in the gas phase. For benzenes functionalized with two substituents, the groups that are strongly activating or deactivating control the site preference and the other groups assume sites that are, to a large degree, dictated by their positions on the benzene ring. The relative stabilities of the ortho, meta, and para positional isomers of disubstituted benzenes can, in some cases, be modified by adsorption to the surface.

  16. Mars Polar Lander Site Surface Details

    NASA Technical Reports Server (NTRS)

    1999-01-01

    This picture is an enlargement of a portion of a MOC image taken in late July 1999, showing the onset of defrosting of the seasonal carbon dioxide frost cap (small, occasionally fan-shaped dark spots seen throughout this image). Two craters are seen in this image, a very rare occurrence on the south polar layered deposits. Shown for comparison at the same scale is a picture of Jack Murphy (now Qualcomm) Stadium in San Diego, California. Clearly visible in the inset is the baseball diamond and pitcher's mound; less clear but certainly visible are a number of automobiles (small light dots) in the parking lot west (to the left) of the stadium. The elevation of the sun in the Mars image is about 10o; the sunlight is coming from the bottom (north) in this image. The shadow of the rims of the craters can be used to determine their depths. The smaller crater in the bottom right corner is about 60 m (197 feet) across and 7 m (23 feet) deep; the large crater just below the inset is 175 m (574 feet) across and 17 m (56 feet) deep. Similar calculations for other features in the images indicate that much of the surface is smooth and flat. Relief is typically much less than 1-2 meters (3-7 feet) in height over areas of 10-15 meters across (33-49 feet).

    Malin Space Science Systems and the California Institute of Technology built the MOC using spare hardware from the Mars Observer mission. MSSS operates the camera from its facilities in San Diego, CA. The Jet Propulsion Laboratory's Mars Surveyor Operations Project operates the Mars Global Surveyor spacecraft with its industrial partner, Lockheed Martin Astronautics, from facilities in Pasadena, CA and Denver, CO.

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

    NASA Astrophysics Data System (ADS)

    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.

  18. Control of Eolian soil erosion from waste site surface barriers

    SciTech Connect

    Ligotke, M.W.

    1994-11-01

    Physical models were tested in a wind tunnel to determine optimum surface-ravel admixtures for protecting silt-loam soil from erosion by, wind and saltating, sand stresses. The tests were performed to support the development of a natural-material surface barrier for and waste sites. Plans call for a 2-m deep silt-loam soil reservoir to retain infiltrating water from rainfall and snowmelt. The objective of the study was to develop a gravel admixture that would produce an erosion-resistant surface layer during, periods of extended dry climatic stress. Thus, tests were performed using simulated surfaces representing dry, unvegetated conditions present just after construction, after a wildfire, or during an extended drought. Surfaces were prepared using silt-loam soil mixed with various grades of sand and Travel. Wind-induced surface shear stresses were controlled over the test surfaces, as were saltating, sand mass flow rates and intensities. Tests were performed at wind speeds that approximated and exceeded local 100-year peak gust intensities. Surface armors produced by pea gravel admixtures were shown to provide the best protection from wind and saltating sand stresses. Compared with unprotected silt-loam surfaces, armored surfaces reduced erosion rates by more than 96%. Based in part on wind tunnel results, a pea gravel admixture of 15% will be added to the top 1 in of soil in a prototype barrier under construction in 1994. Field tests are planned at the prototype site to provide data for comparison with wind tunnel results.

  19. Chemical characterization of the surface sites of coal

    SciTech Connect

    Fowkes, F.M.; Lloyd, T.B.; Cole, D.A.

    1990-08-01

    We propose to do experimental studies in four related areas concerning the acid-base properties of coal surfaces; (1) develop high precision flow microcalorimetric methods for determining the concentrations and strengths of the acidic and basic surface sites of coal powders; (2) develop photo-acoustic FTIR and solid-state NMR spectral shift techniques for determination of the concentrations and strengths of acidic and basic surface sites of coal powders; (3) determine the concentrations and strengths of the acidic and basic surface sites of some of the well-characterized coal samples from Argonne National Labs, comparing the coal samples before and after demineralization treatments with HCl and HF; (4) study the effects of surface acidity and basicity on the coal/water interface, with emphasis on the role of interfacial acid-base interactions in the adsorption of ions, surfactants and coal/water slurry stabilizers. A practical application of the new measurements of the acidity and basicity of surface sites will be to exploit acid-base contributions to preferential wettability for optimizing separation of coal pyrites from the organic components. Work this quarter concentrated on flow microcalorimetry for assessing acidity/basicity of coal powders. 8 refs., 9 figs., 1 tab.

  20. Protein function annotation by local binding site surface similarity.

    PubMed

    Spitzer, Russell; Cleves, Ann E; Varela, Rocco; Jain, Ajay N

    2014-04-01

    Hundreds of protein crystal structures exist for proteins whose function cannot be confidently determined from sequence similarity. Surflex-PSIM, a previously reported surface-based protein similarity algorithm, provides an alternative method for hypothesizing function for such proteins. The method now supports fully automatic binding site detection and is fast enough to screen comprehensive databases of protein binding sites. The binding site detection methodology was validated on apo/holo cognate protein pairs, correctly identifying 91% of ligand binding sites in holo structures and 88% in apo structures where corresponding sites existed. For correctly detected apo binding sites, the cognate holo site was the most similar binding site 87% of the time. PSIM was used to screen a set of proteins that had poorly characterized functions at the time of crystallization, but were later biochemically annotated. Using a fully automated protocol, this set of 8 proteins was screened against ∼60,000 ligand binding sites from the PDB. PSIM correctly identified functional matches that predated query protein biochemical annotation for five out of the eight query proteins. A panel of 12 currently unannotated proteins was also screened, resulting in a large number of statistically significant binding site matches, some of which suggest likely functions for the poorly characterized proteins.

  1. Control of active sites in selective flocculation: I -- Mathematical model

    SciTech Connect

    Behl, S.; Moudgil, B.M.; Prakash, T.S. . Dept. of Materials Science and Engineering)

    1993-12-01

    Heteroflocculation has been determined to be another major reason for loss in selectivity for flocculation process. In a mathematical model developed earlier, conditions for controlling heteroflocculation were discussed. Blocking active sites to control selective adsorption of a flocculant oil a desirable solid surface is discussed. It has been demonstrated that the lower molecular weight fraction of a flocculant which is incapable of flocculating the particles is an efficient site blocking agent. The major application of selective flocculation has been in mineral processing but many potential uses exist in biological and other colloidal systems. These include purification of ceramic powders, separating hazardous solids from chemical waste, and removal of deleterious components from paper pulp.

  2. Active Sites Environmental Monitoring Program: Action levels

    SciTech Connect

    Ashwood, J.S.; Ashwood, T.L.

    1991-10-01

    The Active Sites Environmental Monitoring Program (ASEMP) was established at Oak Ridge National Laboratory to provide for early leak detection and to monitor performance of the active low-level waste disposal facilities in Solid Waste Storage Area (SWSA) 6 and the transuranic waste storage areas in SWSA 5 North. Early leak detection is accomplished by sampling runoff, groundwater, and perched water in burial trenches. Sample results are compared to action levels that represent background contamination by naturally occurring and fallout-derived radionuclides. 15 refs., 3 figs., 12 tabs.

  3. Characterization of active sites in zeolite catalysts

    SciTech Connect

    Eckert, J.; Bug, A.; Nicol, J.M.

    1997-11-01

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). Atomic-level details of the interaction of adsorbed molecules with active sites in catalysts are urgently needed to facilitate development of more effective and/or environmentally benign catalysts. To this end the authors have carried out neutron scattering studies combined with theoretical calculations of the dynamics of small molecules inside the cavities of zeolite catalysts. The authors have developed the use of H{sub 2} as a probe of adsorption sites by observing the hindered rotations of the adsorbed H{sub 2} molecule, and they were able to show that an area near the four-rings is the most likely adsorption site for H{sub 2} in zeolite A while adsorption of H{sub 2} near cations located on six-ring sites decreases in strength as Ni {approximately} Co > Ca > Zn {approximately} Na. Vibrational and rotational motions of ethylene and cyclopropane adsorption complexes were used as a measure for zeolite-adsorbate interactions. Preliminary studies of the binding of water, ammonia, and methylamines were carried out in a number of related guest-host materials.

  4. Binding of oxygen on vacuum fractured pyrite surfaces: Reactivity of iron and sulfur surface sites

    NASA Astrophysics Data System (ADS)

    Berlich, A. G.; Nesbitt, H. W.; Bancroft, G. M.; Szargan, R.

    2013-05-01

    Synchrotron radiation excited photoelectron spectroscopy (SXPS) has been used to study the interaction of oxygen with vacuum fractured pyrite surfaces. Especially valence band spectra obtained with 30 eV photon energy were analyzed to provide a mechanism of the incipient steps of pyrite oxidation. These spectra are far more sensitive to the oxidation than sulfur or iron core level spectra. It is shown that oxygen is adsorbed on Fe(II) surface sites restoring the octahedral coordination of the Fe(II) sites. This process leads to the removal of two surface states in the valence band which are located at the low and high binding energy sides of the outer valence band, respectively. The existence of these surface states which have been proposed by calculations is experimentally proven. Furthermore, it is shown, that the sulfur sites are more reactive than expected. Sulfite like species are already formed after the lowest oxygen exposure of 10 L. This oxidation occurs at sulfur sites neighboring the Fe(II) surface sites. Oxidation of the S2 - surface sites which were considered as the most reactive species in former studies is second. No iron(III) oxides are formed during oxygen exposure, supporting the assumption that water plays an important role in the oxidation mechanism of pyrite surfaces.

  5. Patched bimetallic surfaces are active catalysts for ammonia decomposition

    PubMed Central

    Guo, Wei; Vlachos, Dionisios G.

    2015-01-01

    Ammonia decomposition is often used as an archetypical reaction for predicting new catalytic materials and understanding the very reason of why some reactions are sensitive on material's structure. Core–shell or surface-segregated bimetallic nanoparticles expose outstanding activity for many heterogeneously catalysed reactions but the reasons remain elusive owing to the difficulties in experimentally characterizing active sites. Here by performing multiscale simulations in ammonia decomposition on various nickel loadings on platinum (111), we show that the very high activity of core–shell structures requires patches of the guest metal to create and sustain dual active sites: nickel terraces catalyse N−H bond breaking and nickel edge sites drive atomic nitrogen association. The structure sensitivity on these active catalysts depends profoundly on reaction conditions due to kinetically competing relevant elementary reaction steps. We expose a remarkable difference in active sites between transient and steady-state studies and provide insights into optimal material design. PMID:26443525

  6. Patched bimetallic surfaces are active catalysts for ammonia decomposition

    SciTech Connect

    Guo, Wei; Vlachos, Dionisios G.

    2015-10-07

    In this study, ammonia decomposition is often used as an archetypical reaction for predicting new catalytic materials and understanding the very reason of why some reactions are sensitive on material’s structure. Core–shell or surface-segregated bimetallic nanoparticles expose outstanding activity for many heterogeneously catalysed reactions but the reasons remain elusive owing to the difficulties in experimentally characterizing active sites. Here by performing multiscale simulations in ammonia decomposition on various nickel loadings on platinum (111), we show that the very high activity of core–shell structures requires patches of the guest metal to create and sustain dual active sites: nickel terraces catalyse N-H bond breaking and nickel edge sites drive atomic nitrogen association. The structure sensitivity on these active catalysts depends profoundly on reaction conditions due to kinetically competing relevant elementary reaction steps. We expose a remarkable difference in active sites between transient and steady-state studies and provide insights into optimal material design.

  7. Patched bimetallic surfaces are active catalysts for ammonia decomposition.

    PubMed

    Guo, Wei; Vlachos, Dionisios G

    2015-10-07

    Ammonia decomposition is often used as an archetypical reaction for predicting new catalytic materials and understanding the very reason of why some reactions are sensitive on material's structure. Core-shell or surface-segregated bimetallic nanoparticles expose outstanding activity for many heterogeneously catalysed reactions but the reasons remain elusive owing to the difficulties in experimentally characterizing active sites. Here by performing multiscale simulations in ammonia decomposition on various nickel loadings on platinum (111), we show that the very high activity of core-shell structures requires patches of the guest metal to create and sustain dual active sites: nickel terraces catalyse N-H bond breaking and nickel edge sites drive atomic nitrogen association. The structure sensitivity on these active catalysts depends profoundly on reaction conditions due to kinetically competing relevant elementary reaction steps. We expose a remarkable difference in active sites between transient and steady-state studies and provide insights into optimal material design.

  8. Electrophilic surface sites as precondition for the chemisorption of pyrrole on GaAs(001) surfaces

    SciTech Connect

    Bruhn, Thomas; Fimland, Bjørn-Ove; Vogt, Patrick

    2015-03-14

    We report how the presence of electrophilic surface sites influences the adsorption mechanism of pyrrole on GaAs(001) surfaces. For this purpose, we have investigated the adsorption behavior of pyrrole on different GaAs(001) reconstructions with different stoichiometries and thus different surface chemistries. The interfaces were characterized by x-ray photoelectron spectroscopy, scanning tunneling microscopy, and by reflectance anisotropy spectroscopy in a spectral range between 1.5 and 5 eV. On the As-rich c(4 × 4) reconstruction that exhibits only nucleophilic surface sites, pyrrole was found to physisorb on the surface without any significant modification of the structural and electronic properties of the surface. On the Ga-rich GaAs(001)-(4 × 2)/(6 × 6) reconstructions which exhibit nucleophilic as well as electrophilic surface sites, pyrrole was found to form stable covalent bonds mainly to the electrophilic (charge deficient) Ga atoms of the surface. These results clearly demonstrate that the existence of electrophilic surface sites is a crucial precondition for the chemisorption of pyrrole on GaAs(001) surfaces.

  9. Surface optimization technique for MammoSite breast brachytherapy applicator

    SciTech Connect

    Kirk, Michael . E-mail: Michael_C_Kirk@rush.edu; Hsi, W.C.; Dickler, Adam; Chu, James; Dowlatshahi, Kambiz; Francescatti, Darius; Nguyen, Cam

    2005-06-01

    Purpose: We present a technique to optimize the dwell times and positions of a high-dose-rate {sup 192}Ir source using the MammoSite breast brachytherapy applicator. The surface optimization method used multiple dwell positions and optimization points to conform the 100% isodose line to the surface of the planning target volume (PTV). Methods and materials: The study population consisted of 20 patients treated using the MammoSite device between October 2002 and February 2004. Treatment was delivered in 10 fractions of 3.4 Gy/fraction, twice daily, with a minimum of 6 h between fractions. The treatment of each patient was planned using three optimization techniques. The dosimetric characteristics of the single-point, six-point, and surface optimization techniques were compared. Results: The surface optimization technique increased the PTV coverage compared with the single- and six-point methods (mean percentage of PTV receiving 100% of the prescription dose was 94%, 85%, and 91%, respectively). The surface method, single-point, and six-point method had a mean dose homogeneity index of 0.62, 0.68, and 0.63 and a mean full width at half maximum value of 189, 190, and 192 cGy/fraction, respectively. Conclusion: The surface technique provided greater coverage of the PTV than did the single- and six-point methods. Using the FWHM method, the surface, single-, and six-point techniques resulted in equivalent dose homogeneity.

  10. Surface Landing Site Weather Analysis for NASA's Constellation Program

    NASA Technical Reports Server (NTRS)

    Altino, Karen M.; Burns, K. L.

    2008-01-01

    Weather information is an important asset for NASA's Constellation Program in developing the next generation space transportation system to fly to the International Space Station, the Moon and, eventually, to Mars. Weather conditions can affect vehicle safety and performance during multiple mission phases ranging from pre-launch ground processing of the Ares vehicles to landing and recovery operations, including all potential abort scenarios. Meteorological analysis is art important contributor, not only to the development and verification of system design requirements but also to mission planning and active ground operations. Of particular interest are the surface weather conditions at both nominal and abort landing sites for the manned Orion capsule. Weather parameters such as wind, rain, and fog all play critical roles in the safe landing of the vehicle and subsequent crew and vehicle recovery. The Marshall Space Flight Center (MSFC) Natural Environments Branch has been tasked by the Constellation Program with defining the natural environments at potential landing zones. This paper wiI1 describe the methodology used for data collection and quality control, detail the types of analyses performed, and provide a sample of the results that cab be obtained.

  11. Chemical characterization of the surface sites of coal

    SciTech Connect

    Fowkes, F.M.; Kardos, K.; Riddle, F.L. Jr.; Cole, D.A.

    1990-08-01

    We propose to do experimental studies in four related areas concerning the acid-base properties of coal surfaces: (1) develop high precision flow microcalorimetric methods for determining the concentrations and strengths of the acidic and basic surface sites of coal powders: (2) develop photo-acoustic FTIR and solid-state NMR spectral shift techniques for determination of the concentrations and strengths of acidic and basic surface sites of coal powders; (3) determine the concentrations and strengths of the acidic and basic surface sites of some of the well-characterized coal samples from Argonne National Labs., comparing the coal samples before and after demineralization treatments with HCl and HF; (4) study the effects of surface acidity and basicity on the coal/water interface, with emphasis on the role of interfacial acid-base interactions in the adsorption of ions, surfactants and coal/water slurry stabilizers. From measured heats of interaction, a reasonable estimate can be made of the most prevalent functional groups in coal. This quarter, heats of adsorption of phenols and pyridines were investigated. 2 tabs. (CBS)

  12. Site-directed, on-surface assembly of DNA nanostructures.

    PubMed

    Meyer, Rebecca; Saccà, Barbara; Niemeyer, Christof M

    2015-10-01

    Two-dimensional DNA lattices have been assembled from DNA double-crossover (DX) motifs on DNA-encoded surfaces in a site-specific manner. The lattices contained two types of single-stranded protruding arms pointing into opposite directions of the plane. One type of these protruding arms served to anchor the DNA lattice on the solid support through specific hybridization with surface-bound, complementary capture oligomers. The other type of arms allowed for further attachment of DNA-tethered probe molecules on the opposite side of the lattices exposed to the solution. Site-specific lattice assembly and attachment of fluorophore-labeled oligonucleotides and DNA-protein conjugates was demonstrated using DNA microarrays on flat, transparent mica substrates. Owing to their programmable orientation and addressability over a broad dynamic range from the nanometer to the millimeter length scale, such supramolecular architecture might be used for presenting biomolecules on surfaces, for instance, in biosensor applications. PMID:26306556

  13. Ozone measurements from a global network of surface sites

    NASA Technical Reports Server (NTRS)

    Oltmans, Samuel J.; Levy, Hiram, II

    1994-01-01

    From a network of surface ozone monitoring sites distributed primarily over the Atlantic and Pacific Oceans, the seasonal, day-to-day, and diurnal patterns are delineated. At most of the NH (Northern Hemisphere) sites there is a spring maximum and late summer or autumn minimum. At Barrow, AK (70 deg N) and Barbados (14 deg N), however, there is a winter maximum, but the mechanisms producing the maximum are quite different. All the sites in the SH (Southern Hemisphere) show winter maxima and summer minima. At the subtropical and tropical sites, there are large day-to-day variations that reflect the changes in flow patterns. Air of tropical origin has much lower ozone concentrations than air from higher latitudes. At the two tropical sites (Barbados and Samoa), there is a marked diurnal ozone variation with highest amounts in the early morning and lowest values in the afternoon. At four of the locations (Barrow, AK; Mauna Loa, HI; American Samoa; and South Pole), there are 15- through 20-year records which allow us to look at longer term changes. At Barrow there has been a large summer increase over the 20 years of measurements. At South Pole, on the other hand, summer decreases have led to an overall decline in surface ozone amounts.

  14. Identification of a new hormone-binding site on the surface of thyroid hormone receptor.

    PubMed

    Souza, P C T; Puhl, A C; Martínez, L; Aparício, R; Nascimento, A S; Figueira, A C M; Nguyen, P; Webb, P; Skaf, M S; Polikarpov, I

    2014-04-01

    Thyroid hormone receptors (TRs) are members of the nuclear receptor superfamily of ligand-activated transcription factors involved in cell differentiation, growth, and homeostasis. Although X-ray structures of many nuclear receptor ligand-binding domains (LBDs) reveal that the ligand binds within the hydrophobic core of the ligand-binding pocket, a few studies suggest the possibility of ligands binding to other sites. Here, we report a new x-ray crystallographic structure of TR-LBD that shows a second binding site for T3 and T4 located between H9, H10, and H11 of the TRα LBD surface. Statistical multiple sequence analysis, site-directed mutagenesis, and cell transactivation assays indicate that residues of the second binding site could be important for the TR function. We also conducted molecular dynamics simulations to investigate ligand mobility and ligand-protein interaction for T3 and T4 bound to this new TR surface-binding site. Extensive molecular dynamics simulations designed to compute ligand-protein dissociation constant indicate that the binding affinities to this surface site are of the order of the plasma and intracellular concentrations of the thyroid hormones, suggesting that ligands may bind to this new binding site under physiological conditions. Therefore, the second binding site could be useful as a new target site for drug design and could modulate selectively TR functions.

  15. Active site of ribulosebisphosphate carboxylase/oxygenase

    SciTech Connect

    Hartman, F.C.; Stringer, C.D.; Milanez, S.; Lee, E.H.

    1985-01-01

    Previous affinity labeling studies and comparative sequence analyses have identified two different lysines at the active site of ribulosebisphosphate carboxylase/oxygenase and have suggested their essentiality to function. The essential lysines occupy positions 166 and 329 in the Rhodospirillum rubrum enzyme and positions 175 and 334 in the spinach enzyme. Based on the pH-dependencies of inactivations of the two enzymes by trinitrobenzene sulfonate, Lys-166 (R. rubrum enzyme) exhibits a pK/sub a/ of 7.9 and Lys-334 (spinach enzyme) exhibits a pK/sub a/ of 9.0. These low pK/sub a/ values as well as the enhanced nucleophilicities of the lysyl residues argue that both are important to catalysis rather than to substrate binding. Lys-166 may correspond to the essential base that initiates catalysis and that displays a pK/sub a/ of 7.5 in the pH-curve for V/sub max//K/sub m/. Cross-linking experiments with 4,4'-diisothiocyano-2,2'-disulfonate stilbene demonstrate that the two active-site lysines are within 12 A. 50 refs., 7 figs., 1 tab.

  16. Active Sites Environmental Monitoring Program: Program plan

    SciTech Connect

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

    1992-02-01

    The Active Sites Environmental Monitoring Program (ASEMP), initiated in 1989, provides early detection and performance monitoring of transuranic (TRU) waste and active low-level waste (LLW) facilities at Oak Ridge National Laboratory (ORNL) in accordance with US Department of Energy (DOE) Order 5820.2A. Active LLW facilities in Solid Waste Storage Area (SWSA) 6 include Tumulus I and Tumulus II, the Interim Waste Management Facility (IWMF), LLW silos, high-range wells, asbestos silos, and fissile wells. The tumulus pads and IWMF are aboveground, high-strength concrete pads on which concrete vaults containing metal boxes of LLW are placed; the void space between the boxes and vaults is filled with grout. Eventually, these pads and vaults will be covered by an engineered multilayered cap. All other LLW facilities in SWSA 6 are below ground. In addition, this plan includes monitoring of the Hillcut Disposal Test Facility (HDTF) in SWSA 6, even though this facility was completed prior to the data of the DOE order. In SWSA 5 North, the TRU facilities include below-grade engineered caves, high-range wells, and unlined trenches. All samples from SWSA 6 are screened for alpha and beta activity, counted for gamma-emitting isotopes, and analyzed for tritium. In addition to these analytes, samples from SWSA 5 North are analyzed for specific transuranic elements.

  17. Site-specific retention of colloids at rough rock surfaces.

    PubMed

    Darbha, Gopala Krishna; Fischer, Cornelius; Luetzenkirchen, Johannes; Schäfer, Thorsten

    2012-09-01

    The spatial deposition of polystyrene latex colloids (d = 1 μm) at rough mineral and rock surfaces was investigated quantitatively as a function of Eu(III) concentration. Granodiorite samples from Grimsel test site (GTS), Switzerland, were used as collector surfaces for sorption experiments. At a scan area of 300 × 300 μm(2), the surface roughness (rms roughness, Rq) range was 100-2000 nm, including roughness contribution from asperities of several tens of nanometers in height to the sample topography. Although, an increase in both roughness and [Eu(III)] resulted in enhanced colloid deposition on granodiorite surfaces, surface roughness governs colloid deposition mainly at low Eu(III) concentrations (≤5 × 10(-7) M). Highest deposition efficiency on granodiorite has been found at walls of intergranular pores at surface sections with roughness Rq = 500-2000 nm. An about 2 orders of magnitude lower colloid deposition has been observed at granodiorite sections with low surface roughness (Rq < 500 nm), such as large and smooth feldspar or quartz crystal surface sections as well as intragranular pores. The site-specific deposition of colloids at intergranular pores is induced by small scale protrusions (mean height = 0.5 ± 0.3 μm). These protrusions diminish locally the overall DLVO interaction energy at the interface. The protrusions prevent further rolling over the surface by increasing the hydrodynamic drag required for detachment. Moreover, colloid sorption is favored at surface sections with high density of small protrusions (density (D) = 2.6 ± 0.55 μm(-1), asperity diameter (φ) = 0.6 ± 0.2 μm, height (h) = 0.4 ± 0.1 μm) in contrast to surface sections with larger asperities and lower asperity density (D = 1.2 ± 0.6 μm(-1), φ = 1.4 ± 0.4 μm, h = 0.6 ± 0.2 μm). The study elucidates the importance to include surface roughness parameters into predictive colloid-borne contaminant migration calculations.

  18. Site-specific retention of colloids at rough rock surfaces.

    PubMed

    Darbha, Gopala Krishna; Fischer, Cornelius; Luetzenkirchen, Johannes; Schäfer, Thorsten

    2012-09-01

    The spatial deposition of polystyrene latex colloids (d = 1 μm) at rough mineral and rock surfaces was investigated quantitatively as a function of Eu(III) concentration. Granodiorite samples from Grimsel test site (GTS), Switzerland, were used as collector surfaces for sorption experiments. At a scan area of 300 × 300 μm(2), the surface roughness (rms roughness, Rq) range was 100-2000 nm, including roughness contribution from asperities of several tens of nanometers in height to the sample topography. Although, an increase in both roughness and [Eu(III)] resulted in enhanced colloid deposition on granodiorite surfaces, surface roughness governs colloid deposition mainly at low Eu(III) concentrations (≤5 × 10(-7) M). Highest deposition efficiency on granodiorite has been found at walls of intergranular pores at surface sections with roughness Rq = 500-2000 nm. An about 2 orders of magnitude lower colloid deposition has been observed at granodiorite sections with low surface roughness (Rq < 500 nm), such as large and smooth feldspar or quartz crystal surface sections as well as intragranular pores. The site-specific deposition of colloids at intergranular pores is induced by small scale protrusions (mean height = 0.5 ± 0.3 μm). These protrusions diminish locally the overall DLVO interaction energy at the interface. The protrusions prevent further rolling over the surface by increasing the hydrodynamic drag required for detachment. Moreover, colloid sorption is favored at surface sections with high density of small protrusions (density (D) = 2.6 ± 0.55 μm(-1), asperity diameter (φ) = 0.6 ± 0.2 μm, height (h) = 0.4 ± 0.1 μm) in contrast to surface sections with larger asperities and lower asperity density (D = 1.2 ± 0.6 μm(-1), φ = 1.4 ± 0.4 μm, h = 0.6 ± 0.2 μm). The study elucidates the importance to include surface roughness parameters into predictive colloid-borne contaminant migration calculations. PMID:22861645

  19. Organic solvents identify specific ligand binding sites on protein surfaces.

    PubMed

    Liepinsh, E; Otting, G

    1997-03-01

    Enzymes frequently recognize substrates and pharmaceutical drugs through specific binding interactions in deep pockets on the protein surface. We show how the specificity-determining substrate binding site of hen egg-white lysozyme (HEWL) can be readily identified in aqueous solution by nuclear magnetic resonance spectroscopy using small organic solvent molecules as detection probes. Exchange of magnetization between the 1H nuclei of the protein and the ligands through dipole-dipole interactions is observed which allows the modeling of their position and orientation at the binding site. Combined with site-specific binding constants measured by titration experiments with different organic solvents, the method can provide important information for rational drug design. In addition, the lifetime of nonspecific interactions of HEWL with organic solvents is shown to be in the sub-nanosecond time range. PMID:9062927

  20. FINAL CLOSURE PLAN SURFACE IMPOUNDMENTS CLOSURE, SITE 300

    SciTech Connect

    Lane, J E; Scott, J E; Mathews, S E

    2004-09-29

    Lawrence Livermore National Laboratory of the University of California (LLNL) operates two Class II surface impoundments that store wastewater that is discharged from a number of buildings located on the Site 300 Facility (Site 300). The wastewater is the by-product of explosives processing. Reduction in the volume of water discharged from these buildings over the past several years has significantly reduced the wastewater storage needs. In addition, the impoundments were constructed in 1984, and the high-density polyethylene (HDPE) geomembrane liners are nearing the end of their service life. The purpose of this project is to clean close the surface impoundments and provide new wastewater storage using portable, above ground storage tanks at six locations. The tanks will be installed prior to closure of the impoundments and will include heaters for allowing evaporation during relatively cool weather. Golder Associates (Golder) has prepared this Final Closure Plan (Closure Plan) on behalf of LLNL to address construction associated with the clean closure of the impoundments. This Closure Plan complies with State Water Resources Control Board (SWRCB) Section 21400 of the California Code of Regulations Title 27 (27 CCR {section}21400). As required by these regulations and guidance, this Plan provides the following information: (1) A site characterization, including the site location, history, current operations, and geology and hydrogeology; (2) The regulatory requirements relevant to clean closure of the impoundments; (3) The closure procedures; and, (4) The procedures for validation and documentation of clean closure.

  1. Direct Epoxidation of Propylene over Stabilized Cu+ Surface Sites on Ti Modified Cu2O

    DOE PAGES

    Yang, X.; Kattel, S.; Xiong, K.; Mudiyanselage, K.; Rykov, S.; Senanayake, S. D.; Rodriguez, J. A.; Liu, P.; Stacchiola, D. J.; Chen, J. G.

    2015-07-17

    Direct propylene epoxidation by O2 is a challenging reaction because of the strong tendency for complete combustion. Results from the current study demonstrate the feasibility to tune the epoxidation selectivity by generating highly dispersed and stabilized Cu+ active sites in a TiCuOx mixed oxide. The TiCuOx surface anchors the key surface intermediate, oxametallacycle, leading to higher selectivity for epoxidation of propylene.

  2. Site descriptive modeling as a part of site characterization in Sweden - Concluding the surface based investigations

    SciTech Connect

    Andersson, Johan; Winberg, Anders; Skagius, Kristina; Stroem, Anders; Lindborg, Tobias

    2007-07-01

    The Swedish Nuclear Fuel and Waste Management Co., SKB, is currently finalizing its surface based site investigations for the final repository for spent nuclear fuel in the municipalities of Oestharmnar (the Forsmark area) and Oskarshamn (the Simpevar/Laxemar area). The investigation data are assessed into a Site Descriptive Model, constituting a synthesis of geology, rock mechanics, thermal properties, hydrogeology, hydro-geochemistry, transport properties and a surface system description. Site data constitute a wide range of different measurement results. These data both need to be checked for consistency and to be interpreted into a format more amenable for three-dimensional modeling. The three-dimensional modeling (i.e. estimating the distribution of parameter values in space) is made in a sequence where the geometrical framework is taken from the geological models and in turn used by the rock mechanics, thermal and hydrogeological modeling. These disciplines in turn are partly interrelated, and also provide feedback to the geological modeling, especially if the geological description appears unreasonable when assessed together with the other data. Procedures for assessing the uncertainties and the confidence in the modeling have been developed during the course of the site modeling. These assessments also provide key input to the completion of the site investigation program. (authors)

  3. Human Mars Landing Site and Impacts on Mars Surface Operations

    NASA Technical Reports Server (NTRS)

    Bussey, Ben; Hoffman, Stephen J.

    2016-01-01

    This paper describes NASA's initial steps for identifying and evaluating candidate Exploration Zones (EZs) and Regions of Interests (ROIs) for the first human crews that will explore the surface of Mars. NASA's current effort to define the exploration of this planet by human crews, known as the Evolvable Mars Campaign (EMC), provides the context in which these EZs and ROIs are being considered. The EMC spans all aspects of a human Mars mission including launch from Earth, transit to and from Mars, and operations on the surface of Mars. Studies related to Mars surface operations and related system capabilities have led to the current definition of an EZ as well as ROIs. An EZ is a collection of ROIs that are located within approximately 100 kilometers of a centralized landing site. ROIs are areas that are relevant for scientific investigation and/or development/maturation of capabilities and resources necessary for a sustainable human presence. The EZ also contains one or more landing sites and a habitation site that will be used by multiple human crews during missions to explore and utilize the ROIs within the EZ. With the EMC as a conceptual basis, the EZ model has been refined to a point where specific site selection criteria for scientific exploration and in situ resource utilization can be defined. In 2015 these criteria were distributed to the planetary sciences community and the in situ resource utilization and civil engineering communities as part of a call for EZ proposals. The resulting "First Landing Site/Exploration Zone Workshop for Human Missions to the Surface of Mars" was held in October 2015 during which 47 proposals for EZs and ROIs were presented and discussed. Proposed locations spanned all longitudes and all allowable latitudes (+/- 50 degrees). Proposed justification for selecting one of these EZs also spanned a significant portion of the scientific and resource criteria provided to the community. Workshop results will be used to prepare for

  4. Active Sites Environmental Monitoring Program: FY 1991 report

    SciTech Connect

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

    1992-11-01

    This report summarizes the activities of the Active Sites Environmental Monitoring Program (ASEMP) from April 1991 through September 1991. The ASEMP was established in 1989 by Solid Waste Operations (SWO) and the Environmental Sciences Division, both of Oak Ridge National Laboratory, 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. A new set of action levels was developed on the basis of a statistical analysis of background contamination. These new action levels have been used to evaluate results in this report. Results of ASEMP monitoring continue to demonstrate that no LLW (except [sup 3]H) is being leached from the storage vaults on the tumulus pads. Loading of vaults on Tumulus II, which began in early FY 1991, was >90% complete at the end of September 1991. Results of sampling of groundwater and surface waters is presented.

  5. Surface-material maps of Viking landing sites on Mars

    NASA Technical Reports Server (NTRS)

    Moore, H. J.; Keller, J. M.

    1991-01-01

    Researchers mapped the surface materials at the Viking landing sites on Mars to gain a better understanding of the materials and rock populations at the sites and to provide information for future exploration. The maps extent to about 9 m in front of each lander and are about 15 m wide - an area comparable to the area of a pixel in high resolution Viking Orbiter images. The maps are divided into the near and far fields. Data for the near fields are from 1/10 scale maps, umpublished maps, and lander images. Data for the far fields are from 1/20 scale contour maps, contoured lander camera mosaics, and lander images. Rocks are located on these maps using stereometric measurements and the contour maps. Frequency size distribution of rocks and the responses of soil-like materials to erosion by engine exhausts during landings are discussed.

  6. Surface-material maps of Viking landing sites on Mars

    NASA Astrophysics Data System (ADS)

    Moore, H. J.; Keller, J. M.

    1991-06-01

    Researchers mapped the surface materials at the Viking landing sites on Mars to gain a better understanding of the materials and rock populations at the sites and to provide information for future exploration. The maps extent to about 9 m in front of each lander and are about 15 m wide - an area comparable to the area of a pixel in high resolution Viking Orbiter images. The maps are divided into the near and far fields. Data for the near fields are from 1/10 scale maps, umpublished maps, and lander images. Data for the far fields are from 1/20 scale contour maps, contoured lander camera mosaics, and lander images. Rocks are located on these maps using stereometric measurements and the contour maps. Frequency size distribution of rocks and the responses of soil-like materials to erosion by engine exhausts during landings are discussed.

  7. Titanium surface hydrophilicity enhances platelet activation.

    PubMed

    Alfarsi, Mohammed A; Hamlet, Stephen M; Ivanovski, Saso

    2014-01-01

    Titanium implant surface modification is a key strategy used to enhance osseointegration. Platelets are the first cells that interact with the implant surface whereupon they release a wide array of proteins that influence the subsequent healing process. This study therefore investigated the effect of titanium surface modification on the attachment and activation of human platelets. The surface characteristics of three titanium surfaces: smooth (SMO), micro-rough (SLA) and hydrophilic micro-rough (SLActive) and the subsequent attachment and activation of platelets following exposure to these surfaces were determined. The SLActive surface showed the presence of significant nanoscale topographical features. While attached platelets appeared to be morphologically similar, significantly fewer platelets attached to the SLActive surface compared to both the SMO and SLA surfaces. The SLActive surface however induced the release of the higher levels of chemokines β-thromboglobulin and platelet factor 4 from platelets. This study shows that titanium surface topography and chemistry have a significant effect on platelet activation and chemokine release.

  8. Control of active sites in flocculation: Concept of equivalent active sites''

    SciTech Connect

    Behl, S.; Moudgil, B.M. . Dept. of Materials Science and Engineering)

    1993-12-01

    Flocculation and dispersion of solids are strong functions of the amount and conformation of the adsorbed polymer. Regions of dispersion and flocculation of solids with particular polymer molecules may be deduced from saturation adsorption data. The concept of equivalent active sites'' is proposed to explain flocculation and dispersion behavior irrespective of the amount or conformation of the adsorbed polymer. The concept has been further extended to study the selective flocculation process.

  9. Quantifying the density and utilization of active sites in non-precious metal oxygen electroreduction catalysts

    PubMed Central

    Sahraie, Nastaran Ranjbar; Kramm, Ulrike I.; Steinberg, Julian; Zhang, Yuanjian; Thomas, Arne; Reier, Tobias; Paraknowitsch, Jens-Peter; Strasser, Peter

    2015-01-01

    Carbon materials doped with transition metal and nitrogen are highly active, non-precious metal catalysts for the electrochemical conversion of molecular oxygen in fuel cells, metal air batteries, and electrolytic processes. However, accurate measurement of their intrinsic turn-over frequency and active-site density based on metal centres in bulk and surface has remained difficult to date, which has hampered a more rational catalyst design. Here we report a successful quantification of bulk and surface-based active-site density and associated turn-over frequency values of mono- and bimetallic Fe/N-doped carbons using a combination of chemisorption, desorption and 57Fe Mössbauer spectroscopy techniques. Our general approach yields an experimental descriptor for the intrinsic activity and the active-site utilization, aiding in the catalyst development process and enabling a previously unachieved level of understanding of reactivity trends owing to a deconvolution of site density and intrinsic activity. PMID:26486465

  10. Immobilization of Active Bacteriophages on Polyhydroxyalkanoate Surfaces.

    PubMed

    Wang, Chanchan; Sauvageau, Dominic; Elias, Anastasia

    2016-01-20

    A rapid, efficient technique for the attachment of bacteriophages (phages) onto polyhydroxyalkanoate (PHA) surfaces has been developed and compared to three reported methods for phage immobilization. Polymer surfaces were modified to facilitate phage attachment using (1) plasma treatment alone, (2) plasma treatment followed by activation by 1-ethyl-3-(3-(dimethylamino)propyl)carbodiimide hydrochloride (EDC) and N-hydroxysulfosuccinimide (sulfo-NHS), (3) plasma-initiated acrylic acid grafting, or (4) plasma-initiated acrylic acid grafting with activation by EDC and sulfo-NHS. The impact of each method on the surface chemistry of PHA was investigated using contact angle analysis and X-ray photoelectron spectroscopy. Each of the four treatments was shown to result in both increased hydrophilicity and in the modification of the surface functional groups. Modified surfaces were immersed in suspensions of phage T4 for immobilization. The highest level of phage binding was observed for the surfaces modified by plasma treatment alone. The change in chemical bond states observed for surfaces that underwent plasma treatment is suspected to be the cause of the increased binding of active phages. Plasma-treated surfaces were further analyzed through phage-staining and fluorescence microscopy to assess the surface density of immobilized phages and their capacity to capture hosts. The infective capability of attached phages was confirmed by exposing the phage-immobilized surfaces to the host bacteria Escherichia coli in both plaque and infection dynamic assays. Plasma-treated surfaces with immobilized phages displayed higher infectivity than surfaces treated with other methods; in fact, the equivalent initial multiplicity of infection was 2 orders of magnitude greater than with other methods. Control samples - prepared by immersing polymer surfaces in phage suspensions (without prior plasma treatment) - did not show any bacterial growth inhibition, suggesting they did not bind

  11. Application of Surface-Wave Methods for Seismic Site Characterization

    NASA Astrophysics Data System (ADS)

    Foti, Sebastiano; Parolai, Stefano; Albarello, Dario; Picozzi, Matteo

    2011-11-01

    Surface-wave dispersion analysis is widely used in geophysics to infer a shear wave velocity model of the subsoil for a wide variety of applications. A shear-wave velocity model is obtained from the solution of an inverse problem based on the surface wave dispersive propagation in vertically heterogeneous media. The analysis can be based either on active source measurements or on seismic noise recordings. This paper discusses the most typical choices for collection and interpretation of experimental data, providing a state of the art on the different steps involved in surface wave surveys. In particular, the different strategies for processing experimental data and to solve the inverse problem are presented, along with their advantages and disadvantages. Also, some issues related to the characteristics of passive surface wave data and their use in H/V spectral ratio technique are discussed as additional information to be used independently or in conjunction with dispersion analysis. Finally, some recommendations for the use of surface wave methods are presented, while also outlining future trends in the research of this topic.

  12. Human Mars Landing Site and Impacts on Mars Surface Operations

    NASA Technical Reports Server (NTRS)

    Hoffman, Stephen J.; Bussey, Ben

    2016-01-01

    This paper describes NASA's initial steps for identifying and evaluating candidate Exploration Zones (EZs) and Regions of Interests (ROIs) for the first human crews that will explore the surface of Mars. NASA's current effort to define the exploration of this planet by human crews, known as the Evolvable Mars Campaign (EMC), provides the context in which these EZs and ROIs are being considered. The EMC spans all aspects of a human Mars mission including launch from Earth, transit to and from Mars, and operations on the surface of Mars. An EZ is a collection of ROIs located within approximately 100 kilometers of a centralized landing site. ROIs are areas relevant for scientific investigation and/or development/maturation of capabilities and resources necessary for a sustainable human presence. The EZ also contains one or more landing sites and a habitation site that will be used by multiple human crews during missions to explore and utilize the ROIs within the EZ. With the EMC as a conceptual basis, the EZ model has been refined to a point where specific site selection criteria for scientific exploration and in situ resource utilization can be defined. In 2015 these criteria were distributed to the planetary sciences community and the in situ resource utilization and civil engineering communities as part of a call for EZ proposals. The resulting "First Landing Site/Exploration Zone Workshop for Human Missions to the Surface of Mars" was held in October 2015 during which 47 proposals for EZs and ROIs were presented and discussed. Proposed locations spanned all longitudes and all allowable latitudes (+/- 50 degrees). Proposed justification for selecting one of these EZs also spanned a significant portion of the scientific and resource criteria provided to the community. Several important findings resulted from this Workshop including: (a) a strong consensus that, at a scale of 100 km (radius), multiple places on Mars exist that have both sufficient scientific interest

  13. Electrostatic fields in the active sites of lysozymes.

    PubMed

    Sun, D P; Liao, D I; Remington, S J

    1989-07-01

    Considerable experimental evidence is in support of several aspects of the mechanism that has been proposed for the catalytic activity of lysozyme. However, the enzymatically catalyzed hydrolysis of polysaccharides proceeds over 5 orders of magnitude faster than that of model compounds that mimic the configuration of the substrate in the active site of the enzyme. Although several possible explanations for this rate enhancement have been discussed elsewhere, a definitive mechanism has not emerged. Here we report striking results obtained by classical electrodynamics, which suggest that bond breakage and the consequent separation of charge in lysozyme is promoted by a large electrostatic field across the active site cleft, produced in part by a very asymmetric distribution of charged residues on the enzyme surface. Lysozymes unrelated in amino acid sequence have similar distributions of charged residues and electric fields. The results reported here suggest that the electrostatic component of the rate enhancement is greater than 9 kcal.mol-1. Thus, electrostatic interactions may play a more important role in the enzymatic mechanism than has generally been appreciated.

  14. Surface Plasma Source Electrode Activation by Surface Impurities

    SciTech Connect

    Dudnikov, Vadim; Johnson, Rolland P.; Han, B.; Murray, S. N.; Pennisi, T. R.; Santana, M.; Stockli, Martin P.; Welton, R. F.

    2011-09-26

    In experiments with RF saddle antenna surface plasma sources (SPS), the efficiency of H{sup -} ion generation was increased by up to a factor of 5 by plasma electrode 'activation', without supplying additional Cs, by heating the collar to high temperature for several hours using hot air flow and plasma discharge. Without cracking or heating the cesium ampoule, but likely with Cs recovery from impurities, the achieved energy efficiency was comparable to that of conventionally cesiated SNS RF sources with an external or internal Cs supply. In the experiments, optimum cesiation was produced (without additional Cs) by the collection and trapping of traces of remnant cesium compounds from SPS surfaces. Such activation by accumulation of impurities on electrode surfaces can be a reason for H{sup -} emission enhancement in other so-called 'volume' negative ion sources.

  15. Activity of site-specific endonucleases on complexes of plasmid DNA with multiwalled carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Egorova, V. P.; Krylova, H. V.; Lipnevich, I. V.; Veligura, A. A.; Shulitsky, B. G.; Asayonok, A. A.; Vaskovtsev, E. V.

    2016-08-01

    We have synthesized and investigated structural and functional properties of plasmid DNA complexes with multi-walled carbon nanotubes (MWCNTs) for detection of changes in structural state of the plasmid DNA at its recognition by site-specific endonuclease. It has been also established that the site-specific endonuclease is functionally active on the surface of MWCNTs.

  16. Dissecting the active site of a photoreceptor protein

    NASA Astrophysics Data System (ADS)

    Hoff, Wouter; Hara, Miwa; Ren, Jie; Moghadam, Farzaneh; Xie, Aihua; Kumauchi, Masato

    While enzymes are quite large molecules, functionally important chemical events are often limited to a small region of the protein: the active site. The physical and chemical properties of residues at such active sites are often strongly altered compared to the same groups dissolved in water. Understanding such effects is important for unraveling the mechanisms underlying protein function and for protein engineering, but has proven challenging. Here we report on our ongoing efforts on using photoactive yellow protein (PYP), a bacterial photoreceptor, as a model system for such effects. We will report on the following questions: How many residues affect active site properties? Are these residues in direct physical contact with the active site? Can functionally important residues be recognized in the crystal structure of a protein? What structural resolution is needed to understand active sites? What spectroscopic techniques are most informative? Which weak interactions dominate active site properties?

  17. Photoinduced Charge Transfer from Titania to Surface Doping Site.

    PubMed

    Inerbaev, Talgat; Hoefelmeyer, James D; Kilin, Dmitri S

    2013-05-16

    We evaluate a theoretical model in which Ru is substituting for Ti at the (100) surface of anatase TiO2. Charge transfer from the photo-excited TiO2 substrate to the catalytic site triggers the photo-catalytic event (such as water oxidation or reduction half-reaction). We perform ab-initio computational modeling of the charge transfer dynamics on the interface of TiO2 nanorod and catalytic site. A slab of TiO2 represents a fragment of TiO2 nanorod in the anatase phase. Titanium to ruthenium replacement is performed in a way to match the symmetry of TiO2 substrate. One molecular layer of adsorbed water is taken into consideration to mimic the experimental conditions. It is found that these adsorbed water molecules saturate dangling surface bonds and drastically affect the electronic properties of systems investigated. The modeling is performed by reduced density matrix method in the basis of Kohn-Sham orbitals. A nano-catalyst modeled through replacement defect contributes energy levels near the bottom of the conduction band of TiO2 nano-structure. An exciton in the nano-rod is dissipating due to interaction with lattice vibrations, treated through non-adiabatic coupling. The electron relaxes to conduction band edge and then to the Ru cite with faster rate than hole relaxes to the Ru cite. These results are of the importance for an optimal design of nano-materials for photo-catalytic water splitting and solar energy harvesting. PMID:23795229

  18. Photoinduced Charge Transfer from Titania to Surface Doping Site

    PubMed Central

    Inerbaev, Talgat; Hoefelmeyer, James D.; Kilin, Dmitri S.

    2013-01-01

    We evaluate a theoretical model in which Ru is substituting for Ti at the (100) surface of anatase TiO2. Charge transfer from the photo-excited TiO2 substrate to the catalytic site triggers the photo-catalytic event (such as water oxidation or reduction half-reaction). We perform ab-initio computational modeling of the charge transfer dynamics on the interface of TiO2 nanorod and catalytic site. A slab of TiO2 represents a fragment of TiO2 nanorod in the anatase phase. Titanium to ruthenium replacement is performed in a way to match the symmetry of TiO2 substrate. One molecular layer of adsorbed water is taken into consideration to mimic the experimental conditions. It is found that these adsorbed water molecules saturate dangling surface bonds and drastically affect the electronic properties of systems investigated. The modeling is performed by reduced density matrix method in the basis of Kohn-Sham orbitals. A nano-catalyst modeled through replacement defect contributes energy levels near the bottom of the conduction band of TiO2 nano-structure. An exciton in the nano-rod is dissipating due to interaction with lattice vibrations, treated through non-adiabatic coupling. The electron relaxes to conduction band edge and then to the Ru cite with faster rate than hole relaxes to the Ru cite. These results are of the importance for an optimal design of nano-materials for photo-catalytic water splitting and solar energy harvesting. PMID:23795229

  19. Acidity of edge surface sites of montmorillonite and kaolinite

    NASA Astrophysics Data System (ADS)

    Liu, Xiandong; Lu, Xiancai; Sprik, Michiel; Cheng, Jun; Meijer, Evert Jan; Wang, Rucheng

    2013-09-01

    Acid-base chemistry of clay minerals is central to their interfacial properties, but up to now a quantitative understanding on the surface acidity is still lacking. In this study, with first principles molecular dynamics (FPMD) based vertical energy gap technique, we calculate the acidity constants of surface groups on (0 1 0)-type edges of montmorillonite and kaolinite, which are representatives of 2:1 and 1:1-type clay minerals, respectively. It shows that tbnd Si-OH and tbnd Al-OH2OH groups of kaolinite have pKas of 6.9 and 5.7 and those of montmorillonite have pKas of 7.0 and 8.3, respectively. For each mineral, the calculated pKas are consistent with the experimental ranges derived from fittings of titration curves, indicating that tbnd Si-OH and tbnd Al-OH2OH groups are the major acidic sites responsible to pH-dependent experimental observations. The effect of Mg substitution in montmorillonite is investigated and it is found that Mg substitution increases the pKas of the neighboring tbnd Si-OH and tbnd Si-OH2 groups by 2-3 pKa units. Furthermore, our calculation shows that the pKa of edge tbnd Mg-(OH2)2 is as high as 13.2, indicating the protonated state dominates under common pH. Together with previous adsorption experiments, our derived acidity constants suggest that tbnd Si-O- and tbnd Al-(OH)2 groups are the most probable edge sites for complexing heavy metal cations.

  20. Mars Surveyor Project Landing Site Activities

    NASA Technical Reports Server (NTRS)

    Gulick, Virginia C.; Briggs, Geoffrey; Saunders, R. Stephen; Gilmore, Martha; Soderblom, Larry

    1999-01-01

    The Mars Surveyor Program --now a cooperative program led by NASA and CNES along with other international partners -- is underway. It has the primary science objective of furthering our understanding of the biological potential and possible biological history of Mars and has the complementary objective of improving our understanding of martian climate evolution and planetary history The missions will develop technology and acquire data necessary for eventual human Exploration. Launches of orbiters, landers and rovers will take place in 2001 and in 2003; in 2005 a complete system will be launched capable of returning samples to Earth by 2008. A key aspect of the program is the selection of landing sites. This abstract 1) reports on the status of the landing site selection process that begins with the 2001 lander mission and 2) outlines be opportunities for the Mars community to provide input into the landing site selection process.

  1. Mars Surveyor Project Landing Site Activities

    NASA Technical Reports Server (NTRS)

    Gulick, V. C.; Briggs, Geoffrey; Saunders, R. Stephen; Gilmore, Martha; Soderblom, Larry

    1999-01-01

    The Mars Surveyor Program -- now a cooperative program led by NASA and CNES along with other international partners -- is underway. It has the primary science objective of furthering our understanding of the biological potential and possible biological history of Mars and has the complementary objective of improving our understanding of martian climate evolution and planetary history. The missions will develop technology and acquire data necessary for eventual human exploration. Launches of orbiters, landers and rovers will take place in 2001 and in 2003; in 2005 a complete system will be launched capable of returning samples to Earth by 2008. A key aspect of the program is the selection of landing sites. This abstract 1) reports on the status of the landing site selection process that begins with the 2001 lander mission and 2) outlines the opportunities for the Mars community to provide input into the landing site selection process.

  2. Surface Plasma Source Electrode Activation by Surface Impurities

    SciTech Connect

    Dudnikov, Vadim; Han, Baoxi; Johnson, Rolland P.; Murray Jr, S N; Pennisi, Terry R; Santana, Manuel; Stockli, Martin P; Welton, Robert F

    2011-01-01

    In experiments with RF saddle antenna surface plasma sources (SPS), the efficiency of H- ion generation was increased by up to a factor of 5 by long time plasma electrode activation, without adding Cs from Cs supply, by heating the collar to high temperature using hot air flow and plasma discharge. Without cracking or heating the cesium ampoule, but likely with Cs recovery from impurities, the achieved energy efficiency was comparable to that of conventionally cesiated SNS RF sources with an external or internal Cs supply. In the experiments, perfect cesiation was produced (without additional Cs supply) by the collection and trapping of traces of remnant cesium compounds from SPS surfaces.

  3. Active micromixer using surface acoustic wave streaming

    SciTech Connect

    Branch; Darren W. , Meyer; Grant D. , Craighead; Harold G.

    2011-05-17

    An active micromixer uses a surface acoustic wave, preferably a Rayleigh wave, propagating on a piezoelectric substrate to induce acoustic streaming in a fluid in a microfluidic channel. The surface acoustic wave can be generated by applying an RF excitation signal to at least one interdigital transducer on the piezoelectric substrate. The active micromixer can rapidly mix quiescent fluids or laminar streams in low Reynolds number flows. The active micromixer has no moving parts (other than the SAW transducer) and is, therefore, more reliable, less damaging to sensitive fluids, and less susceptible to fouling and channel clogging than other types of active and passive micromixers. The active micromixer is adaptable to a wide range of geometries, can be easily fabricated, and can be integrated in a microfluidic system, reducing dead volume. Finally, the active micromixer has on-demand on/off mixing capability and can be operated at low power.

  4. The bifunctional active site of s-adenosylmethionine synthetase. Roles of the active site aspartates.

    PubMed

    Taylor, J C; Markham, G D

    1999-11-12

    S-Adenosylmethionine (AdoMet) synthetase catalyzes the biosynthesis of AdoMet in a unique enzymatic reaction. Initially the sulfur of methionine displaces the intact tripolyphosphate chain (PPP(i)) from ATP, and subsequently PPP(i) is hydrolyzed to PP(i) and P(i) before product release. The crystal structure of Escherichia coli AdoMet synthetase shows that the active site contains four aspartate residues. Aspartate residues Asp-16* and Asp-271 individually provide the sole protein ligand to one of the two required Mg(2+) ions (* denotes a residue from a second subunit); aspartates Asp-118 and Asp-238* are proposed to interact with methionine. Each aspartate has been changed to an uncharged asparagine, and the metal binding residues were also changed to alanine, to assess the roles of charge and ligation ability on catalytic efficiency. The resultant enzyme variants all structurally resemble the wild type enzyme as indicated by circular dichroism spectra and are tetramers. However, all have k(cat) reductions of approximately 10(3)-fold in AdoMet synthesis, whereas the MgATP and methionine K(m) values change by less than 3- and 8-fold, respectively. In the partial reaction of PPP(i) hydrolysis, mutants of the Mg(2+) binding residues have >700-fold reduced catalytic efficiency (k(cat)/K(m)), whereas the D118N and D238*N mutants are impaired less than 35-fold. The catalytic efficiency for PPP(i) hydrolysis by Mg(2+) site mutants is improved by AdoMet, like the wild type enzyme. In contrast AdoMet reduces the catalytic efficiency for PPP(i) hydrolysis by the D118N and D238*N mutants, indicating that the events involved in AdoMet activation are hindered in these methionyl binding site mutants. Ca(2+) uniquely activates the D271A mutant enzyme to 15% of the level of Mg(2+), in contrast to the approximately 1% Ca(2+) activation of the wild type enzyme. This indicates that the Asp-271 side chain size is a discriminator between the activating ability of Ca(2+) and the

  5. Boltzmann active walkers and rough surfaces

    NASA Astrophysics Data System (ADS)

    Pochy, R. D.; Kayser, D. R.; Aberle, L. K.; Lam, L.

    1993-06-01

    An active walker model (AWM) was recently proposed by Freimuth and Lam for the generation of various filamentary patterns. In an AWM, the walker changes the landscape as it walks, and its steps are in turn influenced by the changing landscape. The landscape so obtained is a rough surface. In this paper, the properties of such a rough surface (with average height conserved) generated by a Boltzmann active walker in 1 + 1 dimensions is investigated in detail. The scaling properties of the surface thickness σ T is found to belong to a new class quite different from other types of fractal surfaces. For example, σ T is independent of the system size L, but is a function of the “temperature” T. Soliton propagation is found when T = 0.

  6. Patched bimetallic surfaces are active catalysts for ammonia decomposition

    DOE PAGES

    Guo, Wei; Vlachos, Dionisios G.

    2015-10-07

    In this study, ammonia decomposition is often used as an archetypical reaction for predicting new catalytic materials and understanding the very reason of why some reactions are sensitive on material’s structure. Core–shell or surface-segregated bimetallic nanoparticles expose outstanding activity for many heterogeneously catalysed reactions but the reasons remain elusive owing to the difficulties in experimentally characterizing active sites. Here by performing multiscale simulations in ammonia decomposition on various nickel loadings on platinum (111), we show that the very high activity of core–shell structures requires patches of the guest metal to create and sustain dual active sites: nickel terraces catalyse N-Hmore » bond breaking and nickel edge sites drive atomic nitrogen association. The structure sensitivity on these active catalysts depends profoundly on reaction conditions due to kinetically competing relevant elementary reaction steps. We expose a remarkable difference in active sites between transient and steady-state studies and provide insights into optimal material design.« less

  7. Active Flow Control Stator With Coanda Surface

    NASA Technical Reports Server (NTRS)

    Guendogdu; Vorreiter; Seume

    2010-01-01

    Active Flow Control increases the permissible aerodynamic loading. Curved surface near the trailing edge ("Coanda surface"): a) increases turning -> higher pressure ratio. b) controls boundary layer separation -> increased surge margin. Objective: Reduce the number of vanes or compressor stages. Constraints: 1. In a real compressor, the vane must still function entirely without blowing. 2. Maintain the flow exit angle of the reference stator despite the resulting increase in stator loading.

  8. The active site of ribulose-bisphosphate carboxylase/oxygenase

    SciTech Connect

    Hartman, F.C.

    1991-01-01

    The active site of ribulose-bisphosphate carboxylase/oxygenase requires interacting domains of adjacent, identical subunits. Most active-site residues are located within the loop regions of an eight-stranded {beta}/{alpha}-barrel which constitutes the larger C-terminal domain; additional key residues are located within a segment of the smaller N-terminal domain which partially covers the mouth of the barrel. Site-directed mutagenesis of the gene encoding the enzyme from Rhodospirillum rubrum has been used to delineate functions of active-site residues. 6 refs., 2 figs.

  9. Savannah River Site prioritization of transition activities

    SciTech Connect

    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.

  10. Optical Activity of Anisotropic Achiral Surfaces

    SciTech Connect

    Verbiest, T.; Kauranen, M.; Van Rompaey, Y.; Persoons, A. |

    1996-08-01

    Anisotropic achiral surfaces respond differently to left- and right-hand circularly polarized light. This occurs when the orientation of the surface with respect to an otherwise achiral experimental setup makes the total geometry chiral. Such optical activity is demonstrated in second-harmonic generation from an anisotropic thin molecular film. The circular-difference response reverses sign as the handedness of the geometry is reversed and vanishes when the setup possesses a mirror plane. The results are explained within the electric-dipole-allowed second-order surface nonlinearity. {copyright} {ital 1996 The American Physical Society.}

  11. DOE site performance assessment activities. Radioactive Waste Technical Support Program

    SciTech Connect

    Not Available

    1990-07-01

    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.

  12. Safety Oversight of Decommissioning Activities at DOE Nuclear Sites

    SciTech Connect

    Zull, Lawrence M.; Yeniscavich, William

    2008-01-15

    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.

  13. Identification of Glycosylation Sites Essential for Surface Expression of the CaVα2δ1 Subunit and Modulation of the Cardiac CaV1.2 Channel Activity.

    PubMed

    Tétreault, Marie-Philippe; Bourdin, Benoîte; Briot, Julie; Segura, Emilie; Lesage, Sylvie; Fiset, Céline; Parent, Lucie

    2016-02-26

    Alteration in the L-type current density is one aspect of the electrical remodeling observed in patients suffering from cardiac arrhythmias. Changes in channel function could result from variations in the protein biogenesis, stability, post-translational modification, and/or trafficking in any of the regulatory subunits forming cardiac L-type Ca(2+) channel complexes. CaVα2δ1 is potentially the most heavily N-glycosylated subunit in the cardiac L-type CaV1.2 channel complex. Here, we show that enzymatic removal of N-glycans produced a 50-kDa shift in the mobility of cardiac and recombinant CaVα2δ1 proteins. This change was also observed upon simultaneous mutation of the 16 Asn sites. Nonetheless, the mutation of only 6/16 sites was sufficient to significantly 1) reduce the steady-state cell surface fluorescence of CaVα2δ1 as characterized by two-color flow cytometry assays and confocal imaging; 2) decrease protein stability estimated from cycloheximide chase assays; and 3) prevent the CaVα2δ1-mediated increase in the peak current density and voltage-dependent gating of CaV1.2. Reversing the N348Q and N812Q mutations in the non-operational sextuplet Asn mutant protein partially restored CaVα2δ1 function. Single mutation N663Q and double mutations N348Q/N468Q, N348Q/N812Q, and N468Q/N812Q decreased protein stability/synthesis and nearly abolished steady-state cell surface density of CaVα2δ1 as well as the CaVα2δ1-induced up-regulation of L-type currents. These results demonstrate that Asn-663 and to a lesser extent Asn-348, Asn-468, and Asn-812 contribute to protein stability/synthesis of CaVα2δ1, and furthermore that N-glycosylation of CaVα2δ1 is essential to produce functional L-type Ca(2+) channels. PMID:26742847

  14. Active Surfaces and Interfaces of Soft Materials

    NASA Astrophysics Data System (ADS)

    Wang, Qiming

    A variety of intriguing surface patterns have been observed on developing natural systems, ranging from corrugated surface of white blood cells at nanometer scales to wrinkled dog skins at millimeter scales. To mimetically harness functionalities of natural morphologies, artificial transformative skin systems by using soft active materials have been rationally designed to generate versatile patterns for a variety of engineering applications. The study of the mechanics and design of these dynamic surface patterns on soft active materials are both physically interesting and technologically important. This dissertation starts with studying abundant surface patterns in Nature by constructing a unified phase diagram of surface instabilities on soft materials with minimum numbers of physical parameters. Guided by this integrated phase diagram, an electroactive system is designed to investigate a variety of electrically-induced surface instabilities of elastomers, including electro-creasing, electro-cratering, electro-wrinkling and electro-cavitation. Combing experimental, theoretical and computational methods, the initiation, evolution and transition of these instabilities are analyzed. To apply these dynamic surface instabilities to serving engineering and biology, new techniques of Dynamic Electrostatic Lithography and electroactive anti-biofouling are demonstrated.

  15. Investigations of adsorption sites on oxide surfaces using solid-state NMR and TPD-IGC

    NASA Astrophysics Data System (ADS)

    Golombeck, Rebecca A.

    diameters and thermal histories. The bulk structural features in both compositions of glass fibers were identified using high-resolution 29Si, 27Al, and 11B magic-angle spinning (MAS) NMR spectroscopic measurements. In multi-component glasses, the determination of silicon, aluminum, and boron distributions becomes difficult due to the competitive nature of the network-modifying oxides among the network-forming oxides. In pure silicates, 29Si MAS NMR can often resolve resonances arising from silicate tetrahedron having varying numbers of bridging oxygens. In aluminoborosilicate glasses, aluminum is present in four-, five-, and six- coordination with oxygen as neighbors. The speciation of the aluminum can be determined using 27Al MAS NMR. The fraction of tetrahedral boron species in the glass fibers were measured using 11B MAS NMR, which is typically used to study the short-range structure of borate containing glasses such as alkali borate, borosilicate, and aluminoborosilicate glasses. While solid-state NMR is a powerful tool for elucidating bonding environments and coordination changes in the glass structure, it cannot quantitatively probe low to moderate surface area samples due to insufficient spins. Chemical probes either physisorbed or chemisorbed to the fiber's surface can increase the surface selectivity of NMR for analysis of samples with low surface areas and provide information about the local molecular structure of the reactive surface site. Common chemical probe molecules contain NMR active nuclei such as 19F or may be enriched with 13C. A silyating agent, (3,3,3-trifluoropropyl)dimethylchlorosilane (TFS), reacts with reactive surface hydroxyls, which can be quantified by utilizing the NMR active nucleus (19F) contained in the probe molecule. The observed 19F MAS NMR peak area is integrated and compared against a standard of known fluorine spins (concentration), allowing the number of reactive hydroxyl sites to be quantified. IGC is a method used to study the

  16. Mutations of fumarase that distinguish between the active site and a nearby dicarboxylic acid binding site.

    PubMed Central

    Weaver, T.; Lees, M.; Banaszak, L.

    1997-01-01

    Two mutant forms of fumarase C from E. coli have been made using PCR and recombinant DNA. The recombinant form of the protein included a histidine arm on the C-terminal facilitating purification. Based on earlier studies, two different carboxylic acid binding sites, labeled A- and B-, were observed in crystal structures of the wild type and inhibited forms of the enzyme. A histidine at each of the sites was mutated to an asparagine. H188N at the A-site resulted in a large decrease in specific activity, while the H129N mutation at the B-site had essentially no effect. From the results, we conclude that the A-site is indeed the active site, and a dual role for H188 as a potential catalytic base is proposed. Crystal structures of the two mutant proteins produced some unexpected results. Both mutations reduced the affinity for the carboxylic acids at their respective sites. The H129N mutant should be particularly useful in future kinetic studies because it sterically blocks the B-site with the carboxyamide of asparagine assuming the position of the ligand's carboxylate. In the H188N mutation at the active site, the new asparagine side chain still interacts with an active site water that appears to have moved slightly as a result of the mutation. PMID:9098893

  17. Ionizable Side Chains at Catalytic Active Sites of Enzymes

    PubMed Central

    Jimenez-Morales, David; Liang, Jie

    2012-01-01

    Catalytic active sites of enzymes of known structure can be well defined by a modern program of computational geometry. The CASTp program was used to define and measure the volume of the catalytic active sites of 573 enzymes in the Catalytic Site Atlas database. The active sites are identified as catalytic because the amino acids they contain are known to participate in the chemical reaction catalyzed by the enzyme. Acid and base side chains are reliable markers of catalytic active sites. The catalytic active sites have 4 acid and 5 base side chains, in an average volume of 1072 Å3. The number density of acid side chains is 8.3 M (in chemical units); the number density of basic side chains is 10.6 M. The catalytic active site of these enzymes is an unusual electrostatic and steric environment in which side chains and reactants are crowded together in a mixture more like an ionic liquid than an ideal infinitely dilute solution. The electrostatics and crowding of reactants and side chains seems likely to be important for catalytic function. In three types of analogous ion channels, simulation of crowded charges accounts for the main properties of selectivity measured in a wide range of solutions and concentrations. It seems wise to use mathematics designed to study interacting complex fluids when making models of the catalytic active sites of enzymes. PMID:22484856

  18. Green Bank Telescope active surface system

    NASA Astrophysics Data System (ADS)

    Lacasse, Richard J.

    1998-05-01

    During the design phase of the Green Bank Telescope (GBT), various means of providing an accurate surface on a large aperture paraboloid, were considered. Automated jacks supporting the primary reflector were selected as the appropriate technology since they promised greater performance and potentially lower costs than a homologous or carbon fiber design, and had certain advantages over an active secondary. The design of the active surface has presented many challenges. Since the actuators are mounted on a tipping structure, it was required that they support a significant side-load. Such devices were not readily available commercially so they had to be developed. Additional actuator requirements include low backlash, repeatable positioning, and an operational life of at least 230 years. Similarly, no control system capable of controlling the 2209 actuators was commercially available. Again a prime requirement was reliability. Maintaining was also a very important consideration. The system architecture is tree-like. An active surface 'master-computer' controls interaction with the telescope control system, and controls ancillary equipment such as power supplies and temperature monitors. Two slave computers interface with the master- computer, and each closes approximately 1100 position loops. For simplicity, the servo is an 'on/off' type, yet achieves a positioning resolution of 25 microns. Each slave computer interfaces with 4 VME I/O cards, which in turn communicate with 140 control modules. The control modules read out the positions of the actuators every 0.1 sec and control the actuators' DC motors. Initial control of the active surface will be based on an elevation dependant structural model. Later, the model will be improved by holographic observations.Surface accuracy will be improved further by using laser ranging system which will actively measure the surface figure. Several tests have been conducted to assure that the system will perform as desired when

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

    PubMed

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

    2016-07-01

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

  20. Land surface cleanup of plutonium at the Nevada Test Site

    SciTech Connect

    Ebeling, L.L.; Evans, R.B.; Walsh, E.J.

    1991-01-01

    The Nevada Test Site (NTS) covers approximately 3300 km{sup 2} of high desert and is located approximately 100 km northwest of Las Vegas, Nevada. Soil contaminated by plutonium exists on the NTS and surrounding areas from safety tests conducted in the 1950s and 1960s. About 150 curies of contamination have been measured over 1200 hectares of land surface. Most contamination is found in the top 5 cm of soil but may be found deep as 25 cm. The cost of conventional removal and disposal of the full soil volume has been estimated at over $500,000,000. This study is directed toward minimizing the volume of waste which must be further processed and disposed of by precisely controlling soil removal depth. The following soil removal machines were demonstrated at the NTS: (1) a CMI Corporation Model PR-500FL pavement profiler, (2) a CMI Corporation Model Tr-225B trimmer reclaimer, (3) a Caterpillar Model 623 elevating scraper equipped with laser depth control, (4) a Caterpillar Model 14G motor grader equipped with laser depth control, (5) a Caterpillar Model 637 auger scraper, and (6) a XCR Series Guzzler vacuum truck. 5 refs., 5 figs.

  1. Surface-active organics in atmospheric aerosols.

    PubMed

    McNeill, V Faye; Sareen, Neha; Schwier, Allison N

    2014-01-01

    Surface-active organic material is a key component of atmospheric aerosols. The presence of surfactants can influence aerosol heterogeneous chemistry, cloud formation, and ice nucleation. We review the current state of the science on the sources, properties, and impacts of surfactants in atmospheric aerosols. PMID:23408277

  2. Bactericidal activity of biomimetic diamond nanocone surfaces.

    PubMed

    Fisher, Leanne E; Yang, Yang; Yuen, Muk-Fung; Zhang, Wenjun; Nobbs, Angela H; Su, Bo

    2016-03-17

    The formation of biofilms on implant surfaces and the subsequent development of medical device-associated infections are difficult to resolve and can cause considerable morbidity to the patient. Over the past decade, there has been growing recognition that physical cues, such as surface topography, can regulate biological responses and possess bactericidal activity. In this study, diamond nanocone-patterned surfaces, representing biomimetic analogs of the naturally bactericidal cicada fly wing, were fabricated using microwave plasma chemical vapor deposition, followed by bias-assisted reactive ion etching. Two structurally distinct nanocone surfaces were produced, characterized, and the bactericidal ability examined. The sharp diamond nanocone features were found to have bactericidal capabilities with the surface possessing the more varying cone dimension, nonuniform array, and decreased density, showing enhanced bactericidal ability over the more uniform, highly dense nanocone surface. Future research will focus on using the fabrication process to tailor surface nanotopographies on clinically relevant materials that promote both effective killing of a broader range of microorganisms and the desired mammalian cell response. This study serves to introduce a technology that may launch a new and innovative direction in the design of biomaterials with capacity to reduce the risk of medical device-associated infections.

  3. Bactericidal activity of biomimetic diamond nanocone surfaces.

    PubMed

    Fisher, Leanne E; Yang, Yang; Yuen, Muk-Fung; Zhang, Wenjun; Nobbs, Angela H; Su, Bo

    2016-03-01

    The formation of biofilms on implant surfaces and the subsequent development of medical device-associated infections are difficult to resolve and can cause considerable morbidity to the patient. Over the past decade, there has been growing recognition that physical cues, such as surface topography, can regulate biological responses and possess bactericidal activity. In this study, diamond nanocone-patterned surfaces, representing biomimetic analogs of the naturally bactericidal cicada fly wing, were fabricated using microwave plasma chemical vapor deposition, followed by bias-assisted reactive ion etching. Two structurally distinct nanocone surfaces were produced, characterized, and the bactericidal ability examined. The sharp diamond nanocone features were found to have bactericidal capabilities with the surface possessing the more varying cone dimension, nonuniform array, and decreased density, showing enhanced bactericidal ability over the more uniform, highly dense nanocone surface. Future research will focus on using the fabrication process to tailor surface nanotopographies on clinically relevant materials that promote both effective killing of a broader range of microorganisms and the desired mammalian cell response. This study serves to introduce a technology that may launch a new and innovative direction in the design of biomaterials with capacity to reduce the risk of medical device-associated infections. PMID:26992656

  4. Salt Repository Project site study plan for surface geological mapping: Revision 1, December 22, 1987

    SciTech Connect

    Not Available

    1988-03-01

    This site study plan describes the Surface Geological Mapping field activities to be conducted during early stages of Site Characterization for the Deaf Smith County Site, Texas. The field program has been designed to provide data useful in addressing information and design data needs resulting from Federal/State/local regulatory requirements and repository program requirements. Air and ground surveys and an extensive literature search will be conducted to map areas within and hear proposed nuclear waste repository site in the Deaf Smith County. Findings from this study may identify additional areas requiring further investigation, for which a new site study plan will be prepared. The Salt Repository Project (SRP) Networks specify the schedule under which the program will operate. The Technical and Field Services Contractor (TFSC) is responsible for conducting the field program. Data will be handled and reported in accordance with established SRP procedures. A quality assurance program will be utilized to assure that activities affecting quality are performed correctly and the appropriate documentation is maintained. 27 refs., 13 figs., 5 tabs.

  5. Surface Meteorological Station - ANL 10m, (1) Sonics, (1) EBBR, Physics site-3 - Raw Data

    DOE Data Explorer

    Muradyan, Paytsar

    2016-10-25

    Sonic anemometers from Physics Site-3 and Site-9 provide wind components and virtual temperature. The energy balance Bowen ratio (EBBR) station at Physics site-3 provides measurements of the surface fluxes of latent and sensible heat, net radiation, and surface soil heat flux.

  6. Surface Meteorological Station - ANL 10m, (1) Sonic, Physics site-9 - Raw Data

    DOE Data Explorer

    Muradyan, Paytsar

    2016-10-25

    Sonic anemometers from Physics Site-3 and Site-9 provide wind components and virtual temperature. The energy balance Bowen ratio (EBBR) station at Physics site-3 provides measurements of the surface fluxes of latent and sensible heat, net radiation, and surface soil heat flux.

  7. Surface-mediated control of blood coagulation: the role of binding site densities and platelet deposition.

    PubMed Central

    Kuharsky, A L; Fogelson, A L

    2001-01-01

    A mathematical model of the extrinsic or tissue factor (TF) pathway of blood coagulation is formulated and results from a computational study of its behavior are presented. The model takes into account plasma-phase and surface-bound enzymes and zymogens, coagulation inhibitors, and activated and unactivated platelets. It includes both plasma-phase and membrane-phase reactions, and accounts for chemical and cellular transport by flow and diffusion, albeit in a simplified manner by assuming the existence of a thin, well-mixed fluid layer, near the surface, whose thickness depends on flow. There are three main conclusions from these studies. (i) The model system responds in a threshold manner to changes in the availability of particular surface binding sites; an increase in TF binding sites, as would occur with vascular injury, changes the system's production of thrombin dramatically. (ii) The model suggests that platelets adhering to and covering the subendothelium, rather than chemical inhibitors, may play the dominant role in blocking the activity of the TF:VIIa enzyme complex. This, in turn, suggests that a role of the IXa-tenase pathway for activating factor X to Xa is to continue factor Xa production after platelets have covered the TF:VIIa complexes on the subendothelium. (iii) The model gives a kinetic explanation of the reduced thrombin production in hemophilias A and B. PMID:11222273

  8. Enzymatic activity induced by interactions with a nanofabricated hydrophobic Si surface

    NASA Astrophysics Data System (ADS)

    Nishiyama, Katsuhiko

    2013-07-01

    The binding of peptides of 2-10 glycine residues (2-10Gly) to papain on nanofabricated hydrophobic Si surfaces was investigated by molecular dynamics and docking simulations. 5Gly, 7Gly, 9Gly, and 10Gly were distributed on sites near the active center of papain on the Si surface, while 6-10Gly were distributed on sites near the active center of free papain. The Si surface changed the substrate specificity of papain, and modification of this surface should allow full control of substrate specificity. Molecular surgery of proteins in cells may be realized using papain on specially designed surfaces.

  9. Dual Active Surface Heat Flux Gage Probe

    NASA Technical Reports Server (NTRS)

    Liebert, Curt H.; Kolodziej, Paul

    1995-01-01

    A unique plug-type heat flux gage probe was tested in the NASA Ames Research Center 2x9 turbulent flow duct facility. The probe was fabricated by welding a miniature dual active surface heat flux gage body to the end of a hollow metal cylindrical bolt containing a metal inner tube. Cooling air flows through the inner tube, impinges onto the back of the gage body and then flows out through the annulus formed between the inner tube and the hollow bolt wall. Heat flux was generated in the duct facility with a Huels arc heater. The duct had a rectangular cross section and one wall was fabricated from 2.54 centimeter thick thermal insulation rigid surface material mounted onto an aluminum plate. To measure heat flux, the probe was inserted through the plate and insulating materials with the from of the gage located flush with the hot gas-side insulation surface. Absorbed heat fluxes measured with the probe were compared with absorbed heat fluxes measured with six water-cooled reference calorimeters. These calorimeters were located in a water-cooled metal duct wall which was located across from the probe position. Correspondence of transient and steady heat fluxes measured with the reference calorimeters and heat flux gage probe was generally within a satisfactory plus or minus 10 percent. This good correspondence was achieved even though the much cooler probe caused a large surface temperature disruption of 1000K between the metal gage and the insulation. However, this temperature disruption did not seriously effect the accuracy of the heat flux measurement. A current application for dual active surface heat flux gages is for transient and steady absorbed heat flux, surface temperature and heat transfer coefficient measurements on the surface of an oxidizer turbine inlet deflector operating in a space shuttle test bed engine.

  10. Antiviral activity of alcohol for surface disinfection.

    PubMed

    Moorer, W R

    2003-08-01

    Bacteria and viruses from the patient's mouth travel with dental splatter and spills. A surface disinfectant should possess antiviral activity as well as antibacterial action. Because of frequent and 'open' application in the dental office, such a disinfectant should be non-toxic, non-allergenic and safe for the hygienist. It now appears that high-concentration alcohol mixtures (i.e. 80% ethanol + 5% isopropanol) are not only excellent antibacterials, but quickly inactivate HIV as well as hepatitis B and hepatitis C viruses. Compared to alternative surface disinfectants, use of high-concentration alcohol for the spray-wipe-spray method of surface disinfection in dentistry appears safe and efficient. However, dried matter should be wiped and hydrated first.

  11. Active site - a site of binding of affinity inhibitors in baker's yeast inorganic pyrophosphatase

    SciTech Connect

    Svyato, I.E.; Sklyankina, V.A.; Avaeva, S.M.

    1986-03-20

    The interaction of the enzyme-substrate complex with methyl phosphate, O-phosphoethanolamine, O-phosphopropanolamine, N-acetylphosphoserine, and phosphoglyolic acid, as well as pyrophosphatase, modified by monoesters of phosphoric acid, with pyrophosphate and tripolyphosphate, was investigated. It was shown that the enzyme containing the substrate in the active site does not react with monophosphates, but modified pyrophosphatase entirely retains the ability to bind polyanions to the regulatory site. It is concluded that the inactivation of baker's yeast inorganic pyrophosphatase by monoesters of phosphoric acid, which are affinity inhibitors of it, is the result of modification of the active site of the enzyme.

  12. Effect of soil erosion on the long-term stability of FUSRAP near-surface waste-burial sites

    SciTech Connect

    Knight, M.J.

    1983-04-01

    Decontamination of FUSRAP sites could result in the generation of large volumes (in excess of 400,000 m/sup 3/) of low-activity radioactive wastes (primarily contaminated soil and building materials) requiring subsequent disposal. It is likely that near-surface burial will be seriously considered as an option for disposal of these materials. A number of factors - including soil erosion - could adversely affect the long-term stability of a near-surface waste-burial site. The majority of FUSRAP sites are located in the humid eastern United States, where the principal cause of erosion is the action of water. This report examines the effect of soil erosion by water on burial-site stability based on analysis of four hypothetical near-surface burial sites. The Universal Soil Loss Equation was employed to estimate average annual soil loss from burial sites and the 1000-year effects of soil loss on the soil barrier (burial trench cap) placed over low-activity wastes. Results suggest that the land use of the burial site and the slope gradient of the burial trench cap significantly affect the rate of soil erosion. The development of measures limiting the potential land use of a burial site (e.g., mixing large rocks into the burial trench cap) may be required to preserve the integrity of a burial trench for long periods of time.

  13. Geology, physical properties, and surface effects at Discus Thrower Site, Yucca Flat, Nevada test site

    USGS Publications Warehouse

    Carr, Wilfred James; Miller, C.H.; Dodge, Harry W.

    1975-01-01

    Geologic studies in connection with Project Discus Thrower have furnished detailed stratigraphic and structural information about northwestern Yucca Flat. The Paleozoic rocks consist of a lower carbonate sequence, argillite of the Eleana Formation, and an upper carbonate sequence. The distribution of these rocks suggests that both top and bottom of the Eleana are structural contacts, probably thrusts or reverse faults. The overlying tuff includes several units recognized in the subsurface, such as the Fraction Tuff and tuff of Redrock Valley. Other units recognized include bedded tuff associated with the Grouse Canyon Member of Belted Range Tuff, and the Rainier Mesa and Ammonia Tanks Members of the Timber Mountain Tuff. The Timber Mountain and Grouse Canyon are extensively altered to montmorillonite (a swelling clay), possibly as a result of ponding of alkaline water. The overlying alluvium locally contains at the base a clayey, tuffaceous sandstone. Geophysical logs were used as an aid in locating geologic contacts and determining in situ physical properties. Graphic logs are presented that show the correlation of lithology and geophysical logs. Many of the rock units have characteristic log responses, but alteration within rock units affects the logs strikingly in some drill holes. The most significant surface effect of the experiment was the formation of a 4-foot fault scarp northwest of the site.

  14. Estimating Active Layer Thickness from Remotely Sensed Surface Deformation

    NASA Astrophysics Data System (ADS)

    Liu, L.; Schaefer, K. M.; Zhang, T.; Wahr, J. M.

    2010-12-01

    We estimate active layer thickness (ALT) from remotely sensed surface subsidence during thawing seasons derived from interferometric synthetic aperture radar (InSAR) measurements. Ground ice takes up more volume than ground water, so as the soil thaws in summer and the active layer deepens, the ground subsides. The volume of melted ground water during the summer thaw determines seasonal subsidence. ALT is defined as the maximum thaw depth at the end of a thawing season. By using InSAR to measure surface subsidence between the start and end of summer season, one can estimate the depth of thaw over a large area (typically 100 km by 100 km). We developed an ALT retrieval algorithm integrating InSAR-derived surface subsidence, observed soil texture, organic matter content, and moisture content. We validated this algorithm in the continuous permafrost area on the North Slope of Alaska. Based on InSAR measurements using ERS-1/2 SAR data, our estimated values match in situ measurements of ALT within 1--10 cm at Circumpolar Active Layer Monitoring (CALM) sites within the study area. The active layer plays a key role in land surface processes in cold regions. Current measurements of ALT using mechanical probing, frost/thaw tubes, or inferred from temperature measurements are of high quality, but limited in spatial coverage. Using InSAR to estimate ALT greatly expands the spatial coverage of ALT observations.

  15. Sequential and site-specific on-surface synthesis on a bulk insulator.

    PubMed

    Kittelmann, Markus; Nimmrich, Markus; Lindner, Robert; Gourdon, André; Kühnle, Angelika

    2013-06-25

    The bottom-up construction of functional devices from molecular building blocks offers great potential in tailoring materials properties and functionality with utmost control. An important step toward exploiting bottom-up construction for real-life applications is the creation of covalently bonded structures that provide sufficient stability as well as superior charge transport properties over reversibly linked self-assembled structures. On-surface synthesis has emerged as a promising strategy for fabricating stable, covalently bound molecular structure on surfaces. So far, a majority of the structures created by this method have been obtained from a rather simple one-step processing approach. But the on-surface preparation of complex structures will require the possibility to carry out various reaction steps in a sequential manner as done in solution chemistry. Only one example exists in literature in which a hierarchical strategy is followed to enhance structural complexity and reliability on a metallic surface. Future molecular electronic application will, however, require transferring these strategies to nonconducting surfaces. Bulk insulating substrates are known to pose significant challenges to on-surface synthesis due to the absence of a metal catalyst and their low surface energy, frequently resulting in molecule desorption rather than reaction activation. By carefully selecting a suitable precursor molecule, we succeeded in performing a two-step linking reaction on a bulk insulating surface. Besides a firm anchoring toward the substrate surface, the reaction sites and sequential order are encoded in the molecular structure, providing so far unmatched reaction control in on-surface synthesis on a bulk insulating substrate.

  16. Active surfaces: Ferrofluid-impregnated surfaces for active manipulation of droplets

    NASA Astrophysics Data System (ADS)

    Khalil, Karim; Mahmoudi, Seyed Reza; Abu-Dheir, Numan; Varanasi, Kripa

    2014-11-01

    Droplet manipulation and mobility on non-wetting surfaces is of practical importance for diverse applications ranging from micro-fluidic devices, anti-icing, dropwise condensation, and biomedical devices. The use of active external fields has been explored via electric, acoustic, and vibrational, yet moving highly conductive and viscous fluids remains a challenge. Magnetic fields have been used for droplet manipulation; however, usually, the fluid is functionalized to be magnetic, and requires enormous fields of superconducting magnets when transitioning to diamagnetic materials such as water. Here we present a class of active surfaces by stably impregnating active fluids such as ferrofluids into a textured surface. Droplets on such ferrofluid-impregnated surfaces have extremely low hysteresis and high mobility such that they can be propelled by applying relatively low magnetic fields. Our surface is able to manipulate a variety of materials including diamagnetic, conductive and highly viscous fluids, and additionally solid particles.

  17. Active surfaces: Ferrofluid-impregnated surfaces for active manipulation of droplets

    NASA Astrophysics Data System (ADS)

    Khalil, Karim S.; Mahmoudi, Seyed Reza; Abu-dheir, Numan; Varanasi, Kripa K.

    2014-07-01

    Droplet manipulation and mobility on non-wetting surfaces is of practical importance for diverse applications ranging from micro-fluidic devices, anti-icing, dropwise condensation, and biomedical devices. The use of active external fields has been explored via electric, acoustic, and vibrational, yet moving highly conductive and viscous fluids remains a challenge. Magnetic fields have been used for droplet manipulation; however, usually, the fluid is functionalized to be magnetic, and requires enormous fields of superconducting magnets when transitioning to diamagnetic materials such as water. Here we present a class of active surfaces by stably impregnating active fluids such as ferrofluids into a textured surface. Droplets on such ferrofluid-impregnated surfaces have extremely low hysteresis and high mobility such that they can be propelled by applying relatively low magnetic fields. Our surface is able to manipulate a variety of materials including diamagnetic, conductive and highly viscous fluids, and additionally solid particles.

  18. Secondary ion mass spectrometry (SIMS) analysis of hypervelocity microparticle impact sites on LDEF surfaces

    NASA Technical Reports Server (NTRS)

    Simon, C. G.; Buonaquisti, A. J.; Batchelor, D. A.; Hunter, J. L.; Griffis, D. P.; Misra, V.; Ricks, D. R.; Wortman, J. J.; Brownlee, D. E.; Best, S. R.

    1995-01-01

    Two dimensional elemental ion maps have been recorded for hundreds of microparticle impact sites and contamination features on LDEF surfaces. Since the majority of the analyzed surfaces were metal-oxide-silicon (MOS) impact detectors from the Interplanetary Dust Experiment, a series of 'standard' and 'blank' analyses of these surfaces are included. Hypervelocity impacts of forsterite olivine microparticles on activated flight sensors served as standards while stylus and pulsed laser simulated 'impacts' served as analytical blanks. Results showed that despite serious contamination issues, impactor residues can be identified in greater than 1/3 of the impact sites. While aluminum oxide particles could not be detected on aluminum surfaces, they were detected on germanium surfaces from row 12. Remnants of manmade debris impactors consisting of paint chips and bits of metal were identified on surfaces from LDEF Rows 3 (west or trailing side), 6 (south), 9 (ram or leading side), 12 (north) and the space end. Higher than expected ratios of manmade microparticle impacts to total microparticle impacts were found on the space end and the trailing side. These results were consistent with time-tagged and time-segregated microparticle impact data from the IDE and other LDEF experiments. A myriad of contamination interferences were identified and their effects on impactor debris identification mitigated during the course of this study. These interferences include pre-, post and inflight deposited surface contaminants as well as indigenous heterogeneous material contaminants. Non-flight contaminations traced to human origins, including spittle and skin oils, contributed significant levels of alkali-rich carbonaceous interferences. A ubiquitous layer of in-flight deposited silicaceous contamination varied in thickness with location on LDEF, even on a micro scale. In-flight deposited (low velocity) contaminants include urine droplets and bits of metal film from eroded thermal

  19. Surface binding sites in amylase have distinct roles in recognition of starch structure motifs and degradation.

    PubMed

    Cockburn, Darrell; Nielsen, Morten M; Christiansen, Camilla; Andersen, Joakim M; Rannes, Julie B; Blennow, Andreas; Svensson, Birte

    2015-04-01

    Carbohydrate converting enzymes often possess extra substrate binding regions that enhance their activity. These can be found either on separate domains termed carbohydrate binding modules or as so-called surface binding sites (SBSs) situated on the catalytic domain. SBSs are common in starch degrading enzymes and critically important for their function. The affinity towards a variety of starch granules as well as soluble poly- and oligosaccharides of barley α-amylase 1 (AMY1) wild-type and mutants of two SBSs (SBS1 and SBS2) was investigated using Langmuir binding analysis, confocal laser scanning microscopy, affinity gel electrophoresis and surface plasmon resonance to unravel functional roles of the SBSs. SBS1 was critical for binding to different starch types as Kd increased by 7-62-fold or was not measurable upon mutation. By contrast SBS2 was particularly important for binding to soluble polysaccharides and oligosaccharides with α-1,6 linkages, suggesting that branch points are key structural elements in recognition by SBS2. Mutation at both SBS1 and SBS2 eliminated binding to all starch granule types tested. Taken together, the findings indicate that the two SBSs act in concert to localize AMY1 to the starch granule surface and that SBS2 works synergistically with the active site in the degradation of amylopectin.

  20. A novel approach to predict active sites of enzyme molecules.

    PubMed

    Chou, Kuo-Chen; Cai, Yu-dong

    2004-04-01

    Enzymes are critical in many cellular signaling cascades. With many enzyme structures being solved, there is an increasing need to develop an automated method for identifying their active sites. However, given the atomic coordinates of an enzyme molecule, how can we predict its active site? This is a vitally important problem because the core of an enzyme molecule is its active site from the viewpoints of both pure scientific research and industrial application. In this article, a topological entity was introduced to characterize the enzymatic active site. Based on such a concept, the covariant discriminant algorithm was formulated for identifying the active site. As a paradigm, the serine hydrolase family was demonstrated. The overall success rate by jackknife test for a data set of 88 enzyme molecules was 99.92%, and that for a data set of 50 independent enzyme molecules was 99.91%. Meanwhile, it was shown through an example that the prediction algorithm can also be used to find any typographic error of a PDB file in annotating the constituent amino acids of catalytic triad and to suggest a possible correction. The very high success rates are due to the introduction of a covariance matrix in the prediction algorithm that makes allowance for taking into account the coupling effects among the key constituent atoms of active site. It is anticipated that the novel approach is quite promising and may become a useful high throughput tool in enzymology, proteomics, and structural bioinformatics. PMID:14997541

  1. Hanford Site environmental data for calendar year 1993--surface and Columbia River

    SciTech Connect

    Bisping, L.E.

    1994-06-01

    Environmental monitoring at the Hanford Site, located in southeastern Washington State, is conducted by Battelle Memorial Institute, Pacific Northwest Division, as part of its contract to operate the Pacific Northwest Laboratory (PNL) for the U.S. Department of Energy. The data collected provide a historical record of radionuclide and radiation levels attributable to natural causes, worldwide fallout, and Hanford operations. Data are also collected to monitor several chemicals. Pacific Northwest Laboratory publishes an annual environmental report for the Hanford Site each calendar year. The Hanford Site Environmental Report for Calendar Year 1993 describes the Site mission and activities, general environmental features, radiological and chemical releases from operations, status of compliance with environmental regulations, status of programs to accomplish compliance, and environmental monitoring activities and results. The report includes a summary of offsite and onsite environmental monitoring data collected during 1993 by PNL`s Environmental Monitoring Program. Appendix A of that report contains data summaries created from raw surface and river monitoring data. This volume contains the actual raw data used to create the summaries.

  2. Hanford Site environmental data for calendar year 1994: Surface and Columbia River

    SciTech Connect

    Bisping, L.E.

    1995-07-01

    Environmental monitoring at the Hanford Site, located in southeastern Washington State, is conducted by Battelle Memorial Institute, Pacific Northwest Division, as part of its contract to operate the Pacific Northwest Laboratory (PNL) for the US Department of Energy. The data collected provide a historical record of radionuclide and radiation levels attributable to natural causes, worldwide fallout, and Hanford operations. Data are also collected to monitor several chemicals. Pacific Northwest Laboratory publishes an annual environmental report for the Hanford Site each calendar year. The Hanford Site Environmental Report for Calendar Year 1994 describes the Site mission and activities, general environmental features, radiological and chemical releases from operations, status of compliance with environmental regulations, status of programs to accomplish compliance, and environmental monitoring activities and results. The report includes a summary of offsite and onsite environmental monitoring data collected during 1994 b PNL`s Environmental Monitoring Program. Appendix A of that report contains data summaries created from raw surface and river monitoring data. This volume contains the actual raw data used to create the summaries.

  3. A small ribozyme with dual-site kinase activity

    PubMed Central

    Biondi, Elisa; Maxwell, Adam W.R.; Burke, Donald H.

    2012-01-01

    Phosphoryl transfer onto backbone hydroxyls is a recognized catalytic activity of nucleic acids. We find that kinase ribozyme K28 possesses an unusually complex active site that promotes (thio)phosphorylation of two residues widely separated in primary sequence. After allowing the ribozyme to radiolabel itself by phosphoryl transfer from [γ-32P]GTP, DNAzyme-mediated cleavage yielded two radiolabeled cleavage fragments, indicating phosphorylation sites within each of the two cleavage fragments. These sites were mapped by alkaline digestion and primer extension pausing. Enzymatic digestion and mutational analysis identified nucleotides important for activity and established the active structure as being a constrained pseudoknot with unusual connectivity that may juxtapose the two reactive sites. Nuclease sensitivities for nucleotides near the pseudoknot core were altered in the presence of GTPγS, indicating donor-induced folding. The 5′ target site was more strongly favored in full-length ribozyme K28 (128 nt) than in truncated RNAs (58 nt). Electrophoretic mobilities of self-thiophosphorylated products on organomercurial gels are distinct from the 5′ mono-thiophosphorylated product produced by reaction with polynucleotide kinase, potentially indicating simultaneous labeling of both sites within individual RNA strands. Our evidence supports a single, compact structure with local dynamics, rather than global rearrangement, as being responsible for dual-site phosphorylation. PMID:22618879

  4. Surface visualization of electromagnetic brain activity.

    PubMed

    Badea, Alexandra; Kostopoulos, George K; Ioannides, Andreas A

    2003-08-15

    Advances in hardware and software have made possible the reconstruction of brain activity from non-invasive electrophysiological measurements over a large part of the brain. The appreciation of the information content in the data is enhanced when relevant anatomical detail is also available for visualization. Different neuroscientific questions give rise to different requirements for optimal superposition of structure and function. Most available software deal with scalar measures of activity, especially hemodynamic changes. In contrast, the electrophysiological observables are generated by electrical activity, which depends on the synchrony of neuronal assemblies and the geometry of the local cortical surface. We describe methods for segmentation and visualization of spatio-temporal brain activity, which allow the interplay of geometry and scalar as well as vector properties of the current density directly in the representations. The utility of these methods is demonstrated through displays of tomographic reconstructions of early sensory processing in the somatosensory and visual modality extracted from magnetoencephalography (MEG) data. The activation course characteristic to a specific area could be observed as current density or statistical maps independently and/or contrasted to the activity in other areas or the whole brain. MEG and functional magnetic resonance imaging (fMRI) activations were simultaneously visualized. Integrating and visualizing complementary functional data into a single environment helps evaluating analysis and understanding structure/function relationships in normal and diseased brain.

  5. Volcanic Surface Deformation in Dominica From GPS Geodesy: Results From the 2007 NSF- REU Site

    NASA Astrophysics Data System (ADS)

    Murphy, R.; James, S.; Styron, R. H.; Turner, H. L.; Ashlock, A.; Cavness, C.; Collier, X.; Fauria, K.; Feinstein, R.; Staisch, L.; Williams, B.; Mattioli, G. S.; Jansma, P. E.; Cothren, J.

    2007-12-01

    GPS measurements have been collected on the island of Dominica in the Lesser Antilles between 2001 and 2007, with five month-long campaigns completed in June of each year supported in part by a NSF REU Site award for the past two years. All GPS data were collected using dual-frequency, code-phase receivers and geodetic-quality antenna, primarily choke rings. Three consecutive 24 hr observation days were normally obtained for each site. Precise station positions were estimated with GIPSY-OASISII using an absolute point positioning strategy and final, precise orbits, clocks, earth orientation parameters, and x-files. All position estimates were updated to ITRF05 and a revised Caribbean Euler pole was used to place our observations in a CAR-fixed frame. Time series were created to determine the velocity of each station. Forward and inverse elastic half-space models with planar (i.e. dike) and Mogi (i.e. point) sources were investigated. Inverse modeling was completed using a downhill simplex method of function minimization. Selected site velocities were used to create appropriate models for specific regions of Dominica, which correspond to known centers of pre-historic volcanic or recent shallow, seismic activity. Because of the current distribution of GPS sites with robust velocity estimates, we limit our models to possible magmatic activity in the northern, proximal to the volcanic centers of Morne Diablotins and Morne aux Diables, and southern, proximal to volcanic centers of Soufriere and Morne Plat Pays, regions of the island. Surface deformation data from the northernmost sites may be fit with the development of a several km-long dike trending approximately northeast- southwest. Activity in the southern volcanic centers is best modeled by an expanding point source at approximately 1 km depth.

  6. A Frontier Molecular Orbital determination of the active sites on dispersed metal catalysts

    SciTech Connect

    Augustine, R.L.; Lahanas, K.M.

    1992-11-01

    An angular overlap calculation has been used to determine the s, p and d orbital energy levels of the different types of surface sites present on a dispersed metal catalysts. The basis for these calculations is the reported finding that a large number of catalyzed reactions take place on single atom active sites on the metal surface. Thus, these sites can be considered as surface complexes made up of the central active atom surrounded by near-neighbor metal atom ``ligands`` with localized surface orbitals perturbed only by these ``ligands``. These ``complexes`` are based on a twelve coordinate species with the ``ligands`` attached to the t{sub 2g} orbitals and the coordinate axes coincident with the direction of the e{sub g} orbitals on the central atom. These data can permit a Frontier Molecular Orbital treatment of specific site activities as long as the surface orbital availability for overlap with adsorbed substrates is considered along with its energy value and symmetry.

  7. A Frontier Molecular Orbital determination of the active sites on dispersed metal catalysts

    SciTech Connect

    Augustine, R.L.; Lahanas, K.M.

    1992-01-01

    An angular overlap calculation has been used to determine the s, p and d orbital energy levels of the different types of surface sites present on a dispersed metal catalysts. The basis for these calculations is the reported finding that a large number of catalyzed reactions take place on single atom active sites on the metal surface. Thus, these sites can be considered as surface complexes made up of the central active atom surrounded by near-neighbor metal atom ligands'' with localized surface orbitals perturbed only by these ligands''. These complexes'' are based on a twelve coordinate species with the ligands'' attached to the t{sub 2g} orbitals and the coordinate axes coincident with the direction of the e{sub g} orbitals on the central atom. These data can permit a Frontier Molecular Orbital treatment of specific site activities as long as the surface orbital availability for overlap with adsorbed substrates is considered along with its energy value and symmetry.

  8. Surface refractivity measurements at NASA spacecraft tracking sites

    NASA Technical Reports Server (NTRS)

    Schmid, P. E.

    1972-01-01

    High-accuracy spacecraft tracking requires tropospheric modeling which is generally scaled by either estimated or measured values of surface refractivity. This report summarizes the results of a worldwide surface-refractivity test conducted in 1968 in support of the Apollo program. The results are directly applicable to all NASA radio-tracking systems.

  9. Architecture and active site of particulate methane monooxygenase

    PubMed Central

    Culpepper, Megen A.; Rosenzweig, Amy C.

    2012-01-01

    Particulate methane monooxygenase (pMMO) is an integral membrane metalloenzyme that oxidizes methane to methanol in methanotrophic bacteria, organisms that live on methane gas as their sole carbon source. Understanding pMMO function has important implications for bioremediation applications and for the development of new, environmentally friendly catalysts for the direct conversion of methane to methanol. Crystal structures of pMMOs from three different methanotrophs reveal a trimeric architecture, consisting of three copies each of the pmoB, pmoA, and pmoC subunits. There are three distinct metal centers in each protomer of the trimer, mononuclear and dinuclear copper sites in the periplasmic regions of pmoB and a mononuclear site within the membrane that can be occupied by copper or zinc. Various models for the pMMO active site have been proposed within these structural constraints, including dicopper, tricopper, and diiron centers. Biochemical and spectroscopic data on pMMO and recombinant soluble fragments, denoted spmoB proteins, indicate that the active site involves copper and is located at the site of the dicopper center in the pmoB subunit. Initial spectroscopic evidence for O2 binding at this site has been obtained. Despite these findings, questions remain about the active site identity and nuclearity and will be the focus of future studies. PMID:22725967

  10. Detection limit for activation measurements in ultralow background sites

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

    Rajan, Rakhi; Osterman, Amy; Mondragón, Alfonso

    2016-04-20

    Topoisomerase V (Topo-V) is the only topoisomerase with both topoisomerase and DNA repair activities. The topoisomerase activity is conferred by a small alpha-helical domain, whereas the AP lyase activity is found in a region formed by 12 tandem helix-hairpin-helix ((HhH)2) domains. Although it was known that Topo-V has multiple repair sites, only one had been mapped. Here, we show that Topo-V has three AP lyase sites. The atomic structure and Small Angle X-ray Scattering studies of a 97 kDa fragment spanning the topoisomerase and 10 (HhH)2 domains reveal that the (HhH)2 domains extend away from the topoisomerase domain. A combination of biochemical and structural observations allow the mapping of the second repair site to the junction of the 9th and 10th (HhH)2 domains. The second site is structurally similar to the first one and to the sites found in other AP lyases. The 3rd AP lyase site is located in the 12th (HhH)2 domain. The results show that Topo-V is an unusual protein: it is the only known protein with more than one (HhH)2 domain, the only known topoisomerase with dual activities and is also unique by having three AP lyase repair sites in the same polypeptide. PMID:26908655

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

    PubMed Central

    Rajan, Rakhi; Osterman, Amy; Mondragón, Alfonso

    2016-01-01

    Topoisomerase V (Topo-V) is the only topoisomerase with both topoisomerase and DNA repair activities. The topoisomerase activity is conferred by a small alpha-helical domain, whereas the AP lyase activity is found in a region formed by 12 tandem helix-hairpin-helix ((HhH)2) domains. Although it was known that Topo-V has multiple repair sites, only one had been mapped. Here, we show that Topo-V has three AP lyase sites. The atomic structure and Small Angle X-ray Scattering studies of a 97 kDa fragment spanning the topoisomerase and 10 (HhH)2 domains reveal that the (HhH)2 domains extend away from the topoisomerase domain. A combination of biochemical and structural observations allow the mapping of the second repair site to the junction of the 9th and 10th (HhH)2 domains. The second site is structurally similar to the first one and to the sites found in other AP lyases. The 3rd AP lyase site is located in the 12th (HhH)2 domain. The results show that Topo-V is an unusual protein: it is the only known protein with more than one (HhH)2 domain, the only known topoisomerase with dual activities and is also unique by having three AP lyase repair sites in the same polypeptide. PMID:26908655

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

    PubMed

    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.

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

    PubMed

    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

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

    PubMed

    Cockburn, Darrell; Wilkens, Casper; Dilokpimol, Adiphol; Nakai, Hiroyuki; Lewińska, Anna; Abou Hachem, Maher; Svensson, Birte

    2016-01-01

    Carbohydrate active enzymes often contain auxiliary binding sites located either on independent domains termed carbohydrate binding modules (CBMs) or as so-called surface binding sites (SBSs) on the catalytic module at a certain distance from the active site. The SBSs are usually critical for the activity of their cognate enzyme, though they are not readily detected in the sequence of a protein, but normally require a crystal structure of a complex for their identification. A variety of methods, including affinity electrophoresis (AE), insoluble polysaccharide pulldown (IPP) and surface plasmon resonance (SPR) have been used to study auxiliary binding sites. These techniques are complementary as AE allows monitoring of binding to soluble polysaccharides, IPP to insoluble polysaccharides and SPR to oligosaccharides. Here we show that these methods are useful not only for analyzing known binding sites, but also for identifying new ones, even without structural data available. We further verify the chosen assays discriminate between known SBS/CBM containing enzymes and negative controls. Altogether 35 enzymes are screened for the presence of SBSs or CBMs and several novel binding sites are identified, including the first SBS ever reported in a cellulase. This work demonstrates that combinations of these methods can be used as a part of routine enzyme characterization to identify new binding sites and advance the study of SBSs and CBMs, allowing them to be detected in the absence of structural data. PMID:27504624

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

    PubMed Central

    Wilkens, Casper; Dilokpimol, Adiphol; Nakai, Hiroyuki; Lewińska, Anna; Abou Hachem, Maher; Svensson, Birte

    2016-01-01

    Carbohydrate active enzymes often contain auxiliary binding sites located either on independent domains termed carbohydrate binding modules (CBMs) or as so-called surface binding sites (SBSs) on the catalytic module at a certain distance from the active site. The SBSs are usually critical for the activity of their cognate enzyme, though they are not readily detected in the sequence of a protein, but normally require a crystal structure of a complex for their identification. A variety of methods, including affinity electrophoresis (AE), insoluble polysaccharide pulldown (IPP) and surface plasmon resonance (SPR) have been used to study auxiliary binding sites. These techniques are complementary as AE allows monitoring of binding to soluble polysaccharides, IPP to insoluble polysaccharides and SPR to oligosaccharides. Here we show that these methods are useful not only for analyzing known binding sites, but also for identifying new ones, even without structural data available. We further verify the chosen assays discriminate between known SBS/CBM containing enzymes and negative controls. Altogether 35 enzymes are screened for the presence of SBSs or CBMs and several novel binding sites are identified, including the first SBS ever reported in a cellulase. This work demonstrates that combinations of these methods can be used as a part of routine enzyme characterization to identify new binding sites and advance the study of SBSs and CBMs, allowing them to be detected in the absence of structural data. PMID:27504624

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

    SciTech Connect

    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.

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

    PubMed

    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.

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

    PubMed

    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

  20. Studies on the active site of pig plasma amine oxidase.

    PubMed Central

    Collison, D; Knowles, P F; Mabbs, F E; Rius, F X; Singh, I; Dooley, D M; Cote, C E; McGuirl, M

    1989-01-01

    Amine oxidase from pig plasma (PPAO) has two bound Cu2+ ions and at least one pyrroloquinoline quinone (PQQ) moiety as cofactors. It is shown that recovery of activity by copper-depleted PPAO is linear with respect to added Cu2+ ions. Recovery of e.s.r. and optical spectral characteristics of active-site copper parallel the recovery of catalytic activity. These results are consistent with both Cu2+ ions contributing to catalysis. Further e.s.r. studies indicate that the two copper sites in PPAO, unlike those in amine oxidases from other sources, are chemically distinct. These comparative studies establish that non-identity of the Cu2+ ions in PPAO is not a requirement for amine oxidase activity. It is shown through the use of a new assay procedure that there are two molecules of PQQ bound per molecule of protein in PPAO; only the more reactive of these PQQ moieties is required for activity. PMID:2559715

  1. Using temperature-programmed desorption and the condensation approximation to determine surface site-energy distributions: examining the approximation's bases.

    SciTech Connect

    Brown, L. F.; Travis, B. J.

    2004-01-01

    Investigators (e.g., Seebauer 1994, Bogillo and Shkilev 1999) have used the condensation approximation (CA) successfully for determining broad nonuniform surface site-energy distributions (SEDs) from temperature-programmed desorption (TPD) spectra and for identifying constant pre-exponential factors from peak analysis. The CA assumes that at any temperature T, desorption occurs only at sites with a single desorption activation energy (E{sub cdn}). E{sub cdn} is of course a function of T. Further, the approximation assumes that during TPD all sites with desorption energy E{sub cdn} empty at T.

  2. Does Titan have an Active Surface?

    NASA Astrophysics Data System (ADS)

    Nelson, R.

    2009-12-01

    ammonia, a compound expected in Titan’s interior. This, combined with the previous evidence from VIMS and RADAR images, creates a strong case for Titan having a presently active surface, possibly due to cryovolcanism. Cassini encountered Titan at very close range on 2008-11-19-13:58 and again on 2008-12-05-12:38. These epochs are called T47 and T48. Comparison of earlier lower resolution data (T5) with the recent T47 and T48 data reveal changes of the surface reflectance and morphology in the Hotei region. This is the first evidence from VIMS that confirms the RADAR report that Hotei Reggio has morphology consistent with volcanic terrain. It has not escaped our attention that ammonia, in association with methane and nitrogen, the principal species of Titan’s atmosphere, closely replicates the environment at the time that live first emerged on earth. If Titan is currently active then these results raise the following questions: What is the full extent of current geologic activity? What are the ongoing processes? Are Titan’s chemical processes today supporting a prebiotic chemistry similar to that under which life evolved on Earth? This work done at JPL under contract with NASA. Refs: [1]R. M. Nelson et al., Icarus 199 (2009) 429-441. [2]R. M. Nelson et al., GRL, VOL. 36, L04202, doi:10.1029/2008GL036206, 2009. [3]S. D. Wall GRL, VOL. 36, L04203, doi:10.1029/2008GL036415, 2009

  3. Surface Forcing from CH4 at the North Slope of Alaska and Southern Great Plains Sites

    NASA Astrophysics Data System (ADS)

    Collins, W.; Feldman, D.; Turner, D. D.

    2014-12-01

    Recent increases in atmospheric CH4 have been spatially heterogeneous as indicated by in situ flask measurements and space-borne remote-sensing retrievals from the AIRS instrument, potentially leading to increased radiative forcing. We present detailed, specialized measurements at the DOE ARM North Slope of Alaska (NSA) and Southern Great Plains (SGP) sites to derive the time-series of both CH4 atmospheric concentrations and associated radiative implications at highly-contrasting natural and anthropogenic sources. Using a combination of spectroscopic measurements, in situ observations, and ancillary data for the atmospheric thermodynamic state from radiosondes and cloud-clearing from active sounders, we can separate out the contribution of CH4 to clear-sky downwelling radiance spectra and its infrared surface forcing. The time-series indicates year-to-year variation in shoulder season increases of CH4 concentration and forcing at NSA and large signals from anthropogenic activity at SGP.

  4. Computer simulation of the active site of human serum cholinesterase

    SciTech Connect

    Kefang Jiao; Song Li; Zhengzheng Lu

    1996-12-31

    The first 3D-structure of acetylchelinesterase from Torpedo California electric organ (T.AChE) was published by JL. Sussman in 1991. We have simulated 3D-structure of human serum cholinesterase (H.BuChE) and the active site of H.BuChE. It is discovered by experiment that the residue of H.BuChE is still active site after a part of H.BuChE is cut. For example, the part of 21KD + 20KD is active site of H.BuChE. The 20KD as it is. Studies on these peptides by Hemelogy indicate that two active peptides have same negative electrostatic potential maps diagram. These negative electrostatic areas attached by acetyl choline with positive electrostatic potency. We predict that 147...236 peptide of AChE could be active site because it was as 20KD as with negative electrostatic potential maps. We look forward to proving from other ones.

  5. Near-surface gas mapping studies of salt geologic features at Weeks Island and other sites

    SciTech Connect

    Molecke, M.A.; Carney, K.R.; Autin, W.J.; Overton, E.B.

    1996-10-01

    Field sampling and rapid gas analysis techniques were used to survey near-surface soil gases for geotechnical diagnostic purposes at the Weeks Island Strategic Petroleum Reserve (SPR) site and other salt dome locations in southern Louisiana. This report presents the complete data, results and interpretations obtained during 1995. Weeks Island 1994 gas survey results are also briefly summarized; this earlier study did not find a definitive correlation between sinkhole No. 1 and soil gases. During 1995, several hundred soil gas samples were obtained and analyzed in the field by gas chromatography, for profiling low concentrations and gas anomalies at ppm to percent levels. The target gases included hydrogen, methane, ethane and ethylene. To supplement the field data, additional gas samples were collected at various site locations for laboratory analysis of target gases at ppb levels. Gases in the near-surface soil originate predominantly from the oil, from petrogenic sources within the salt, or from surface microbial activity. Surveys were conducted across two Weeks Island sinkholes, several mapped anomalous zones in the salt, and over the SPR repository site and its perimeter. Samples were also taken at other south Louisiana salt dome locations for comparative purposes. Notable results from these studies are that elevated levels of hydrogen and methane (1) were positively associated with anomalous gassy or shear zones in the salt dome(s) and (2) are also associated with suspected salt fracture (dilatant) zones over the edges of the SPR repository. Significantly elevated areas of hydrogen, methane, plus some ethane, were found over anomalous shear zones in the salt, particularly in a location over high pressure gas pockets in the salt, identified in the mine prior to SPR operations. Limited stable isotope ratio analyses, SIRA, were also conducted and determined that methane samples were of petrogenic origin, not biogenic.

  6. Multi-site Phosphorylation Regulates Bim Stability and Apoptotic Activity

    PubMed Central

    Hübner, Anette; Barrett, Tamera; Flavell, Richard A.; Davis, Roger J.

    2008-01-01

    The pro-apoptotic BH3-only protein Bim is established to be an important mediator of signaling pathways that induce cell death. Multi-site phosphorylation of Bim by several members of the MAP kinase group is implicated as a regulatory mechanism that controls the apoptotic activity of Bim. To test the role of Bim phosphorylation in vivo, we constructed mice with a series of mutant alleles that express phosphorylation-defective Bim proteins. We show that mutation of the phosphorylation site Thr-112 causes decreased binding of Bim to the anti-apoptotic protein Bcl2 and can increase cell survival. In contrast, mutation of the phosphorylation sites Ser-55, Ser-65, and Ser-73 can cause increased apoptosis because of reduced proteasomal degradation of Bim. Together, these data indicate that phosphorylation can regulate Bim by multiple mechanisms and that the phosphorylation of Bim on different sites can contribute to the sensitivity of cellular apoptotic responses. PMID:18498746

  7. C¹ Positive Surface over Positive Scattered Data Sites

    PubMed Central

    Ibraheem, Farheen; Hussain, Malik Zawwar; Bhatti, Akhlaq Ahmad

    2015-01-01

    The aim of this paper is to develop a local positivity preserving scheme when the data amassed from different sources is positioned at sparse points. The proposed algorithm first triangulates the irregular data using Delauny triangulation method, therewith interpolates each boundary and radial curve of the triangle by C¹ rational trigonometric cubic function. Half of the parameters in the description of the interpolant are constrained to keep up the positive shape of data while the remaining half are set free for users’ requirement. Orthogonality of trigonometric function assures much smoother surface as compared to polynomial functions. The proposed scheme can be of great use in areas of surface reconstruction and deformation, signal processing, CAD/CAM design, solving differential equations, and image restoration. PMID:26057122

  8. Active Site Dependent Reaction Mechanism over Ru/CeO2 Catalyst toward CO2 Methanation.

    PubMed

    Wang, Fei; He, Shan; Chen, Hao; Wang, Bin; Zheng, Lirong; Wei, Min; Evans, David G; Duan, Xue

    2016-05-18

    Oxygen vacancy on the surface of metal oxides is one of the most important defects which acts as the reactive site in a variety of catalytic reactions. In this work, operando spectroscopy methodology was employed to study the CO2 methanation reaction catalyzed by Ru/CeO2 (with oxygen vacancy in CeO2) and Ru/α-Al2O3 (without oxygen vacancy), respectively, so as to give a thorough understanding on active site dependent reaction mechanism. In Ru/CeO2 catalyst, operando XANES, IR, and Raman were used to reveal the generation process of Ce(3+), surface hydroxyl, and oxygen vacancy as well as their structural evolvements under practical reaction conditions. The steady-state isotope transient kinetic analysis (SSITKA)-type in situ DRIFT infrared spectroscopy undoubtedly substantiates that CO2 methanation undergoes formate route over Ru/CeO2 catalyst, and the formate dissociation to methanol catalyzed by oxygen vacancy is the rate-determining step. In contrast, CO2 methanation undergoes CO route over Ru surface in Ru/α-Al2O3 with the absence of oxygen vacancy, demonstrating active site dependent catalytic mechanism toward CO2 methanation. In addition, the catalytic activity evaluation and the oscillating reaction over Ru/CeO2 catalyst further prove that the oxygen vacancy catalyzes the rate-determining step with a much lower activation temperature compared with Ru surface in Ru/α-Al2O3 (125 vs 250 °C).

  9. Rapid comparison of protein binding site surfaces with Property Encoded Shape Distributions (PESD)

    PubMed Central

    Das, Sourav; Kokardekar, Arshad

    2009-01-01

    Patterns in shape and property distributions on the surface of binding sites are often conserved across functional proteins without significant conservation of the underlying amino-acid residues. To explore similarities of these sites from the viewpoint of a ligand, a sequence and fold-independent method was created to rapidly and accurately compare binding sites of proteins represented by property-mapped triangulated Gauss-Connolly surfaces. Within this paradigm, signatures for each binding site surface are produced by calculating their property-encoded shape distributions (PESD), a measure of the probability that a particular property will be at a specific distance to another on the molecular surface. Similarity between the signatures can then be treated as a measure of similarity between binding sites. As postulated, the PESD method rapidly detected high levels of similarity in binding site surface characteristics even in cases where there was very low similarity at the sequence level. In a screening experiment involving each member of the PDBBind 2005 dataset as a query against the rest of the set, PESD was able to retrieve a binding site with identical E.C. (Enzyme Commission) numbers as the top match in 79.5% of cases. The ability of the method in detecting similarity in binding sites with low sequence conservations were compared with state-of-the-art binding site comparison methods. PMID:19919089

  10. Surface activation of Concorde by Be-7

    NASA Technical Reports Server (NTRS)

    Truscott, P. R.; Dyer, C. S.; Flatman, J. C.

    1992-01-01

    Activation analysis of two airframe components from the Concorde aircraft has identified the presence of Be-7, a nuclide found by other investigators that was deposited on the forward edge of the Long Duration Exposure Facility (LDEF) structure. The results of the Concorde analysis indicate that this phenomenon is very much a surface effect, and that the areal densities of the Be-7 are comparable to those found for LDEF. The collection of Be-7 by the aircraft must be greater than in the case of LDEF (since duration for which Concorde is accumulating the nuclide is shorter) and is of the order of 1.2 to 41 nuclei/sq cm(-)s(exp -1) depending upon assumptions made regarding the altitude at which collection becomes appreciable, and the efficiency of the process which removes the radionuclide.

  11. Water in the Active Site of Ketosteroid Isomerase

    PubMed Central

    Hanoian, Philip; Hammes-Schiffer, Sharon

    2011-01-01

    Classical molecular dynamics simulations were utilized to investigate the structural and dynamical properties of water in the active site of ketosteroid isomerase (KSI) to provide insight into the role of these water molecules in the enzyme-catalyzed reaction. This reaction is thought to proceed via a dienolate intermediate that is stabilized by hydrogen bonding with residues Tyr16 and Asp103. A comparative study was performed for the wild-type (WT) KSI and the Y16F, Y16S, and Y16F/Y32F/Y57F (FFF) mutants. These systems were studied with three different bound ligands: equilenin, which is an intermediate analog, and the intermediate states of two steroid substrates. Several distinct water occupation sites were identified in the active site of KSI for the WT and mutant systems. Three additional sites were identified in the Y16S mutant that were not occupied in WT KSI or the other mutants studied. The number of water molecules directly hydrogen bonded to the ligand oxygen was approximately two waters in the Y16S mutant, one water in the Y16F and FFF mutants, and intermittent hydrogen bonding of one water molecule in WT KSI. The molecular dynamics trajectories of the Y16F and FFF mutants reproduced the small conformational changes of residue 16 observed in the crystal structures of these two mutants. Quantum mechanical/molecular mechanical calculations of 1H NMR chemical shifts of the protons in the active site hydrogen-bonding network suggest that the presence of water in the active site does not prevent the formation of short hydrogen bonds with far-downfield chemical shifts. The molecular dynamics simulations indicate that the active site water molecules exchange much more frequently for WT KSI and the FFF mutant than for the Y16F and Y16S mutants. This difference is most likely due to the hydrogen-bonding interaction between Tyr57 and an active site water molecule that is persistent in the Y16F and Y16S mutants but absent in the FFF mutant and significantly less

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

    PubMed

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

    2014-12-16

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

  13. PEP-SiteFinder: a tool for the blind identification of peptide binding sites on protein surfaces.

    PubMed

    Saladin, Adrien; Rey, Julien; Thévenet, Pierre; Zacharias, Martin; Moroy, Gautier; Tufféry, Pierre

    2014-07-01

    Peptide-protein interactions are important to many processes of life, particularly for signal transmission or regulatory mechanisms. When no information is known about the interaction between a protein and a peptide, it is of interest to propose candidate sites of interaction at the protein surface, to assist the design of biological experiments to probe the interaction, or to serve as a starting point for more focused in silico approaches. PEP-SiteFinder is a tool that will, given the structure of a protein and the sequence of a peptide, identify protein residues predicted to be at peptide-protein interface. PEP-SiteFinder relies on the 3D de novo generation of peptide conformations given its sequence. These conformations then undergo a fast blind rigid docking on the complete protein surface, and we have found, as the result of a benchmark over 41 complexes, that the best poses overlap to some extent the experimental patch of interaction for close to 90% complexes. In addition, PEP-SiteFinder also returns a propensity index we have found informative about the confidence of the prediction. The PEP-SiteFinder web server is available at http://bioserv.rpbs.univ-paris-diderot.fr/PEP-SiteFinder.

  14. PEP-SiteFinder: a tool for the blind identification of peptide binding sites on protein surfaces

    PubMed Central

    Saladin, Adrien; Rey, Julien; Thévenet, Pierre; Zacharias, Martin; Moroy, Gautier; Tufféry, Pierre

    2014-01-01

    Peptide–protein interactions are important to many processes of life, particularly for signal transmission or regulatory mechanisms. When no information is known about the interaction between a protein and a peptide, it is of interest to propose candidate sites of interaction at the protein surface, to assist the design of biological experiments to probe the interaction, or to serve as a starting point for more focused in silico approaches. PEP-SiteFinder is a tool that will, given the structure of a protein and the sequence of a peptide, identify protein residues predicted to be at peptide–protein interface. PEP-SiteFinder relies on the 3D de novo generation of peptide conformations given its sequence. These conformations then undergo a fast blind rigid docking on the complete protein surface, and we have found, as the result of a benchmark over 41 complexes, that the best poses overlap to some extent the experimental patch of interaction for close to 90% complexes. In addition, PEP-SiteFinder also returns a propensity index we have found informative about the confidence of the prediction. The PEP-SiteFinder web server is available at http://bioserv.rpbs.univ-paris-diderot.fr/PEP-SiteFinder. PMID:24803671

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

    ERIC Educational Resources Information Center

    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…

  16. Energy transfer at the active sites of heme proteins

    SciTech Connect

    Dlott, D.D.; Hill, J.R.

    1995-12-31

    Experiments using a picosecond pump-probe apparatus at the Picosecond Free-electron Laser Center at Stanford University, were performed to investigate the relaxation of carbon monoxide bound to the active sites of heme proteins. The significance of these experiments is two-fold: (1) they provide detailed information about molecular dynamics occurring at the active sites of proteins; and (2) they provide insight into the nature of vibrational relaxation processes in condensed matter. Molecular engineering is used to construct various molecular systems which are studied with the FEL. We have studied native proteins, mainly myoglobin obtained from different species, mutant proteins produced by genetic engineering using recombinant DNA techniques, and a variety of model systems which mimic the structures of the active sites of native proteins, which are produced using molecular synthesis. Use of these different systems permits us to investigate how specific molecular structural changes affect dynamical processes occurring at the active sites. This research provides insight into the problems of how different species needs are fulfilled by heme proteins which have greatly different functionality, which is induced by rather small structural changes.

  17. Remaining Sites Verification Package for the 100-B-23, 100-B/C Area Surface Debris, Waste Site, Waste Site Reclassification Form 2008-027

    SciTech Connect

    J. M. Capron

    2008-06-16

    The 100-B-23, 100-B/C Surface Debris, waste consisted of multiple locations of surface debris and chemical stains that were identified during an Orphan Site Evaluation of the 100-B/C Area. Evaluation of the collected information for the surface debris features yielded four generic waste groupings: asbestos-containing material, lead debris, oil and oil filters, and treated wood. Focused verification sampling was performed concurrently with remediation. Site remediation was accomplished by selective removal of the suspect hazardous items and potentially impacted soils. In accordance with this evaluation, the verification sampling results support a reclassification of this site to Interim Closed Out. The results of verification sampling show that residual contaminant concentrations do not preclude any future uses and allow for unrestricted use of shallow zone soils. The results also demonstrate that residual contaminant concentrations are protective of groundwater and the Columbia River.

  18. Changes in active site histidine hydrogen bonding trigger cryptochrome activation.

    PubMed

    Ganguly, Abir; Manahan, Craig C; Top, Deniz; Yee, Estella F; Lin, Changfan; Young, Michael W; Thiel, Walter; Crane, Brian R

    2016-09-01

    Cryptochrome (CRY) is the principal light sensor of the insect circadian clock. Photoreduction of the Drosophila CRY (dCRY) flavin cofactor to the anionic semiquinone (ASQ) restructures a C-terminal tail helix (CTT) that otherwise inhibits interactions with targets that include the clock protein Timeless (TIM). All-atom molecular dynamics (MD) simulations indicate that flavin reduction destabilizes the CTT, which undergoes large-scale conformational changes (the CTT release) on short (25 ns) timescales. The CTT release correlates with the conformation and protonation state of conserved His378, which resides between the CTT and the flavin cofactor. Poisson-Boltzmann calculations indicate that flavin reduction substantially increases the His378 pKa Consistent with coupling between ASQ formation and His378 protonation, dCRY displays reduced photoreduction rates with increasing pH; however, His378Asn/Arg variants show no such pH dependence. Replica-exchange MD simulations also support CTT release mediated by changes in His378 hydrogen bonding and verify other responsive regions of the protein previously identified by proteolytic sensitivity assays. His378 dCRY variants show varying abilities to light-activate TIM and undergo self-degradation in cellular assays. Surprisingly, His378Arg/Lys variants do not degrade in light despite maintaining reactivity toward TIM, thereby implicating different conformational responses in these two functions. Thus, the dCRY photosensory mechanism involves flavin photoreduction coupled to protonation of His378, whose perturbed hydrogen-bonding pattern alters the CTT and surrounding regions. PMID:27551082

  19. Rapid binding of a cationic active site inhibitor to wild type and mutant mouse acetylcholinesterase: Brownian dynamics simulation including diffusion in the active site gorge.

    PubMed

    Tara, S; Elcock, A H; Kirchhoff, P D; Briggs, J M; Radic, Z; Taylor, P; McCammon, J A

    1998-12-01

    It is known that anionic surface residues play a role in the long-range electrostatic attraction between acetylcholinesterase and cationic ligands. In our current investigation, we show that anionic residues also play an important role in the behavior of the ligand within the active site gorge of acetylcholinesterase. Negatively charged residues near the gorge opening not only attract positively charged ligands from solution to the enzyme, but can also restrict the motion of the ligand once it is inside of the gorge. We use Brownian dynamics techniques to calculate the rate constant kon, for wild type and mutant acetylcholinesterase with a positively charged ligand. These calculations are performed by allowing the ligand to diffuse within the active site gorge. This is an extension of previously reported work in which a ligand was allowed to diffuse only to the enzyme surface. By setting the reaction criteria for the ligand closer to the active site, better agreement with experimental data is obtained. Although a number of residues influence the movement of the ligand within the gorge, Asp74 is shown to play a particularly important role in this function. Asp74 traps the ligand within the gorge, and in this way helps to ensure a reaction.

  20. Conformational Transitions in Human AP Endonuclease 1 and Its Active Site Mutant during Abasic Site Repair†

    PubMed Central

    Kanazhevskaya, Lyubov Yu.; Koval, Vladimir V.; Zharkov, Dmitry O.; Strauss, Phyllis R.; Fedorova, Olga S.

    2010-01-01

    AP endonuclease 1 (APE 1) is a crucial enzyme of the base excision repair pathway (BER) in human cells. APE1 recognizes apurinic/apyrimidinic (AP) sites and makes a nick in the phosphodiester backbone 5′ to them. The conformational dynamics and presteady-state kinetics of wild-type APE1 and its active site mutant, Y171F-P173L-N174K, have been studied. To observe conformational transitions occurring in the APE1 molecule during the catalytic cycle, we detected intrinsic tryptophan fluorescence of the enzyme under single turnover conditions. DNA duplexes containing a natural AP site, its tetrahydrofuran analogue, or a 2′-deoxyguanosine residue in the same position were used as specific substrates or ligands. The stopped-flow experiments have revealed high flexibility of the APE1 molecule and the complexity of the catalytic process. The fluorescent traces indicate that wild-type APE1 undergoes at least four conformational transitions during the processing of abasic sites in DNA. In contrast, nonspecific interactions of APE1 with undamaged DNA can be described by a two-step kinetic scheme. Rate and equilibrium constants were extracted from the stopped-flow and fluorescence titration data for all substrates, ligands, and products. A replacement of three residues at the enzymatic active site including the replacement of tyrosine 171 with phenylalanine in the enzyme active site resulted in a 2 × 104-fold decrease in the reaction rate and reduced binding affinity. Our data indicate the important role of conformational changes in APE1 for substrate recognition and catalysis. PMID:20575528

  1. Surface Radiation Survey at the Shepley’s Hill Remediation Site, Devens, Massachusettes

    SciTech Connect

    J. R. Giles; C. P. Oertel; L. G. Roybal

    2009-09-01

    The Idaho National Laboratory (INL) provided technical support for ongoing environmental remediation activities at the Shepley’s Hill remediation site, near Devens, MA. The technical support included the completion of a radiation survey of naturally occurring radioactive materials (NORM) at Shepley’s Hill, Shepley’s Hill landfill cover, and Red Cove areas. The objective of the radiation survey was to assess the ability of the INL backpack sodium iodide spectroscopy (BaSIS) system to detect elevated levels of NORM that may be associated with radon-222 emanation from near surface and subsurface fractures in the area. It is postulated that these fracture zones provide subsurface conduits for the transport of environmental contaminants. As such, location of these fracture sets will proved EPA Region 1 with the means for completing the development of an accurate site conceptual model. The results of the radiological survey show that some of the radiological anomalies correlate with currently mapped rock outcrops; however, not all of the rock outcrops in the surveyed area have been mapped. As such, it is not conclusive that all of the radiological anomalies correspond with surface rock outcrops. EPA Region 1 intends to perform a more comprehensive correlation of the radiation data collected with the BaSIS system with additional data sets such as detailed bedrock structural mapping, 2-dimensional resistivity profiling, and high-resolution topographic mapping. The results of this effort will be used in consideration of designing a potential follow-on effort for mapping of radon.

  2. INORGANIC PLUME DELINEATION USING SURFACE HIGH RESOLUTION ELECTRICAL RESISTIVITY AT THE BC CRIBS & TRENCHES SITE HANFORD

    SciTech Connect

    BENECKE, M.W.

    2007-05-29

    A surface resistivity survey was conducted on the Hanford Site over a waste disposal trench that received a large volume of liquid inorganic waste. The objective of the survey was to map the extent of the plume that resulted from the disposal activities approximately 50 years earlier. The survey included six resistivity transects of at least 200m, where each transect provided two-dimensional profile information of subsurface electrical properties. The results of the survey indicated that a low resistivity plume resides at a depth of approximately 25-44 m below ground surface. The target depth was calibrated with borehole data of pore-water electrical conductivity. Due to the high correlation of the pore-water electrical conductivity to nitrate concentration and the high correlation of measured apparent resistivity to pore-water electrical conductivity, inferences were made that proposed the spatial distribution of the apparent resistivity was due to the distribution of nitrate. Therefore, apparent resistivities were related to nitrate, which was subsequently rendered in three dimensions to show that the nitrate likely did not reach the water table and the bounds of the highest concentrations are directly beneath the collection of waste sites.

  3. Site-selective biofunctionalization of aluminum nitride surfaces using patterned organosilane self-assembled monolayers.

    PubMed

    Chiu, Chi-Shun; Lee, Hong-Mao; Gwo, Shangjr

    2010-02-16

    Surface biochemical functionalization of group-III nitride semiconductors has recently attracted much interest because of their biocompatibility, nontoxicity, and long-term chemical stability under demanding physiochemical conditions for chemical and biological sensing. Among III-nitrides, aluminum nitride (AlN) and aluminum gallium nitride (AlGaN) are particularly important because they are often used as the sensing surfaces for sensors based on field-effect transistor or surface acoustic wave (SAW) sensor structures. To demonstrate the possibility of site-selective biofunctionalization on AlN surfaces, we have fabricated two-dimensional antibody micropatterns on AlN surfaces by using patterned self-assembled monolayer (SAM) templates. Patterned SAM templates are composed of two types of organosilane molecules terminated with different functional groups (amino and methyl), which were fabricated on AlN/sapphire substrates by combining photolithography, lift-off process, and self-assembly technique. Because the patterned SAM templates have different surface properties on the same surface, clear imaging contrast of SAM micropatterns can be observed by field-emission scanning electron microscopy (FE-SEM) operating at a low accelerating voltage in the range of 0.5-1.5 kV. Furthermore, the contrast in surface potential of the binary SAM microstructures was confirmed by selective adsorption of negatively charged colloidal gold nanoparticles (AuNPs). The immobilization of AuNPs was limited on the positively charged amino-terminated regions, while they were scarcely found on the surface regions terminated by methyl groups. In this work, selective immobilization of green fluorescent protein (GFP) antibodies was demonstrated by the specific protein binding of enhanced GFP (EGFP) labeling. The observed strong fluorescent signal from antibody functionalized regions on the SAM-patterned AlN surface indicates the retained biological activity of specific molecular recognition

  4. Anisotropic capillary barrier for waste site surface covers

    DOEpatents

    Stormont, John C.

    1996-01-01

    Waste sites are capped or covered upon closure. The cover structure incorporates a number of different layers each having a contributory function. One such layer is the barrier layer. Traditionally the barriers have been compacted soil and geosynthetics. These types of barriers have not been successfully implemented in unsaturated ground conditions like those found in dry climates. Capillary barriers have been proposed as barrier layers in dry environments, but the divergence length of these barriers has been found to be inadequate. An alternative to the capillary barrier is a anisotropic capillary barrier. An anisotropic capillary barrier has an increased divergence length which results in more water being diverted laterally preventing the majority of water from percolating in a downward direction through the barrier.

  5. Anisotropic capillary barrier for waste site surface covers

    DOEpatents

    Stormont, J.C.

    1996-08-27

    Waste sites are capped or covered upon closure. The cover structure incorporates a number of different layers each having a contributory function. One such layer is the barrier layer. Traditionally the barriers have been compacted soil and geosynthetics. These types of barriers have not been successfully implemented in unsaturated ground conditions like those found in dry climates. Capillary barriers have been proposed as barrier layers in dry environments, but the divergence length of these barriers has been found to be inadequate. An alternative to the capillary barrier is a anisotropic capillary barrier. An anisotropic capillary barrier has an increased divergence length which results in more water being diverted laterally preventing the majority of water from percolating in a downward direction through the barrier. 10 figs.

  6. Surface active properties of chitosan and its derivatives.

    PubMed

    Elsabee, Maher Z; Morsi, Rania Elsayed; Al-Sabagh, A M

    2009-11-01

    This review discusses the definition of surface active agents and specifically natural polymeric surface active agents. Chitosan by itself was found to have weak surface activity since it has no hydrophobic segments. Chemical modifications of chitosan could improve such surface activity. This is achieved by introducing hydrophobic substituents in its glucosidic group. Several examples of chitosan derivatives with surfactant activity have been surveyed. The surface active polymers form micelles and aggregates which have enormous importance in the entrapment of water-insoluble drugs and consequently applications in the controlled drug delivery and many biomedical fields. Chitosan also interacts with several substrates by electrostatic and hydrophobic interactions with considerable biomedical applications.

  7. The origin of summertime crust and surface hoar formation at the WAIS Divide site, West Antarctica

    NASA Astrophysics Data System (ADS)

    Fegyveresi, J. M.; Alley, R. B.; Spencer, M. K.

    2013-12-01

    Summertime field observations at the WAIS Divide site, West Antarctica, indicate a very active surface. Over five consecutive seasons (2008-2013), daily surface measurements were made along with photography of the surface and of back-lit snowpits, where densities were measured. The Automatic Weather Station in the University of Wisconsin network was supplemented by various independent sensors deployed on site, including pyranometer sensor arrays and net-radiometers in order to better quantify the short-wave and long-wave radiation conditions surrounding near-surface metamorphism. Prominent 'glazed' crusts occur frequently. Surface and pit observations show that such crusts form in summertime during relative low-wind, low-humidity, high-temperature episodes that immediately follow a succession of strong wind events. During each documented case of formation, these episodes were also brought about during clear-sky days with maximum diurnal variability of incoming solar energy. Shallow firn temperature measurements indicate strong inversions during crust formation that likely lead to increased vapor transport. Furthermore, distinct hoar frost growth was observed on crusts that were exposed to multiple clear-sky days, likely as a result of increased insolation, humidity, and vertical vapor transport in the near-surface. There was no obvious indication of melt associated with glazed features during initial inspection. Examination of the WDC06A ice core and its associated ECM record indicates that numerous crusts are present very regularly throughout the core and in all seasons. Crusts are about 40% more abundant in summertime than in wintertime deposits, likely due to the formation of 'glazed' surfaces; formation mechanisms of the less-common wintertime crusts have not been observed and are not known. Over the ice-core record, there is little change in frequency of occurrence of wintertime crusts, but some changes in summertime, perhaps indicating changes in occurrence

  8. N-methyl-D-aspartate recognition site ligands modulate activity at the coupled glycine recognition site.

    PubMed

    Hood, W F; Compton, R P; Monahan, J B

    1990-03-01

    In synaptic plasma membranes from rat forebrain, the potencies of glycine recognition site agonists and antagonists for modulating [3H]1-[1-(2-thienyl)cyclohexyl]piperidine ([3H]TCP) binding and for displacing strychnine-insensitive [3H]glycine binding are altered in the presence of N-methyl-D-aspartate (NMDA) recognition site ligands. The NMDA competitive antagonist, cis-4-phosphonomethyl-2-piperidine carboxylate (CGS 19755), reduces [3H]glycine binding, and the reduction can be fully reversed by the NMDA recognition site agonist, L-glutamate. Scatchard analysis of [3H]glycine binding shows that in the presence of CGS 19755 there is no change in Bmax (8.81 vs. 8.79 pmol/mg of protein), but rather a decrease in the affinity of glycine (KD of 0.202 microM vs. 0.129 microM). Similar decreases in affinity are observed for the glycine site agonists, D-serine and 1-aminocyclopropane-1-carboxylate, in the presence of CGS 19755. In contrast, the affinity of glycine antagonists, 1-hydroxy-3-amino-2-pyrrolidone and 1-aminocyclobutane-1-carboxylate, at this [3H]glycine recognition site increases in the presence of CGS 19755. The functional consequence of this change in affinity was addressed using the modulation of [3H]TCP binding. In the presence of L-glutamate, the potency of glycine agonists for the stimulation of [3H]TCP binding increases, whereas the potency of glycine antagonists decreases. These data are consistent with NMDA recognition site ligands, through their interactions at the NMDA recognition site, modulating activity at the associated glycine recognition site.

  9. Near-surface wave velocity structure of Faial (Azores - Portugal) Island for site effect studies

    NASA Astrophysics Data System (ADS)

    Borges, José; Neves, Samuel; Caldeira, Bento; Bezzeghoud, Mourad; Carvalho, João; Carvalho, Alexandra

    2015-04-01

    Throughout history, the life of the Azorean people has been marked by earthquakes that have had different effects depending on their proximity and magnitude. This seismic activity, which may have volcanic or tectonic origins, has affected the population of these islands by destroying infrastructure and claiming lives. The social and economic impacts of these phenomena are enormous. The last significant event affecting the Azores (Portugal) was the July 1998 Mw=6.2 earthquake causing major destruction affecting more than 5000 people, causing 8 deaths, 150 persons injured and 1500 homeless. Ground motion simulations are mainly based on source characteristics and are heavily dependent on the medium, which is still poorly understood. Subsurface soil condition can amplify the seismic waves, so, for seismic response analysis, it is necessary to know the shallow soil properties and its spatial variability. For this purpose, we applied P and S-wave refraction, Multichannel Analysis of Surface Waves (MASW) to characterize shear wave velocity at different sites in the Faial Island, in particular, in sites where already occurred amplification. Ambient vibrations can also be used to estimate physical properties of the shallower geological formations. With this goal, the obtained velocity models were confirmed by comparison between real H/V curves with synthetic ones. We concluded that the anomalous intensities observed in some sites are strongly related to thick layers of soft sediments of pyroclastic deposits produced by old volcanic eruptions occurred in the Faial Island.

  10. [Ventricular activation sequence estimated by body surface isochrone map].

    PubMed

    Hayashi, H; Ishikawa, T; Takami, K; Kojima, H; Yabe, S; Ohsugi, S; Miyachi, K; Sotobata, I

    1985-06-01

    This study was performed to evaluate the usefulness of the body surface isochrone map (VAT map) for identifying the ventricular activation sequence, and it was correlated with the isopotential map. Subjects consisted of 42 normal healthy adults, 18 patients with artificial ventricular pacemakers, and 100 patients with ventricular premature beats (VPB). The sites of pacemaker implantations were the right ventricular endocardial apex (nine cases), right ventricular epicardial apex (five cases), right ventricular inflow tract (one case), left ventricular epicardial apex (one case), and posterior base of the left ventricle via the coronary sinus (two cases). An isopotential map was recorded by the mapper HPM-6500 (Chunichi-Denshi Co.) on the basis of an 87 unipolar lead ECG, and a VAT isochrone map was drawn by a minicomputer. The normal VAT map was classified by type according to alignment of isochrone lines, and their frequency was 57.1% for type A, 16.7% for type B, and 26.2% for type C. In the VAT map of ventricular pacing, the body surface area of initial isochrone lines represented well the sites of pacemaker stimuli. In the VAT map of VPB, the sites of origin of VPB agreed well with those as determined by the previous study using an isopotential map. The density of the isochrone lines suggested the mode of conduction via the specialized conduction system or ventricular muscle. The VAT map is a very useful diagnostic method to predict the ventricular activation sequence more directly in a single sheet of the map. PMID:2419457

  11. An in situ vapour phase hydrothermal surface doping approach for fabrication of high performance Co3O4 electrocatalysts with an exceptionally high S-doped active surface.

    PubMed

    Tan, Zhijin; Liu, Porun; Zhang, Haimin; Wang, Yun; Al-Mamun, Mohammad; Yang, Hua Gui; Wang, Dan; Tang, Zhiyong; Zhao, Huijun

    2015-04-01

    A facile in situ vapour phase hydrothermal (VPH) surface doping approach has been developed for fabrication of high performance S-doped Co3O4 electrocatalysts with an unprecedentedly high surface S content (>47%). The demonstrated VPH doping approach could be useful for enrichment of surface active sites for other metal oxide electrocatalysts. PMID:25714902

  12. Controlled release of biologically active silver from nanosilver surfaces.

    PubMed

    Liu, Jingyu; Sonshine, David A; Shervani, Saira; Hurt, Robert H

    2010-11-23

    Major pathways in the antibacterial activity and eukaryotic toxicity of nanosilver involve the silver cation and its soluble complexes, which are well established thiol toxicants. Through these pathways, nanosilver behaves in analogy to a drug delivery system, in which the particle contains a concentrated inventory of an active species, the ion, which is transported to and released near biological target sites. Although the importance of silver ion in the biological response to nanosilver is widely recognized, the drug delivery paradigm has not been well developed for this system, and there is significant potential to improve nanosilver technologies through controlled release formulations. This article applies elements of the drug delivery paradigm to nanosilver dissolution and presents a systematic study of chemical concepts for controlled release. After presenting thermodynamic calculations of silver species partitioning in biological media, the rates of oxidative silver dissolution are measured for nanoparticles and macroscopic foils and used to derive unified area-based release kinetics. A variety of competing chemical approaches are demonstrated for controlling the ion release rate over 4 orders of magnitude. Release can be systematically slowed by thiol and citrate ligand binding, formation of sulfidic coatings, or the scavenging of peroxy-intermediates. Release can be accelerated by preoxidation or particle size reduction, while polymer coatings with complexation sites alter the release profile by storing and releasing inventories of surface-bound silver. Finally, the ability to tune biological activity is demonstrated through a bacterial inhibition zone assay carried out on selected formulations of controlled release nanosilver.

  13. Effect of Surface-Active Pseudomonas spp. on Leaf Wettability

    PubMed Central

    Bunster, Lillian; Fokkema, Nyckle J.; Schippers, Bob

    1989-01-01

    Different strains of Pseudomonas putida and P. fluorescens isolated from the rhizosphere and phyllosphere were tested for surface activity in droplet cultures on polystyrene. Droplets of 6 of the 12 wild types tested spread over the surface during incubation, and these strains were considered surface active; strains not showing this reaction were considered non-surface active. Similar reactions were observed on pieces of wheat leaves. Supernatants from centrifuged broth cultures behaved like droplets of suspensions in broth; exposure to 100°C destroyed the activity. Average contact angles of the supernatants of surface-active and non-surface-active strains on polystyrene were 24° and 72°, respectively. The minimal surface tension of supernatants of the surface-active strains was about 46 mN/m, whereas that of the non-surface-active strains was 64 mN/m (estimations from Zisman plots). After 6 days of incubation, wheat flag leaves sprayed with a dilute suspension of a surface-active strain of P. putida (WCS 358RR) showed a significant increase in leaf wettability, which was determined by contact angle measurements. Increasing the initial concentration of bacteria and the amount of nutrients in the inoculum sprayed on leaves reduced the contact angles from 138° on leaves treated with antibiotics (control) to 43° on leaves treated with surface-active bacteria. A closely related strain with no surface activity on polystyrene did not affect leaf wettability, although it was present in densities similar to those of the surface-active strain. Nutrients alone could occasionally also increase leaf wettability, apparently by stimulating naturally occurring surface-active bacteria. When estimating densities of Pseudomonas spp. underneath droplets with low contact angles, it appeared that populations on leaves treated with a surface-active strain could vary from about 104 to 106 CFU cm−2, suggesting that the surface effect may be prolonged after a decline of the

  14. The site of activation of factor X by cancer procoagulant.

    PubMed

    Gordon, S G; Mourad, A M

    1991-12-01

    Cancer procoagulant (CP) is a cysteine proteinase found in a variety of malignant cells and tissues and in human amnion-chorion tissue. It initiates coagulation by activating factor X. However, the amino acid sequence of the substrate protein that determines the cleavage site of cysteine proteinases is different from that of the serine proteinases that normally activate factor X, such as factor IXa, VIIa and Russell's Viper Venom (RVV). Therefore, it was of interest to determine the site of cleavage of human factor X by CP. Purified CP was incubated with purified factor X and the reaction mixture was electrophoresed on a 10% Tris-tricine SDS-PAGE gel. The proteins were electroeluted on to a polyvinylidene difluoride (PVDF) membrane, and stained with Coomassie blue. The heavy chain of activated factor X was cut out of the PVDF membrane and sequenced with an Applied Biosystems 477A with on-line HPLC. The primary cleavage sequence was Asp-Ala-Ala-Asp-Leu-Asp-Pro-; two other secondary sequences Ser-Ile-Thr-Trp-Lys-Pro- and Glu-Asn-Pro-Phe-Asp-Leu were found. The penultimate amino acid on the carbonyl side of the hydrolysed amide bond plays a critical role for the recognition of the cleavage site of cysteine proteinases. These data indicate that the penultimate amino acid for the primary cleavage site of factor X by CP is proline-20 and for the secondary sites, proline-13 and proline-28. This is in contrast to arginine-52 that determines the specificity of the cleavage by normal serine proteinase activation.(ABSTRACT TRUNCATED AT 250 WORDS)

  15. Comparison of surface fluxes and boundary-layer measurements at Arctic terrestrial sites

    NASA Astrophysics Data System (ADS)

    Grachev, Andrey; Uttal, Taneil; Persson, Ola; Stone, Robert; Crepinsek, Sara; Albee, Robert; Makshtas, Alexander; Kustov, Vasily; Repina, Irina; Artamonov, Arseniy

    2014-05-01

    Observational evidence suggests that atmospheric energy fluxes are a major contributor to the decrease of the Arctic pack ice, seasonal land snow cover and the warming of the surrounding land areas and permafrost layers. To better understand the atmosphere-surface exchange mechanisms, improve models, and to diagnose climate variability in the Arctic, accurate measurements are required of all components of the net surface energy budget and the carbon dioxide cycle over representative areas and over multiple years. This study analyzes and discusses variability of surface fluxes and basic meteorological parameters based on measurements made at several long-term research observatories near the coast of the Arctic Ocean located in USA (Barrow), Canada (Eureka), and Russia (Tiksi). Tower-based eddy covariance and solar radiation measurements provide a long-term near continuous temporal record of hourly average mass and energy fluxes respectively. The turbulent fluxes of the momentum, sensible heat, water vapor, and carbon dioxide are supported by additional atmospheric and surface/snow/permafrost measurements (mean wind speed, air temperature and humidity, upwelling and downwelling short-wave and long-wave atmospheric and surface radiation, snow depth, surface albedo, soil heat flux, active layer temperature profiles etc.) In this study we compare annual cycles of surface fluxes including solar radiation and other ancillary data to describe four seasons in the Arctic including spring onset of melt and fall onset of snow accumulation. Particular interest is a transition through freezing point, i.e. during transition from winter to spring and from summer to fall, when the carbon dioxide and/or water vapor turbulent fluxes change their direction. According to our data, in a summer period observed temporal variability of the carbon dioxide flux was generally in anti-phase with water vapor flux (downward CO2 flux and upward H2O flux). On average the turbulent flux of carbon

  16. Summary of activities. [Mars surface sampling

    NASA Technical Reports Server (NTRS)

    1989-01-01

    Four space projects' activities are summarized. Design work on the Mars Penetrator Project, in cooperation with the NASA Ames Research Center, is being continued. Efforts are focused on the drilling mechanism which must penetrate the martian subsurface soil to collect and retrieve an uncontaminated sample. The new design consists of a rotary-percussive drill mechanism. This mechanism is optimum for dry drilling, necessary to avoid contamination of the soil sample, in many different soil types. The need for a small, relatively inexpensive device to study the chemical structure of this martian soil was also established. The egg design was chosen for its low cost compared to other systems and potential for a large number of eggs to be deployed on the martian surface. The design process included analysis of the dynamics of reentry, dissipation of heat during reentry, impact with the surface, access to undisturbed soil samples, and ability to gather samples from the soil at three depths. The egg consists of the reentry systems, soil probe lifting system, soil probe package, gas chromatograph, transmitter, and battery power supply. The egg must function only once, but is designed to withstand one martian year. The Mars Mole is designed as a rover-based device which penetrates the martian soil to a depth of up to 10 m, obtains a sample of soil, and returns it to the surface for analysis. The mole was designed to meet the following specifications: (1) weight less than 10 kg; (2) size less than 20 x 20 x 30 cm; (3) power less than 100 W; (4) ability to obtain a sample of at least 5 cc; (5) ability to penetrate fine, loose sand; and (6) need to obtain at least one sample. The space station umbilical connector project is a device which provides the translational motion of the connectors on the Space Station Freedom to allow engagement for power and data transfer. The design is capable of delivering a 20 lb force within the necessary tolerances and will operate reliably in the

  17. Enhanced oxygen evolution activity of IrO2 and RuO2 (100) surfaces

    SciTech Connect

    Stoerzinger, Kelsey; Qiao, Liang; Biegalski, Michael D; Christen, Hans M; Shao-Horn, Yang

    2014-01-01

    The activities of the oxygen evolution reaction (OER) on IrO2 and RuO2 catalysts are among the highest known to date. However, the intrinsic OER activities of surfaces with defined crystallographic orientations are not well established experimentally. Here we report that the (100) surface of IrO2 and RuO2 is more active than the (110) surface that has been traditionally explored by density functional theory studies. The relation between the OER activity and density of coordinatively undersaturated metal sites exposed on each rutile crystallographic facet is discussed. The surface-orientation dependent activities can guide the design of high-surface-area catalysts with increased activity for electrolyzers, metal-air batteries, and photoelectrochemical water splitting applications.

  18. Comparison of surface fluxes and conductances at two contrasting sites within the FIFE area

    NASA Technical Reports Server (NTRS)

    Stewart, J. B.; Verma, S. B.

    1992-01-01

    Surface flux measurements from two contrasting sites within the FIFE study area are analyzed. The seasonal variation of midday latent heat fluxes and surface conductances at the two sites was found to be very similar even though the ratio of their average total leaf area indices was greater than two to one. Concurrent measurements made at another six flat sites within the FIFE area confirmed the independence of latent heat flux with respect to leaf area index. The surface conductance stress function related to specific humidity deficit was the same for the two sites, whereas the solar radiation stress function showed a difference of 30 percent at a solar radiation input of 300 W/sq m and the soil moisture stress function showed a difference of 16 percent when half the extractable soil moisture had been taken up. However, when the stress functions were combined to determine the surface conductance, these differences virtually canceled out.

  19. Elemental analyses of hypervelocity micro-particle impact sites on interplanetary dust experiment sensor surfaces

    NASA Technical Reports Server (NTRS)

    Simon, Charles G.; Hunter, J. L.; Griffis, D. P.; Misra, V.; Ricks, D. R.; Wortman, Jim J.

    1992-01-01

    The Interplanetary Dust Experiment (IDE) had over 450 electrically active ultra-high purity metal-oxide-silicon impact detectors located on the six primary sides of the Long Duration Exposure Facility (LDEF). Hypervelocity micro-particles that struck the active sensors with enough energy to breakdown the 0.4 to 1.0 micron thick SiO2 insulator layer separating the silicon base (the negative electrode), and the 1000 A thick surface layer of aluminum (the positive electrode) caused electrical discharges that were recorded for the first year of orbit. These discharge features, which include 50 micron diameter areas where the aluminum top layer has been vaporized, facilitate the location of the impacts. The high purity Al-SiO2-Si substrates allow detection of trace (ppm) amounts of hypervelocity impactor residues. After sputtering through a layer of surface contamination, secondary ion mass spectrometry (SIMS) is used to create two-dimensional elemental ion intensity maps of micro-particle impact sites on the IDE sensors. The element intensities in the central craters of the impacts are corrected for relative ion yields and instrumental conditions and then normalized to silicon. The results are used to classify the particles' origins as 'manmade', 'natural' or 'indeterminate'. The last classification results from the presence of too little impactor residue (a frequent occurrence on leading edge impacts), analytical interference from high background contamination, the lack of information on silicon residue, the limited usefulness of data on aluminum in the central craters, or a combination of these circumstances. Several analytical 'blank' discharges were induced on flight sensors by pressing down on the sensor surface with a pure silicon shard. Analyses of these blank discharges showed that the discharge energy blasts away the layer of surface contamination. Only Si and Al were detected inside the discharge zones, including the central craters, of these features. A

  20. Closure Report for Corrective Action Unit 300: Surface Release Areas Nevada Test Site, Nevada

    SciTech Connect

    NSTec Environmental Restoration

    2007-07-01

    Corrective Action Unit (CAU) 300 is located in Areas 23, 25, and 26 of the Nevada Test Site, which is located approximately 65 miles northwest of Las Vegas, Nevada. CAU 300 is listed in the Federal Facility Agreement and Consent Order of 1996 as Surface Release Areas and is comprised of the following seven Corrective Action Sites (CASs), which are associated with the identified Building (Bldg): {sm_bullet} CAS 23-21-03, Bldg 750 Surface Discharge {sm_bullet} CAS 23-25-02, Bldg 750 Outfall {sm_bullet} CAS 23-25-03, Bldg 751 Outfall {sm_bullet} CAS 25-60-01, Bldg 3113A Outfall {sm_bullet} CAS 25-60-02, Bldg 3901 Outfall {sm_bullet} CAS 25-62-01, Bldg 3124 Contaminated Soil {sm_bullet} CAS 26-60-01, Bldg 2105 Outfall and Decon Pad The Nevada Division of Environmental Protection (NDEP)-approved corrective action alternative for CASs 23-21-03, 23-25-02, and 23-25-03 is no further action. As a best management practice, approximately 48 feet of metal piping was removed from CAS 23-25-02 and disposed of as sanitary waste. The NDEP-approved corrective action alternative for CASs 25-60-01, 25-60-02, 25-62-01, and 26-60-01, is clean closure. Closure activities for these CASs included removing and disposing of soil impacted with total petroleum hydrocarbons-diesel range organics (TPH-DRO), polychlorinated biphenyls (PCBs), semivolatile organic compounds (SVOCs), and cesium (Cs)-137, concrete impacted with TPH-DRO, and associated piping impacted with TPH-DRO. CAU 300 was closed in accordance with the NDEP-approved CAU 300 Corrective Action Plan (CAP) (U.S. Department of Energy, National Nuclear Security Administration Nevada Site Office [NNSA/NSO], 2006). The closure activities specified in the CAP were based on the recommendations presented in the CAU 300 Corrective Action Decision Document (NNSA/NSO, 2005). This Closure Report documents CAU 300 closure activities. During closure activities, approximately 40 cubic yards (yd3) of low-level waste consisting of TPH-DRO-, PCB

  1. Active-Site-Accessible, Porphyrinic Metal;#8722;Organic Framework Materials

    SciTech Connect

    Farha, Omar K.; Shultz, Abraham M.; Sarjeant, Amy A.; Nguyen, SonBinh T.; Hupp, Joseph T.

    2012-02-06

    On account of their structural similarity to cofactors found in many metallo-enzymes, metalloporphyrins are obvious potential building blocks for catalytically active, metal-organic framework (MOF) materials. While numerous porphyrin-based MOFs have already been described, versions featuring highly accessible active sites and permanent microporosity are remarkably scarce. Indeed, of the more than 70 previously reported porphyrinic MOFs, only one has been shown to be both permanently microporous and contain internally accessible active sites for chemical catalysis. Attempts to generalize the design approach used in this single successful case have failed. Reported here, however, is the synthesis of an extended family of MOFs that directly incorporate a variety of metalloporphyrins (specifically Al{sup 3+}, Zn{sup 2+}, Pd{sup 2+}, Mn{sup 3+}, and Fe{sup 3+} complexes). These robust porphyrinic materials (RPMs) feature large channels and readily accessible active sites. As an illustrative example, one of the manganese-containing RPMs is shown to be catalytically competent for the oxidation of alkenes and alkanes.

  2. Identification of active sites in gold-catalyzed hydrogenation of acrolein.

    PubMed

    Mohr, Christian; Hofmeister, Herbert; Radnik, Jörg; Claus, Peter

    2003-02-19

    The active sites of supported gold catalysts, favoring the adsorption of C=O groups of acrolein and subsequent reaction to allyl alcohol, have been identified as edges of gold nanoparticles. After our recent finding that this reaction preferentially occurs on single crystalline particles rather than multiply twinned ones, this paper reports on a new approach to distinguish different features of the gold particle morphology. Elucidation of the active site issue cannot be simply done by varying the size of gold particles, since the effects of faceting and multiply twinned particles may interfere. Therefore, modification of the gold particle surface by indium has been used to vary the active site characteristics of a suitable catalyst, and a selective decoration of gold particle faces has been observed, leaving edges free. This is in contradiction to theoretical predictions, suggesting a preferred occupation of the low-coordinated edges of the gold particles. On the bimetallic catalyst, the desired allyl alcohol is the main product (selectivity 63%; temperature 593 K, total pressure p(total) = 2 MPa). From the experimentally proven correlation between surface structure and catalytic behavior, the edges of single crystalline gold particles have been identified as active sites for the preferred C=O hydrogenation. PMID:12580618

  3. Data-Driven Surface Traversability Analysis for Mars 2020 Landing Site Selection

    NASA Technical Reports Server (NTRS)

    Ono, Masahiro; Rothrock, Brandon; Almeida, Eduardo; Ansar, Adnan; Otero, Richard; Huertas, Andres; Heverly, Matthew

    2015-01-01

    The objective of this paper is three-fold: 1) to describe the engineering challenges in the surface mobility of the Mars 2020 Rover mission that are considered in the landing site selection processs, 2) to introduce new automated traversability analysis capabilities, and 3) to present the preliminary analysis results for top candidate landing sites. The analysis capabilities presented in this paper include automated terrain classification, automated rock detection, digital elevation model (DEM) generation, and multi-ROI (region of interest) route planning. These analysis capabilities enable to fully utilize the vast volume of high-resolution orbiter imagery, quantitatively evaluate surface mobility requirements for each candidate site, and reject subjectivity in the comparison between sites in terms of engineering considerations. The analysis results supported the discussion in the Second Landing Site Workshop held in August 2015, which resulted in selecting eight candidate sites that will be considered in the third workshop.

  4. Functional constituents of the active site of human neutrophil collagenase.

    PubMed

    Mookhtiar, K A; Wang, F; Van Wart, H E

    1986-05-01

    A series of chemical modification reactions has been carried out to identify functional constituents of the active site of human neutrophil collagenase. The enzyme is reversibly inhibited by the transition metal chelating agent 1,10-phenanthroline, and inhibition is fully reversed by zinc. Removal of weakly bound metal ions by gel filtration inactivates collagenase, and activity is fully restored on immediate readdition of calcium. The enzyme is unaffected by reagents that modify serine, cysteine, and arginine residues. However, reaction with the carboxyl reagents cyclohexylmorpholinocarbodiimide and Woodward's Reagent K lowers the activity of the enzyme substantially. Acetylimidazole inactivates the enzyme, but activity is completely restored on addition of hydroxylamine. The enzyme is also inactivated by tetranitromethane, indicating that it contains an essential tyrosine residue. Acylation of collagenase with diethyl pyrocarbonate, diketene, acetic anhydride, or trinitrobenzenesulfonate inactivates the enzyme, and activity is not restored on addition of hydroxylamine, indicating the presence of an essential lysine residue.

  5. Nest predation increases with parental activity: Separating nest site and parental activity effects

    USGS Publications Warehouse

    Martin, T.E.; Scott, J.; Menge, C.

    2000-01-01

    Alexander Skutch hypothesized that increased parental activity can increase the risk of nest predation. We tested this hypothesis using ten open-nesting bird species in Arizona, USA. Parental activity was greater during the nestling than incubation stage because parents visited the nest frequently to feed their young during the nestling stage. However, nest predation did not generally increase with parental activity between nesting stages across the ten study species. Previous investigators have found similar results. We tested whether nest site effects might yield higher predation during incubation because the most obvious sites are depredated most rapidly. We conducted experiments using nest sites from the previous year to remove parental activity. Our results showed that nest sites have highly repeatable effects on nest predation risk; poor nest sites incurred rapid predation and caused predation rates to be greater during the incubation than nestling stage. This pattern also was exhibited in a bird species with similar (i.e. controlled) parental activity between nesting stages. Once nest site effects are taken into account, nest predation shows a strong proximate increase with parental activity during the nestling stage within and across species. Parental activity and nest sites exert antagonistic influences on current estimates of nest predation between nesting stages and both must be considered in order to understand current patterns of nest predation, which is an important source of natural selection.

  6. Surface Complexation Modeling of U(VI) Adsorption onto Savannah River Site Sediments

    NASA Astrophysics Data System (ADS)

    Dong, W.; Wan, J.; Tokunaga, T. K.; Denham, M.; Davis, J.; Hubbard, S. S.

    2011-12-01

    The Savannah River Site (SRS) was a U.S. Department of Energy facility for plutonium production during the Cold War. Waste plumes containing low-level radioactivity and acidic waste solutions were discharged to a series of unlined seepage basins in the F-Area of the SRS from 1955 to 1988. Although the site has undergone many years of active remediation, the groundwater remains acidic, and the concentrations of U and other radionuclides are still significantly higher than their Maximum Contaminant Levels (MCLs). The objective of this effort is to understand and predict U(VI) mobility in acidic waste plumes through developing surface complexation models (SCMs). Laboratory batch experiments were conducted to evaluate U adsorption behavior over the pH range of 3.0 to 9.5. Ten sorbent samples were selected including six contaminated sediment samples from three boreholes drilled within the plume and along the groundwater flow direction, two uncontaminated (pristine) sediment samples from a borehole outside of the plume, and two reference minerals, goethite and kaolinite (identified as the dominant minerals in the clay size fraction of the F-Area sediments). The results show that goethite and kaolinite largely control U partitioning behavior. In comparison with the pristine sediment, U(VI) adsorption onto contaminated sediments exhibits adsorption edges shifted toward lower pH by about 1.0 unit (e.g., from pH≈4.5 to pH≈3.5). We developed a SCMs based component additivity (CA) approach, which can successfully predict U(VI) adsorption onto uncontaminated SRS sediments. However, application of the same SCMs based CA approach to contaminated sediments resulted in underestimates of U(VI) adsorption at acidic pH conditions. The model sensitivity analyses indicate that both goethite and kaolinite surfaces co-contributed to U(VI) adsorption under acidic pH conditions. In particular, the exchange sites of clay minerals might play an important role in adsorption of U(VI) at p

  7. An Integrated Approach to Quantify Groundwater - Surface Water Interactions: the Norman Research Site, Oklahoma

    NASA Astrophysics Data System (ADS)

    Mendoza-Sanchez, I.; Phanikumar, M. S.; Masoner, J.; Cozzarelli, I.; McGuire, J. T.

    2009-12-01

    An intensive investigation of hydrogeologic and biogeochemical processes controlling contaminant migration and attenuation is in progress at the Norman Landfill Research Site in Oklahoma. The site involves a wetland that overlies a landfill leachate plume. The wetland-aquifer system actively exchanges contaminants and nutrients. These chemicals move from the wetland to the aquifer and vice versa depending on the groundwater-surface water (GW-SW) exchange rate and flow direction. The GW-SW flux has to be quantified to better understand the fate and transport of contaminants and nutrients. Different types of data have been collected at the site over a period of ten years including meteorological data, isotopic composition of water samples, water levels, pan evaporation rates, and seepage fluxes. This paper reports the development and application of a process-based water balance model based on long-term climate, soil, vegetation and hydrological dynamics of the system to determine the GW-SW flow rates. Our integrated approach involved model evaluation by means of the following independent measurements: (a) groundwater inflow calculation using stable isotopes of oxygen and hydrogen ( ) (b) seepage flux measurements in the wetland hyporheic sediment and c) pan evaporation measurements on land and in the wetland. The approach was found to be useful for identifying the dominant hydrological processes at the site, including recharge and subsurface flows. Recharge results from the model compared well with estimates obtained using isotope methods from previous studies and allowed us to identify specific annual signatures of this important process during the period of study. Results indicate that subsurface flow components in the system are seasonal and readily respond to rainfall events. The wetland water balance is dominated by local groundwater inputs and regional groundwater flow contributes little to the overall water balance.

  8. Site-Specific Scaling Relations for Hydrocarbon Adsorption on Hexagonal Transition Metal Surfaces

    SciTech Connect

    Montemore, Matthew M.; Medlin, James W.

    2013-10-03

    Screening a large number of surfaces for their catalytic performance remains a challenge, leading to the need for simple models to predict adsorption properties. To facilitate rapid prediction of hydrocarbon adsorption energies, scaling relations that allow for calculation of the adsorption energy of any intermediate attached to any symmetric site on any hexagonal metal surface through a carbon atom were developed. For input, these relations require only simple electronic properties of the surface and of the gas-phase reactant molecules. Determining adsorption energies consists of up to four steps: (i) calculating the adsorption energy of methyl in the top site using density functional theory or by simple relations based on the electronic structure of the surface; (ii) using modified versions of classical scaling relations to scale between methyl in the top site and C₁ species with more metal-surface bonds (i.e., C, CH, CH₂) in sites that complete adsorbate tetravalency; (iii) using gas-phase bond energies to predict adsorption energies of longer hydrocarbons (i.e., CR, CR₂, CR₃); and (iv) expressing energetic changes upon translation of hydrocarbons to various sites in terms of the number of agostic interactions and the change in the number of carbon-metal bonds. Combining all of these relations allows accurate scaling over a wide range of adsorbates and surfaces, resulting in efficient screening of catalytic surfaces and a clear elucidation of adsorption trends. The relations are used to explain trends in methane reforming, hydrocarbon chain growth, and propane dehydrogenation.

  9. Twinning in fcc lattice creates low-coordinated catalytically active sites in porous gold.

    PubMed

    Krajčí, Marian; Kameoka, Satoshi; Tsai, An-Pang

    2016-08-28

    We describe a new mechanism for creation of catalytically active sites in porous gold. Samples of porous gold prepared by de-alloying Al2Au exhibit a clear correlation between the catalytic reactivity towards CO oxidation and structural defects in the fcc lattice of Au. We have found that on the stepped {211} surfaces quite common twin boundary defects in the bulk structure of porous gold can form long close-packed rows of atoms with the coordination number CN = 6. DFT calculations confirm that on these low-coordinated Au sites dioxygen chemisorbs and CO oxidation can proceed via the Langmuir-Hinshelwood mechanism with the activation energy of 37 kJ/mol or via the CO-OO intermediate with the energy barrier of 19 kJ/mol. The existence of the twins in porous gold is stabilized by the surface energy.

  10. Twinning in fcc lattice creates low-coordinated catalytically active sites in porous gold

    NASA Astrophysics Data System (ADS)

    Krajčí, Marian; Kameoka, Satoshi; Tsai, An-Pang

    2016-08-01

    We describe a new mechanism for creation of catalytically active sites in porous gold. Samples of porous gold prepared by de-alloying Al2Au exhibit a clear correlation between the catalytic reactivity towards CO oxidation and structural defects in the fcc lattice of Au. We have found that on the stepped {211} surfaces quite common twin boundary defects in the bulk structure of porous gold can form long close-packed rows of atoms with the coordination number CN = 6. DFT calculations confirm that on these low-coordinated Au sites dioxygen chemisorbs and CO oxidation can proceed via the Langmuir-Hinshelwood mechanism with the activation energy of 37 kJ/mol or via the CO-OO intermediate with the energy barrier of 19 kJ/mol. The existence of the twins in porous gold is stabilized by the surface energy.

  11. Twinning in fcc lattice creates low-coordinated catalytically active sites in porous gold.

    PubMed

    Krajčí, Marian; Kameoka, Satoshi; Tsai, An-Pang

    2016-08-28

    We describe a new mechanism for creation of catalytically active sites in porous gold. Samples of porous gold prepared by de-alloying Al2Au exhibit a clear correlation between the catalytic reactivity towards CO oxidation and structural defects in the fcc lattice of Au. We have found that on the stepped {211} surfaces quite common twin boundary defects in the bulk structure of porous gold can form long close-packed rows of atoms with the coordination number CN = 6. DFT calculations confirm that on these low-coordinated Au sites dioxygen chemisorbs and CO oxidation can proceed via the Langmuir-Hinshelwood mechanism with the activation energy of 37 kJ/mol or via the CO-OO intermediate with the energy barrier of 19 kJ/mol. The existence of the twins in porous gold is stabilized by the surface energy. PMID:27586937

  12. Active sites in char gasification: Final technical report

    SciTech Connect

    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.

  13. ICR SS protozoan data site-by-site: a picture of Cryptosporidium and Giardia in U.S. surface water.

    PubMed

    Ongerth, Jerry E

    2013-09-17

    The U.S. Environmental Protection Agency (USEPA) Information Collection Rule Supplemental Survey (ICR SS) required analysis of Cryptosporidium and Giardia in 10 L surface water samples twice a week for a year by USEPA Method 1623 at 80 representative U.S. public water systems (PWS). The resulting data are examined site-by-site in relation to objectives of the Federal drinking water regulation, The Long-Term (2) Enhanced Surface Water Treatment Rule (LT2), currently under formal 6-year review by the USEPA. The data describe Cryptosporidium and Giardia in watersheds nation-wide over a single annual cycle. Due to limited recovery efficiency measurement results are not fully quantified. In the required sample volumes of 10 L no Cryptosporidium were found in 86% of samples and no Giardia were found in 67% of samples. Yet, organisms were found in enough samples at 34 of 80 sites to detail a specrtum of occurrence and variability for both organisms. The data are shown to describe indivudual site risk essential for guidance of watershed and water treatment management by PWSs. The span of median occurrence for both organisms was about 2 orders of magnitude above the limit of detection (LD), ca. 0.05 raw no's/L for Cryptosporidium and ca. 0.10 raw no's/L for Giardia. Data analysis illustrates key features of Cryptosporidium and Giardia in surface water: presence is continuous not intermittent; zeros indicate presence below the LD; occurrence level and variations depend on watershed sources; risk depends on both magnitude and variability of concentration; accurate estimation of risk requires routine measurement of recovery efficiency and calculation of concentration. The data and analysis illustrate features of Cryptosporidium and Giardia occurrence in surface water relevant to their effective regulation for public health protection.

  14. Elemental Analyses of Hypervelocity Microparticle Impact Sites on Interplanetary Dust Experiment Sensor Surfaces

    NASA Technical Reports Server (NTRS)

    Simon, C. G.; Hunter, J. L.; Griffis, D. P.; Misra, V.; Ricks, D. A.; Wortman, J. J.; Brownlee, D. E.

    1992-01-01

    The Interplanetary Dust Experiment (IDE) had over 450 electrically active ultra-high purity metal-oxide-silicon impact detectors located on the six primary sides of the Long Duration Exposure Facility (LDEF). Hypervelocity microparticles (approximately 0.2 to approximately 100 micron diameter) that struck the active sensors with enough energy to breakdown the 0.4 or 1.0 micron thick SiO2 insulator layer separating the silicon base (the negative electrode), and the 1000 A thick surface layer of aluminum (the positive electrode) caused electrical discharges that were recorded for the first year of orbit. The high purity Al-SiO2-Si substrates allowed detection of trace (ppm) amounts of hypervelocity impactor residues. After sputtering through a layer of surface contamination, secondary ion mass spectrometry (SIMS) was used to create two-dimensional elemental ion intensity maps of microparticle sites on the IDE sensors. The element intensities in the central craters of the impacts were corrected for relative ion yields and instrumental conditions and then normalized to silicon. The results classification resulted from the particles' origins as 'manmade', 'natural', or 'indeterminate'. The last classification resulted from the presence of too little impactor residue, analytical interference from high background contamination, the lack of information on silicon and aluminum residues, or a combination of these circumstances. Several analytical 'blank' discharges were induced on flight sensors by pressing down on the sensor surface with a pure silicon shard. Analyses of these blank discharges showed that the discharge energy blasts away the layer of surface contamination. Only Si and Al were detected inside the discharge zones, including the central craters, of these features. Thus far, a total of 79 randomly selected microparticle impact sites from the six primary sides of the LDEF were analyzed: 36 from tray C-9 (Leading (ram), or east, side), 18 from tray C-3 (Trailing

  15. Elemental analyses of hypervelocity microparticle impact sites on Interplanetary Dust Experiment sensor surfaces

    NASA Technical Reports Server (NTRS)

    Simon, Charles G.; Hunter, J. L.; Griffis, D. P.; Misra, V.; Ricks, D. A.; Wortman, Jim J.; Brownlee, D. E.

    1993-01-01

    The Interplanetary Dust Experiment (IDE) had over 450 electrically active ultra-high purity metal-oxide-silicon impact detectors located on the six primary sides of the Long Duration Exposure Facility (LDEF). Hypervelocity microparticles (approximately 0.2 to approximately 100 micron diameter) that struck the active sensors with enough energy to break down the 0.4 or 1.0 micron thick SIO2 insulator layer separating the silicon base (the negative electrode), and the 1000 A thick surface layer of aluminum (the positive electrode) caused electrical discharges that were recorded for the first year of orbit. The high purity Al-SiO2-Si substrates allowed detection of trace (ppm) amounts of hypervelocity impactor residues. After sputtering through a layer of surface contamination, secondary ion mass spectrometry (SIMS) was used to create two-dimensional elemental ion intensity maps of microparticle impact sites on the IDE sensors. The element intensities in the central craters of the impacts were corrected for relative ion yields and instrumental conditions and then normalized to silicon. The results were used to classify the particles' origins as 'manmade,' 'natural,' or 'indeterminate.' The last classification resulted from the presence of too little impactor residue, analytical interference from high background contamination, the lack of information on silicon and aluminum residues, or a combination of these circumstances. Several analytical 'blank' discharges were induced on flight sensors by pressing down on the sensor surface with a pure silicon shard. Analyses of these blank discharges showed that the discharge energy blasts away the layer of surface contamination. Only Si and Al were detected inside the discharge zones, including the central craters of these features. Thus far a total of 79 randomly selected microparticle impact sites from the six primary sides of the LDEF have been analyzed: 36 from tray C-9 (Leading (ram), or East, side), 18 from tray C-3

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

    SciTech Connect

    Nekrasov, Vyacheslav M.; Yurkin, Maxim A.; Chernyshev, Andrei V.; Polshchitsin, Alexey A.; Yakovleva, Galina E.; Maltsev, Valeri P.

    2014-08-14

    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.

  17. Inhibition and active-site modelling of prolidase.

    PubMed

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

    1989-03-15

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

  18. Surface and subsurface characterization of uranium contamination at the Fernald environmental management site

    SciTech Connect

    Schilk, A.J.; Perkins, R.W.; Abel, K.H.; Brodzinski, R.L.

    1993-04-01

    The past operations of uranium production and support facilities at several Department of Energy (DOE) sites have occasionally resulted in the local contamination of some surface and subsurface soils, and the three-dimensional distribution of the uranium at these sites must be thoroughly characterized before any effective remedial protocols can be established. To this end, Pacific Northwest Laboratory (PNL) has been tasked by the DOE`s Office of Technology Development with adapting, developing, and demonstrating technologies for the measurement of uranium in surface and subsurface soils at the Fernald Uranium in Soils Integrated Demonstration site. These studies are detailed in this report.

  19. Brominated lipids identify lipid binding sites on the surface of the reaction center from Rhodobacter sphaeroides.

    PubMed

    Roszak, Aleksander W; Gardiner, Alastair T; Isaacs, Neil W; Cogdell, Richard J

    2007-03-20

    This study describes the use of brominated phospholipids to distinguish between lipid and detergent binding sites on the surface of a typical alpha-helical membrane protein. Reaction centers isolated from Rhodobacter sphaeroides were cocrystallized with added brominated phospholipids. X-ray structural analysis of these crystals has revealed the presence of two lipid binding sites from the characteristic strong X-ray scattering from the bromine atoms. These results demonstrate the usefulness of this approach to mapping lipid binding sites at the surface of membrane proteins.

  20. VARIABLE BOUND-SITE CHARGING CONTRIBUTIONS TO SURFACE COMPLEXATION MASS ACTION EXPRESSIONS

    EPA Science Inventory

    One and two pK models of surface complexation reactions between reactive surface sites (>SOH) and the proton (H+) use mass action expressions of the form: Ka={[>SOHn-1z-1]g>SOH(0-1)aH+EXP(-xeY/kT)}/{[>SOHnz]g>SOH(n)} where Ka=the acidity constant, [ ]=reactive species concentrati...

  1. Basement Surface Faulting and Topography for Savannah River Site and Vicinity

    SciTech Connect

    Cumbest, R.J.

    1998-12-17

    This report integrates the data from more than 60 basement borings and over 100 miles of seismic reflection profiling acquired on the Savannah River Site to map the topography of the basement (unweathered rock) surface and faulting recorded on this surface.

  2. Root-surface phosphatase activity in shrublands across a European gradient: effects of warming.

    PubMed

    Estiarte, M; Peuuelas, J; Sardans, J; Emmett, B A; Sowerby, A; Beier, C; Schmidt, I K; Tietema, A; Van Meeteren, M J M; Kovacs-Lang, E; Mathe, P; De Angelis, P; De Dato, G

    2008-01-01

    Root-surface phosphatase activities were measured in natural and semi-natural shrublands across an European climatic gradient of temperature and rainfall including Wales (WL), Denmark (DK), Netherlands (NL), Hungary (HU), Italy (IT) and Spain (SP). In each site a warming experiment was conducted since 1999 or 2001 by means of passive night-time warming using reflective curtains that covered the vegetation at night. The treatments increased yearly average soil temperatures around 0. 8 degrees C in most of sites. Root-surface phosphatase activity values ranged between 56 mg PNP g(-1) h(-1) in IT and 3.5 mg PNP g(-1) h(-1) in HU. Warming had no effect on root-surface phosphatase activity across the sites and only in Hungary a slight increase was detected. Plants at Mediterranean sites (IT, SP) showed a higher root-surface phosphatase activity than plants at temperate sites (WL, NL, DK). We suggest it might be an adaptation of plant species evolved under Mediterranean climate that allows them a) to compensate in wet period for the decrease in phosphatase activity, and thus P uptake, during drought periods, and/or b) to benefit from soluble organic P flushes following the frequent drying-rewetting episodes experienced by soils in Mediterranean ecosystems. PMID:18831327

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

    PubMed

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

    2015-03-19

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

  4. Identification of Ice Nucleation Active Sites on Feldspar Dust Particles

    PubMed Central

    2015-01-01

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

  5. Passive and active EO sensing close to the sea surface

    NASA Astrophysics Data System (ADS)

    Steinvall, Ove; Persson, Rolf; Berglund, Folke; Öhgren, Johan; Gustafsson, Frank

    2014-10-01

    The present paper investigates the use of an eye-safe laser rangefinder at 1.5 μm and TV/IR imaging to obtain information on atmospheric properties at various paths close to the sea surface. On one day active/passive imaging NIR and SWIR systems were also used. The paper will describe the experimental equipment and the results from measurements of atmospheric backscatter as well as TV and IR images of test targets along a 1.8 km path close to the Baltic Sea. The site also contained a weather station and a scintillometer for logging weather and turbulence parameters. Results correlating the lidar attenuation with the imaging performance will be given and compared with models.

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

    SciTech Connect

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

    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.

  7. Land surface model over forest and lake surfaces in a boreal site - Evaluation of the tiling method

    NASA Astrophysics Data System (ADS)

    Manrique Suñén, A.; Nordbo, A.; Balsamo, G.; Beljaars, A.; Mammarella, I.

    2012-04-01

    Land surface model over forest and lake surfaces in a boreal site - Evaluation of the tiling method Andrea Manrique Suñén1, Annika Nordbo2, Gianpaolo Balsamo1, Anton Beljaars1 and Ivan Mammarella2 1 ECMWF, Reading, UK 2 University of Helsinki, Finland The tiling method is used by many models to represent the surface heterogeneity. Each grid-box is divided into fractions of different types of surface, and an area-weighted average of the energy fluxes is computed to couple with the atmosphere. This method provides a flexible characterisation of land complexity, and separate information of sub grid variables. However, not much assessment of its validity has been carried out. To evaluate results for two contrasting surfaces, the Hydrology Tiled ECMWF Scheme for Surface Exchanges has been run offline for the year 2006, forced by the ERA-Interim reanalysis data over a boreal site in southern Finland for two cases. The first one corresponds to a full coverage of the grid-box by high vegetation, and the second one to a full coverage by a lake. The lake model Flake was incorporated into the system to represent inland water processes. It uses a simple parameterisation which has proved to perform well for numerical weather prediction. The resulting fluxes for both cases have been compared to observational data from two stations situated near each other in a Scots pine forest (Hyytiälä) and in a small boreal lake (Valkea-Kotinen), in southern Finland. The turbulent fluxes at the sites were measured using the Eddy-covariance technique. Net radiation, change in heat storage, wind speed, air temperature, and specific humidity and surface pressure were also available for each site. The diurnal and seasonal cycles of the energy fluxes for these contrasting surfaces have been evaluated, and the different energy partitioning has been explained. In general, the effect of the lake's thermal inertia is well represented by the model. The only shortcoming of the lake model appears to

  8. Pioneering Objectives and Activities on the Surface of Mars

    NASA Technical Reports Server (NTRS)

    Toups, Larry; Hoffman, Stephen J.

    2015-01-01

    Human Mars missions have been a topic of sustained interest within NASA, which continues to use its resources to examine many different mission objectives, trajectories, vehicles, and technologies, the combinations of which are often referred to as reference missions or architectures. The current investigative effort, known as the Evolvable Mars Campaign (EMC), is examining alternatives that can pioneer an extended human presence on Mars that is Earth independent. These alternatives involve combinations of all the factors just mentioned. This paper is focused on the subset of these factors involved with objectives and activities that take place on the surface of Mars. "Pioneering" is a useful phrase to encapsulate the current approach being used to address this situation - one of its primary definitions is "a person or group that originates or helps open up a new line of thought or activity or a new method or technical development". Thus, in this scenario, NASA would be embarking on a path to "pioneer" a suite of technologies and operations that will result in an Earth independent, extended stay capability for humans on Mars. This paper will describe (a) the concept of operation determined to be best suited for the initial emplacement, (b) the functional capabilities determined to be necessary for this emplacement, with representative examples of systems that could carry out these functional capabilities and one implementation example (i.e., delivery sequence) at a representative landing site, and will (c) discuss possible capabilities and operations during subsequent surface missions.

  9. Seismic site characterization of an urban dedimentary basin, Livermore Valley, California: Site tesponse, basin-edge-induced surface waves, and 3D simulations

    USGS Publications Warehouse

    Hartzell, Stephen; Leeds, Alena L.; Ramirez-Guzman, Leonardo; Allen, James P.; Schmitt, Robert G.

    2016-01-01

    Thirty‐two accelerometers were deployed in the Livermore Valley, California, for approximately one year to study sedimentary basin effects. Many local and near‐regional earthquakes were recorded, including the 24 August 2014 Mw 6.0 Napa, California, earthquake. The resulting ground‐motion data set is used to quantify the seismic response of the Livermore basin, a major structural depression in the California Coast Range Province bounded by active faults. Site response is calculated by two methods: the reference‐site spectral ratio method and a source‐site spectral inversion method. Longer‐period (≥1  s) amplification factors follow the same general pattern as Bouguer gravity anomaly contours. Site response spectra are inverted for shallow shear‐wave velocity profiles, which are consistent with independent information. Frequency–wavenumber analysis is used to analyze plane‐wave propagation across the Livermore Valley and to identify basin‐edge‐induced surface waves with back azimuths different from the source back azimuth. Finite‐element simulations in a 3D velocity model of the region illustrate the generation of basin‐edge‐induced surface waves and point out strips of elevated ground velocities along the margins of the basin.

  10. Surface site diffusion and reaction on molecular "organizates" and colloidal catalysts: A geometrical perspective.

    PubMed

    Politowicz, P A; Kozak, J J

    1987-12-01

    We study surface-mediated, diffusion-controlled reactive processes on particles whose overall geometry is homeomorphic to a sphere. Rather than assuming that a coreactant can diffuse freely over the surface of the particle to a target site (reaction center), we consider the case where the coreactant can migrate only among N - 1 satellite sites that are networked to the reaction site by means of a number of pathways or reaction channels. Five distinct lattice topologies are considered and we study the reaction efficiency both for the case where the satellite sites are passive and for the case where reaction may occur with finite probability at these sites. The results obtained for this class of surface problems are compared with those obtained by assuming that the reaction-diffusion process takes place on a planar, two-dimensional surface (lattice). The applicability of our results to surface-mediated processes on "organizates" (cells, vesicles, micelles) and on colloidally dispersed catalyst particles is brought out in the Introduction, and the correspondence between the lattice-based, Markovian approach developed here and Fickian models of surface diffusion, particularly with regard to the exponentiality of the decay, is discussed in the concluding section.

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  12. Hanford Site Permanent Isolation Surface Barrier Development Program: Fiscal year 1992 and 1993 highlights

    SciTech Connect

    Cadwell, L.L.; Link, S.O.; Gee, G.W.

    1993-09-01

    The Hanford Site Permanent Isolation Surface Barrier Development Program was jointly developed by the Pacific Northwest Laboratory and Westinghouse Hanford Company to design and test an earthen cover system that can be used to inhibit water infiltration; plant, animal, and human intrusion; and wind and water erosion. Kaiser Engineers Hanford Company provided engineering design support for the program. Work on barrier design has been under way at Hanford for nearly 10 years. The comprehensive development of a long-term barrier, formerly the Hanford Site Protective Barrier Development Program, was initiated in FY 1986, and a general field-tested design is expected to be completed by FY 1998. Highlights of efforts in FY 1992 and FY 1993 included the resumption of field testing, the completion of the prototype barrier design, and the convening of an external peer review panel, which met twice with the barrier development team. The review panel provided helpful guidance on current and future barrier development activities, while commending the program for its significant technical contributions to innovative barrier technology development.

  13. A modular treatment of molecular traffic through the active site of cholinesterase

    PubMed Central

    Botti, SA; Felder, CE; Lifson, S; Sussman, JL; Silman, I

    1999-01-01

    We present a model for the molecular traffic of ligands, substrates, and products through the active site of cholinesterases (ChEs). First, we describe a common treatment of the diffusion to a buried active site of cationic and neutral species. We then explain the specificity of ChEs for cationic ligands and substrates by introducing two additional components to this common treatment. The first module is a surface trap for cationic species at the entrance to the active-site gorge that operates through local, short-range electrostatic interactions and is independent of ionic strength. The second module is an ionic-strength-dependent steering mechanism generated by long-range electrostatic interactions arising from the overall distribution of charges in ChEs. Our calculations show that diffusion of charged ligands relative to neutral isosteric analogs is enhanced approximately 10-fold by the surface trap, while electrostatic steering contributes only a 1.5- to 2-fold rate enhancement at physiological salt concentration. We model clearance of cationic products from the active-site gorge as analogous to the escape of a particle from a one-dimensional well in the presence of a linear electrostatic potential. We evaluate the potential inside the gorge and provide evidence that while contributing to the steering of cationic species toward the active site, it does not appreciably retard their clearance. This optimal fine-tuning of global and local electrostatic interactions endows ChEs with maximum catalytic efficiency and specificity for a positively charged substrate, while at the same time not hindering clearance of the positively charged products. PMID:10545346

  14. Druggability analysis and classification of protein tyrosine phosphatase active sites

    PubMed Central

    Ghattas, Mohammad A; Raslan, Noor; Sadeq, Asil; Al Sorkhy, Mohammad; Atatreh, Noor

    2016-01-01

    Protein tyrosine phosphatases (PTP) play important roles in the pathogenesis of many diseases. The fact that no PTP inhibitors have reached the market so far has raised many questions about their druggability. In this study, the active sites of 17 PTPs were characterized and assessed for its ability to bind drug-like molecules. Consequently, PTPs were classified according to their druggability scores into four main categories. Only four members showed intermediate to very druggable pocket; interestingly, the rest of them exhibited poor druggability. Particularly focusing on PTP1B, we also demonstrated the influence of several factors on the druggability of PTP active site. For instance, the open conformation showed better druggability than the closed conformation, while the tight-bound water molecules appeared to have minimal effect on the PTP1B druggability. Finally, the allosteric site of PTP1B was found to exhibit superior druggability compared to the catalytic pocket. This analysis can prove useful in the discovery of new PTP inhibitors by assisting researchers in predicting hit rates from high throughput or virtual screening and saving unnecessary cost, time, and efforts via prioritizing PTP targets according to their predicted druggability. PMID:27757011

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

    SciTech Connect

    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.

  16. Comparison of Grab, Air, and Surface Results for Radiation Site Characterization

    NASA Astrophysics Data System (ADS)

    Glassford, Eric Keith

    2011-12-01

    The use of proper sampling methods and sample types for evaluating sites believed to be contaminated with radioactive materials is necessary to avoid misrepresenting conditions at the site. This study was designed to investigate if the site characterization, based upon uranium contamination measured in different types of samples, is dependent upon the mass of the sample collected. A bulk sample of potentially contaminated interior dirt was collected from an abandoned metal processing mill that rolled uranium between 1948 and 1956. The original mill dates from 1910 and has a dirt floor. The bulk sample was a mixture of dirt, black and yellow particles of metal dust, and small fragments of natural debris. Small mass (approximately 0.75 grams (g)) and large mass (approximately 70g) grab samples were prepared from the bulk sample material to simulate collection of a "grab" type sample. Air sampling was performed by re-suspending a portion of the bulk sample material using a vibration table to simulate airborne contamination that might be present during site remediation. Additionally, samples of removable contaminated surface dust were collected on 47 mm diameter filter paper by wiping the surfaces of the exposure chamber used to resuspend the bulk material. Certified reference materials, one containing a precisely known quantity of U 3O8 and one containing a known quantity of natural uranium, were utilized to calibrate the gamma spectrometry measurement system. Non-destructive gamma spectrometry measurements were used to determine the content of uranium-235 (235U) at 185 keV and 143 keV, thorium-234 (234Th) at 63 keV, and protactinium-234m (234mPa) at 1001 keV in each sample. Measurement of natural uranium in small, 1 g samples is usually accomplished by radiochemical analysis in order to measure alpha particles emitted by 238U, 235U, and 234U. However, uranium in larger bulk samples can also be measured non-destructively using gamma spectrometry to detect the low

  17. Site-dependent catalytic activity of graphene oxides towards oxidative dehydrogenation of propane.

    PubMed

    Tang, Shaobin; Cao, Zexing

    2012-12-28

    Graphene oxides (GOs) may offer extraordinary potential in the design of novel catalytic systems due to the presence of various oxygen functional groups and their unique electronic and structural properties. Using first-principles calculations, we explore the plausible mechanisms for the oxidative dehydrogenation (ODH) of propane to propene by GOs and the diffusion of the surface oxygen-containing groups under an external electric field. The present results show that GOs with modified oxygen-containing groups may afford high catalytic activity for the ODH of propane to propene. The presence of hydroxyl groups around the active sites provided by epoxides can remarkably enhance the C-H bond activation of propane and the activity enhancement exhibits strong site dependence. The sites of oxygen functional groups on the GO surface can be easily tuned by the diffusion of these groups under an external electric field, which increases the reactivity of GOs towards ODH of propane. The chemically modified GOs are thus quite promising in the design of metal-free catalysis. PMID:22801590

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

    PubMed

    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

  19. CO Oxidation on Au/TiO2: Condition-Dependent Active Sites and Mechanistic Pathways.

    PubMed

    Wang, Yang-Gang; Cantu, David C; Lee, Mal-Soon; Li, Jun; Glezakou, Vassiliki-Alexandra; Rousseau, Roger

    2016-08-24

    We present results of ab initio electronic structure and molecular dynamics simulations (AIMD), as well as a microkinetic model of CO oxidation catalyzed by TiO2 supported Au nanocatalysts. A coverage-dependent microkinetic analysis, based on energetics obtained with density functional methods, shows that the dominant kinetic pathway, activated oxygen species, and catalytic active sites are all strongly depended on both temperature and oxygen partial pressure. Under oxidizing conditions and T < 400 K, the prevalent pathway involves a dynamic single atom catalytic mechanism. This reaction is catalyzed by a transient Au-CO species that migrates from the Au-cluster onto a surface oxygen adatom. It subsequently reacts with the TiO2 support via a Mars van Krevelen mechanism to form CO2 and finally the Au atom reintegrates back into the gold cluster to complete the catalytic cycle. At 300 ≤ T ≤ 600 K, oxygen-bound single Oad-Au(+)-CO sites and the perimeter Au-sites of the nanoparticle work in tandem to optimally catalyze the reaction. Above 600 K, a variety of alternate pathways associated with both single-atom and the perimeter sites of the Au nanoparticle are found to be active. Under low oxygen pressures, Oad-Au(+)-CO species can be a source of catalyst deactivation and the dominant pathway involves only Au-perimeter sites. A detailed comparison of the current model and the existing literature resolves many apparent inconsistencies in the mechanistic interpretations. PMID:27480512

  20. Histidine at the active site of Neurospora tyrosinase.

    PubMed

    Pfiffner, E; Lerch, K

    1981-10-13

    The involvement of histidyl residues as potential ligands to the binuclear active-site copper of Neurospora tyrosinase was explored by dye-sensitized photooxidation. The enzymatic activity of the holoenzyme was shown to be unaffected by exposure to light in the presence of methylene blue; however, irradiation of the apoenzyme under the same conditions led to a progressive loss of its ability to be reactivated with Cu2+. This photoinactivation was paralleled by a decrease in the histidine content whereas the number of histidyl residues in the holoenzyme remained constant. Copper measurements of photooxidized, reconstituted apoenzyme demonstrated the loss of binding of one copper atom per mole of enzyme as a consequence of photosensitized oxidation of three out of nine histidine residues. Their sequence positions were determined by a comparison of the relative yields of the histidine containing peptides of photooxidized holo- and apotyrosinases. The data obtained show the preferential modification of histidyl residues 188, 193, and 289 and suggest that they constitute metal ligands to one of the two active-site copper atoms. Substitution of copper by cobalt was found to afford complete protection of the histidyl residues from being modified by dye-sensitized photooxidation. PMID:6458322

  1. A site energy distribution function from Toth isotherm for adsorption of gases on heterogeneous surfaces.

    PubMed

    Kumar, K Vasanth; de Castro, M Monteiro; Martinez-Escandell, M; Molina-Sabio, M; Rodriguez-Reinoso, F

    2011-04-01

    A site energy distribution function based on a condensation approximation method is proposed for gas-phase adsorption systems following the Toth isotherm. The proposed model is successfully applied to estimate the site energy distribution of three pitch-based activated carbons (PA, PFeA and PBA) developed in our laboratory and also for other common adsorbent materials for different gas molecules. According to the proposed model the site energy distribution curves of the activated carbons are found to be exponential for hydrogen at 77 K. The site energy distribution of some of the activated carbon fibers, ambersorb, Dowex optipore, 13X Zeolite for different adsorbate molecules represents a quasi-Gaussian curve with a widened left hand side, indicating that most sites have adsorption energies lower than a statistical mean value.

  2. Surface Properties and Characteristics of Mars Landing Sites from Remote Sensing Data and Ground Truth

    NASA Astrophysics Data System (ADS)

    Golombek, M. P.; Haldemann, A. F.; Simpson, R. A.; Furgason, R. L.; Putzig, N. E.; Huertas, A.; Arvidson, R. E.; Heet, T.; Bell, J. F.; Mellon, M. T.; McEwen, A. S.

    2008-12-01

    Surface characteristics at the six sites where spacecraft have successfully landed on Mars can be related favorably to their signatures in remotely sensed data from orbit and from the Earth. Comparisons of the rock abundance, types and coverage of soils (and their physical properties), thermal inertia, albedo, and topographic slope all agree with orbital remote sensing estimates and show that the materials at the landing sites can be used as ground truth for the materials that make up most of the equatorial and mid- to moderately high-latitude regions of Mars. The six landing sites sample two of the three dominant global thermal inertia and albedo units that cover ~80% of the surface of Mars. The Viking, Spirit, Mars Pathfinder, and Phoenix landing sites are representative of the moderate to high thermal inertia and intermediate to high albedo unit that is dominated by crusty, cloddy, blocky or frozen soils (duricrust that may be layered) with various abundances of rocks and bright dust. The Opportunity landing site is representative of the moderate to high thermal inertia and low albedo surface unit that is relatively dust free and composed of dark eolian sand and/or increased abundance of rocks. Rock abundance derived from orbital thermal differencing techniques in the equatorial regions agrees with that determined from rock counts at the surface and varies from ~3-20% at the landing sites. The size-frequency distributions of rocks >1.5 m diameter fully resolvable in HiRISE images of the landing sites follow exponential models developed from lander measurements of smaller rocks and are continuous with these rock distributions indicating both are part of the same population. Interpretation of radar data confirms the presence of load bearing, relatively dense surfaces controlled by the soil type at the landing sites, regional rock populations from diffuse scattering similar to those observed directly at the sites, and root-mean-squared slopes that compare favorably

  3. Active Site Dependent Reaction Mechanism over Ru/CeO2 Catalyst toward CO2 Methanation.

    PubMed

    Wang, Fei; He, Shan; Chen, Hao; Wang, Bin; Zheng, Lirong; Wei, Min; Evans, David G; Duan, Xue

    2016-05-18

    Oxygen vacancy on the surface of metal oxides is one of the most important defects which acts as the reactive site in a variety of catalytic reactions. In this work, operando spectroscopy methodology was employed to study the CO2 methanation reaction catalyzed by Ru/CeO2 (with oxygen vacancy in CeO2) and Ru/α-Al2O3 (without oxygen vacancy), respectively, so as to give a thorough understanding on active site dependent reaction mechanism. In Ru/CeO2 catalyst, operando XANES, IR, and Raman were used to reveal the generation process of Ce(3+), surface hydroxyl, and oxygen vacancy as well as their structural evolvements under practical reaction conditions. The steady-state isotope transient kinetic analysis (SSITKA)-type in situ DRIFT infrared spectroscopy undoubtedly substantiates that CO2 methanation undergoes formate route over Ru/CeO2 catalyst, and the formate dissociation to methanol catalyzed by oxygen vacancy is the rate-determining step. In contrast, CO2 methanation undergoes CO route over Ru surface in Ru/α-Al2O3 with the absence of oxygen vacancy, demonstrating active site dependent catalytic mechanism toward CO2 methanation. In addition, the catalytic activity evaluation and the oscillating reaction over Ru/CeO2 catalyst further prove that the oxygen vacancy catalyzes the rate-determining step with a much lower activation temperature compared with Ru surface in Ru/α-Al2O3 (125 vs 250 °C). PMID:27135417

  4. A study of surface and subsurface ground motions at Calico Hills, Nevada Test Site

    USGS Publications Warehouse

    King, Kenneth W.

    1982-01-01

    A study of earthquake ground motions recorded at depth in a drill hole and at the ground surface has derived the surface to subsurface transfer functions such as might be expected at a potential nuclear waste repository in a similar setting. The site under investigation has small seismic velocity contrasts in the layers of rock between the surface and the subsurface seismometer location. The subsurface seismic motions were similar in spectral characteristics to the surface motions and were lower in amplitude across the recorded band-width by a factor of 1.5.

  5. Low temperature adsorption and site-conversion process of CO on the Ni(111) surface

    NASA Astrophysics Data System (ADS)

    Beniya, Atsushi; Isomura, Noritake; Hirata, Hirohito; Watanabe, Yoshihide

    2012-12-01

    Low-temperature (25 K) adsorption states and the site conversion of adsorbed CO between the ontop and the hollow sites on Ni(111) were studied by means of temperature programmed desorption and infrared reflection absorption spectroscopy. The activation energy and pre-exponential factor of desorption were estimated to be 1.2 eV and 2.6 × 1013 s- 1, respectively, in the limit of zero coverage. At low coverage, CO molecules preferentially adsorbed at the hollow sites below 100 K. With increasing temperature, the ontop sites were also occupied. Using a van't Hoff plot, the enthalpy and the entropy differences between the hollow and ontop CO were estimated to be 36 meV and 0.043 meV K- 1, respectively, and the vibrational entropy difference was estimated to be 0.085 meV K- 1. The positive entropy difference was the result of the low-energy frustrated translational mode of the ontop CO, which was estimated to be 4.6 ± 0.3 meV. With the harmonic approximation, the upper limit of the activation energy of site hopping from ontop sites to hollow sites was estimated to be 61 meV. In addition, it was suggested that the activation energy of hollow-to-hollow site hopping via a bridge site was less than 37 meV.

  6. Trichodiene synthase. Identification of active site residues by site-directed mutagenesis.

    PubMed

    Cane, D E; Shim, J H; Xue, Q; Fitzsimons, B C; Hohn, T M

    1995-02-28

    Derivatization of 5,5'-dithiobis(2-nitrobenzoic acid)-treated trichodiene synthase with [methyl-14C]methyl methanethiosulfonate and analysis of the derived tryptic peptides suggested the presence of two cysteine residues at the active site. The corresponding C146A and C190A mutants were constructed by site-directed mutagenesis. The C190A mutant displayed partial but significantly reduced activity, with a reduction in kcat/Km of 3000 compared to the wild-type trichodiene synthase, while the C146A mutant was essentially inactive. A hybrid trichodiene synthase, constructed from amino acids 1-309 of the Fusarium sporotrichioides enzyme and amino acids 310-383 of the Gibberella pulicaris cyclase, had steady state kinetic parameters nearly identical to those of the wild-type F. sporotrichioides enzyme. From this parent hybrid, a series of mutants was constructed by site-directed mutagenesis in which the amino acids in the base-rich region, 302-306 (DRRYR), were systematically modified. Three of these mutants were overexpressed and purified to homogeneity. The importance of Arg304 for catalysis was established by the observation that the R304K mutant showed a more than 25-fold increase in Km, as well as a 200-fold reduction in kcat. In addition, analysis of the incubation products of the R304K mutant by gas chromatography-mass spectrometry (GC-MS) indicated that farnesyl diphosphate was converted not only to trichodiene but to at least two additional C15H24 hydrocarbons, mle 204. Replacement of the Tyr305 residue of trichodiene synthase with Phe had little effect on kcat, while increasing the Km by a factor of ca. 7-8.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:7873527

  7. May 2012 Groundwater and Surface Water Sampling at the Rio Blanco, Colorado, Site (Data Validation Package)

    SciTech Connect

    2012-12-01

    Annual sampling was conducted at the Rio Blanco, Colorado, site for the Long-Term Hydrologic Monitoring Program May 9-10, 2012, to monitor groundwater and surface water for potential radionuclide contamination. Sampling and analyses were conducted as specified in Sampling and Analysis Plan for the U.S. Department of Energy Office of Legacy Management Sites (LMS/PRO/S04351, continually updated). A duplicate sample was collected from location Johnson Artesian WL. Samples were analyzed for gamma-emitting radionuclides by high-resolution gamma spectrometry and for tritium using the conventional and enrichment methods. Results of this monitoring at the Rio Blanco site demonstrate that groundwater and surface water outside the site boundaries have not been affected by project-related contaminants.

  8. The copper active site of CBM33 polysaccharide oxygenases.

    PubMed

    Hemsworth, Glyn R; Taylor, Edward J; Kim, Robbert Q; Gregory, Rebecca C; Lewis, Sally J; Turkenburg, Johan P; Parkin, Alison; Davies, Gideon J; Walton, Paul H

    2013-04-24

    The capacity of metal-dependent fungal and bacterial polysaccharide oxygenases, termed GH61 and CBM33, respectively, to potentiate the enzymatic degradation of cellulose opens new possibilities for the conversion of recalcitrant biomass to biofuels. GH61s have already been shown to be unique metalloenzymes containing an active site with a mononuclear copper ion coordinated by two histidines, one of which is an unusual τ-N-methylated N-terminal histidine. We now report the structural and spectroscopic characterization of the corresponding copper CBM33 enzymes. CBM33 binds copper with high affinity at a mononuclear site, significantly stabilizing the enzyme. X-band EPR spectroscopy of Cu(II)-CBM33 shows a mononuclear type 2 copper site with the copper ion in a distorted axial coordination sphere, into which azide will coordinate as evidenced by the concomitant formation of a new absorption band in the UV/vis spectrum at 390 nm. The enzyme's three-dimensional structure contains copper, which has been photoreduced to Cu(I) by the incident X-rays, confirmed by X-ray absorption/fluorescence studies of both aqueous solution and intact crystals of Cu-CBM33. The single copper(I) ion is ligated in a T-shaped configuration by three nitrogen atoms from two histidine side chains and the amino terminus, similar to the endogenous copper coordination geometry found in fungal GH61. PMID:23540833

  9. Activation of muscarinic acetylcholine receptors via their allosteric binding sites.

    PubMed Central

    Jakubík, J; Bacáková, L; Lisá, V; el-Fakahany, E E; Tucek, S

    1996-01-01

    Ligands that bind to the allosteric-binding sites on muscarinic acetylcholine receptors alter the conformation of the classical-binding sites of these receptors and either diminish or increase their affinity for muscarinic agonists and classical antagonists. It is not known whether the resulting conformational change also affects the interaction between the receptors and the G proteins. We have now found that the muscarinic receptor allosteric modulators alcuronium, gallamine, and strychnine (acting in the absence of an agonist) alter the synthesis of cAMP in Chinese hamster ovary (CHO) cells expressing the M2 or the M4 subtype of muscarinic receptors in the same direction as the agonist carbachol. In addition, most of their effects on the production of inositol phosphates in CHO cells expressing the M1 or the M3 muscarinic receptor subtypes are also similar to (although much weaker than) those of carbachol. The agonist-like effects of the allosteric modulators are not observed in CHO cells that have not been transfected with the gene for any of the subtypes of muscarinic receptors. The effects of alcuronium on the formation of cAMP and inositol phosphates are not prevented by the classical muscarinic antagonist quinuclidinyl benzilate. These observations demonstrate for the first time that the G protein-mediated functional responses of muscarinic receptors can be evoked not only from their classical, but also from their allosteric, binding sites. This represents a new mechanism of receptor activation. PMID:8710935

  10. Lunar Surface Traverse and Exploration Planning: What Makes a "Good" Landing Site?

    NASA Astrophysics Data System (ADS)

    Lawrence, S. J.; Stopar, J. D.; Jolliff, B. L.; Speyerer, E. J.; Robinson, M. S.

    2015-10-01

    As part of a campaign to determine landing site locations for science and ISRU activity, we develop a defensible morphometric envelope for landed missions using LRO data to analyze the morphometric parameters of historical lunar landing locations.

  11. Surface wind characteristics of some Aleutian Islands. [for selection of windpowered machine sites

    NASA Technical Reports Server (NTRS)

    Wentink, T., Jr.

    1973-01-01

    The wind power potential of Alaska is assessed in order to determine promising windpower sites for construction of wind machines and for shipment of wind derived energy. Analyses of near surface wind data from promising Aleutian sites accessible by ocean transport indicate probable velocity regimes and also present deficiencies in available data. It is shown that winds for some degree of power generation are available 77 percent of the time in the Aleutians with peak velocities depending on location.

  12. Aerosol measurements at the Southern Great Plains Site: Design and surface installation

    SciTech Connect

    Leifer, R.; Knuth, R.H.; Guggenheim, S.F.; Albert, B.

    1996-04-01

    To impropve the predictive capabilities of the Atmospheric Radiation Measurements (ARM) program radiation models, measurements of awserosol size distributions, condensation particle concentrations, aerosol scattering coefficients at a number of wavelenghts, and the aerosol absorption coefficients are needed at the Southern Great Plains (SGP) site. Alos, continuous measurements of ozone concnetrations are needed for model validation. The environmental Measuremenr Laboratory (EMK) has the responsibility to establish the surface aerosol measurements program at the SGP site. EML has designed a special sampling manifold.

  13. Radiation inactivation study of aminopeptidase: probing the active site

    NASA Astrophysics Data System (ADS)

    Jamadar, V. K.; Jamdar, S. N.; Mohan, Hari; Dandekar, S. P.; Harikumar, P.

    2004-04-01

    Ionizing radiation inactivated purified chicken intestinal aminopeptidase in media saturated with gases in the order N 2O>N 2>air. The D 37 values in the above conditions were 281, 210 and 198 Gy, respectively. OH radical scavengers such as t-butanol and isopropanol effectively nullified the radiation-induced damage in N 2O. The radicals (SCN) 2•-, Br 2•- and I 2•- inactivated the enzyme, pointing to the involvement of aromatic amino acids and cysteine in its catalytic activity. The enzyme exhibited fluorescence emission at 340 nm which is characteristic of tryptophan. The radiation-induced loss of activity was accompanied by a decrease in the fluorescence of the enzyme suggesting a predominant influence on tryptophan residues. The enzyme inhibition was associated with a marked increase in the Km and a decrease in the Vmax and kcat values, suggesting an irreversible alteration in the catalytic site. The above observations were confirmed by pulse radiolysis studies.

  14. Simulation and preparation of surface EVA in reduced gravity at the Marseilles Bay subsea analogue sites

    NASA Astrophysics Data System (ADS)

    Weiss, P.; Gardette, B.; Chirié, B.; Collina-Girard, J.; Delauze, H. G.

    2012-12-01

    Extravehicular activity (EVA) of astronauts during space missions is simulated nowadays underwater in neutral buoyancy facilities. Certain aspects of weightlessness can be reproduced underwater by adding buoyancy to a diver-astronaut, therefore exposing the subject to the difficulties of working without gravity. Such tests were done at the COMEX' test pool in Marseilles in the 1980s to train for a French-Russian mission to the MIR station, for the development of the European HERMES shuttle and the COLUMBUS laboratory. However, space agencies are currently studying missions to other destinations than the International Space Station in orbit, such as the return to the Moon, NEO (near-Earth objects) or Mars. All these objects expose different gravities: Moon has one sixth of Earth's gravity, Mars has a third of Earth's gravity and asteroids have virtually no surface gravity; the astronaut "floats" above the ground. The preparation of such missions calls for a new concept in neutral buoyancy training, not on man-made structures, but on natural terrain, underwater, to simulate EVA operations such as sampling, locomotion or even anchoring in low gravity. Underwater sites can be used not only to simulate the reduced gravity that astronauts will experience during their field trips, also human factors like stress are more realistically reproduced in such environment. The Bay of Marseille hosts several underwater sites that can be used to simulate various geologic morphologies, such as sink-holes which can be used to simulate astronaut descends into craters, caves where explorations of lava tubes can be trained or monolithic rock structures that can be used to test anchoring devices (e.g., near Earth objects). Marseilles with its aerospace and maritime/offshore heritage hosts the necessary logistics and expertise that is needed to perform such simulations underwater in a safe manner (training of astronaut-divers in local test pools, research vessels, subsea robots and

  15. Spatial Variability of Surface Irradiance Measurements at the Manus ARM Site

    SciTech Connect

    Riihimaki, Laura D.; Long, Charles N.

    2014-05-16

    The location of the Atmospheric Radiation Measurement (ARM) site on Manus island in Papua New Guinea was chosen because it is very close the coast, in a geographically at, near-sea level area of the island, minimizing the impact of local island effects on the meteorology of the measurements [Ackerman et al., 1999]. In this study, we confirm that the Manus site is in deed less impacted by the island meteorology than slightly inland by comparing over a year of broadband surface irradiance and ceilometer measurements and derived quantities at the standard Manus site and a second location 7 km away as part of the AMIE-Manus campaign. The two sites show statistically similar distributions of irradiance and other derived quantities for all wind directions except easterly winds, when the inland site is down wind from the standard Manus site. Under easterly wind conditions, which occur 17% of the time, there is a higher occurrence of cloudiness at the down wind site likely do to land heating and orographic effects. This increased cloudiness is caused by shallow, broken clouds often with bases around 700 m in altitude. While the central Manus site consistently measures a frequency of occurrence of low clouds (cloud base height less than 1200 m) about 25+4% regardless of wind direction, the AMIE site has higher frequencies of low clouds (38%) when winds are from the east. This increase in low, locally produced clouds causes an additional -20 W/m2 shortwave surface cloud radiative effect at the AMIE site in easterly conditions than in other meteorological conditions that exhibit better agreement between the two sites.

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed Central

    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

  18. Spectroscopic Definition of the Ferroxidase Site in M Ferritin: Comparison of Binuclear Substrate vs. Cofactor Active Sites

    PubMed Central

    Schwartz, Jennifer K.; Liu, Xiaofeng S.; Tosha, Takehiko; Theil, Elizabeth C.; Solomon, Edward I.

    2008-01-01

    Maxi ferritins, 24 subunit protein nanocages, are essential in humans, plants, bacteria, and other animals for the concentration and storage of iron as hydrated ferric oxide, while minimizing free radical generation or use by pathogens. Formation of the precursors to these ferric oxides is catalyzed at a non-heme biferrous substrate site, which has some parallels with the cofactor sites in other biferrous enzymes. A combination of circular dichroism (CD), magnetic circular dichroism (MCD), and variable-temperature, variable-field MCD (VTVH MCD) has been used to probe Fe(II) binding to the substrate active site in frog M ferritin. These data determined that the active site within each subunit consists of two inequivalent five-coordinate (5C) ferrous centers that are weakly anti-ferromagnetically coupled, consistent with a μ-1,3 carboxylate bridge. The active site ligand set is unusual and likely includes a terminal water bound to each Fe(II) center. The Fe(II) ions bind to the active sites in a concerted manner, and cooperativity among the sites in each subunit is observed, potentially providing a mechanism for the control of ferritin iron loading. Differences in geometric and electronic structure – including a weak ligand field, availability of two water ligands at the biferrous substrate site, and the single carboxylate bridge in ferritin – coincide with the divergent reaction pathways observed between this substrate site and the previously studied cofactor active sites. PMID:18576633

  19. An active-site lysine in avian liver phosphoenolpyruvate carboxykinase

    SciTech Connect

    Guidinger, P.F.; Nowak, T. )

    1991-09-10

    The participation of lysine in the catalysis by avian liver phosphoenolpyruvate carboxykinase was studied by chemical modification and by a characterization of the modified enzyme. The rate of inactivation by 2,4-pentanedione is pseudo-first-order and linearly dependent on reagent concentration with a second-order rate constant of 0.36 {plus minus} 0.025 M{sup {minus}1} min{sup {minus}1}. Inactivation by pyridoxal 5{prime}-phosphate of the reversible reaction catalyzed by phosphoenolpyruvate carboxykinase follows bimolecular kinetics with a second-order rate constant of 7,700 {plus minus} 860 m{sup {minus}1} min{sup {minus}1}. Treatment of the enzyme or one lysine residue modified concomitant with 100% loss in activity. A stoichiometry of 1:1 is observed when either the reversible or the irreversible reactions catalyzed by the enzyme are monitored. A study of k{sub obs} vs pH suggests this active-site lysine has a pK{sub a} of 8.1 and a pH-independent rate constant of inactivation of 47,700 m{sup {minus}1} min{sup {minus}1}. Proton relaxation rate measurements suggest that pyridoxal 5{prime}-phosphate modification alters binding of the phosphate-containing substrates. {sup 31}P NMR relaxation rate measurements show altered binding of the substrates in the ternary enzyme {center dot}Mn{sup 2+}{center dot}substrate complex. Circular dichroism studies show little change in secondary structure of pyridoxal 5{prime}-phosphate modified phosphoenolpyruvate carboxykinase. These results indicate that avian liver phosphoenolpyruvate carboxykinase has one reactive lysine at the active site and it is involved in the binding and activation of the phosphate-containing substrates.

  20. Near Surface Swimming of Salmonella Typhimurium Explains Target-Site Selection and Cooperative Invasion

    PubMed Central

    Kreibich, Saskia; Vonaesch, Pascale; Andritschke, Daniel; Rout, Samuel; Weidner, Kerstin; Sormaz, Milos; Songhet, Pascal; Horvath, Peter; Chabria, Mamta; Vogel, Viola; Spori, Doris M.; Jenny, Patrick; Hardt, Wolf-Dietrich

    2012-01-01

    Targeting of permissive entry sites is crucial for bacterial infection. The targeting mechanisms are incompletely understood. We have analyzed target-site selection by S. Typhimurium. This enteropathogenic bacterium employs adhesins (e.g. fim) and the type III secretion system 1 (TTSS-1) for host cell binding, the triggering of ruffles and invasion. Typically, S. Typhimurium invasion is focused on a subset of cells and multiple bacteria invade via the same ruffle. It has remained unclear how this is achieved. We have studied target-site selection in tissue culture by time lapse microscopy, movement pattern analysis and modeling. Flagellar motility (but not chemotaxis) was required for reaching the host cell surface in vitro. Subsequently, physical forces trapped the pathogen for ∼1.5–3 s in “near surface swimming”. This increased the local pathogen density and facilitated “scanning” of the host surface topology. We observed transient TTSS-1 and fim-independent “stopping” and irreversible TTSS-1-mediated docking, in particular at sites of prominent topology, i.e. the base of rounded-up cells and membrane ruffles. Our data indicate that target site selection and the cooperative infection of membrane ruffles are attributable to near surface swimming. This mechanism might be of general importance for understanding infection by flagellated bacteria. PMID:22911370

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

    PubMed

    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.

  2. Eel calcitonin binding site distribution and antinociceptive activity in rats

    SciTech Connect

    Guidobono, F.; Netti, C.; Sibilia, V.; Villa, I.; Zamboni, A.; Pecile, A.

    1986-03-01

    The distribution of binding site for (/sup 125/I)-eel-calcitonin (ECT) to rat central nervous system, studied by an autoradiographic technique, showed concentrations of binding in the diencephalon, the brain stem and the spinal cord. Large accumulations of grains were seen in the hypothalamus, the amygdala, in the fasciculus medialis prosencephali, in the fasciculus longitudinalis medialis, in the ventrolateral part of the periventricular gray matter, in the lemniscus medialis and in the raphe nuclei. The density of grains in the reticular formation and in the nucleus tractus spinalis nervi trigemini was more moderate. In the spinal cord, grains were scattered throughout the dorsal horns. Binding of the ligand was displaced equally by cold ECT and by salmon CT(sCT), indicating that both peptides bind to the same receptors. Human CT was much weaker than sCT in displacing (/sup 125/I)-ECT binding. The administration of ECT into the brain ventricles of rats dose-dependently induced a significant and long-lasting enhancement of hot-plate latencies comparable with that obtained with sCT. The antinociceptive activity induced by ECT is compatible with the topographical distribution of binding sites for the peptide and is a further indication that fish CTs are active in the mammalian brain.

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

    PubMed

    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

  4. A Climatology of Surface Cloud Radiative Effects at the ARM Tropical Western Pacific Sites

    SciTech Connect

    McFarlane, Sally A.; Long, Charles N.; Flaherty, Julia E.

    2013-04-01

    Cloud radiative effects on surface downwelling fluxes are investigated using long-term datasets from the three Atmospheric Radiation Measurement (ARM) sites in the Tropical Western Pacific (TWP) region. The Nauru and Darwin sites show significant variability in sky cover, downwelling radiative fluxes, and surface cloud radiative effect (CRE) due to El Niño and the Australian monsoon, respectively, while the Manus site shows little intra-seasonal or interannual variability. Cloud radar measurement of cloud base and top heights are used to define cloud types so that the effect of cloud type on the surface CRE can be examined. Clouds with low bases contribute 71-75% of the surface shortwave (SW) CRE and 66-74% of the surface longwave (LW) CRE at the three TWP sites, while clouds with mid-level bases contribute 8-9% of the SW CRE and 12-14% of the LW CRE, and clouds with high bases contribute 16-19% of the SW CRE and 15-21% of the LW CRE.

  5. [Field measurement of Gobi surface emissivity spectrum at Dunhuang calibration site of China].

    PubMed

    Zhang, Yong; Li, Yuan; Rong, Zhi-guo; Hu, Xiu-qing; Zhang, Li-jun; Liu, Jing-jing

    2009-05-01

    Gobi surface emissivity spectrum of Dunhuang radiometric calibration site of China is one of the key factors to calibrate the thermal infrared remote sensors using land surface. Based on the iterative spectrally smooth temperature/emissivity separation (ISSTES)algorithm, Dunhuang Gobi surface emissivity spectrum was measured using BOMEM MR154 Fourier transform spectroradiometer and Infrared Golden Board. Emissivity spectrum data were obtained at different time and locations. These spectrum data were convolved with the channel response function of CE312 radiometer and compared with the channel emissivity measured by the same instrument. The results showed that the difference between these two kinds of channel emissivity was within 0.012 and exhibited a good consistency. With these measured emissivity spectra, all of the mainstream thermal infrared remote sensors can be calibrated using Dunhuang Gobi surface at radiometric calibration site of China.

  6. Acid-base site detection and mapping on solid surfaces by Kelvin force microscopy (KFM).

    PubMed

    Gouveia, Rubia F; Bernardes, Juliana S; Ducati, Telma R D; Galembeck, Fernando

    2012-12-01

    Electrostatic potential at the surface of acidic or basic solids changes under higher relative humidity (RH), as determined by using Kelvin force microscopy (KFM). The potential on acid surfaces becomes more negative as the water vapor pressure increases, while it becomes more positive on basic solids. These results verify the following hypothesis: OH(-) or H(+) ions associated with atmospheric water ion clusters are selectively adsorbed on solid surfaces, depending on the respective Brønsted acid or base character. Therefore, Kelvin microscopy, under variable humidity, is a rigorous but convenient alternative to determine the acid-base character of solid surfaces, with a great advantage: it uses only one amphoteric and simple reagent to determine both the acid and base sites. Moreover, this technique provides information on the spatial distribution of acid-base sites, which is currently inaccessible to any other method.

  7. An Active Site Water Network in the Plasminogen Activator Pla from Yersinia pestis

    SciTech Connect

    Eren, Elif; Murphy, Megan; Goguen, Jon; van den Berg, Bert

    2010-08-13

    The plasminogen activator Pla from Yersinia pestis is an outer membrane protease (omptin) that is important for the virulence of plague. Here, we present the high-resolution crystal structure of wild-type, enzymatically active Pla at 1.9 {angstrom}. The structure shows a water molecule located between active site residues D84 and H208, which likely corresponds to the nucleophilic water. A number of other water molecules are present in the active site, linking residues important for enzymatic activity. The R211 sidechain in loop L4 is close to the nucleophilic water and possibly involved in the stabilization of the oxyanion intermediate. Subtle conformational changes of H208 result from the binding of lipopolysaccharide to the outside of the barrel, explaining the unusual dependence of omptins on lipopolysaccharide for activity. The Pla structure suggests a model for the interaction with plasminogen substrate and provides a more detailed understanding of the catalytic mechanism of omptin proteases.

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

    SciTech Connect

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

    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.

  9. Rapid Determination of RNA Accessible Sites by Surface Plasmon Resonance Detection of Hybridization to DNA arrays

    PubMed Central

    Mandir, Joshua B.; Lockett, Matthew R.; Phillips, Margaret F.; Allawi, Hatim T.; Lyamichev, Victor I.; Smith, Lloyd M.

    2009-01-01

    RNA accessible sites are the regions in an RNA molecule, which are available for hybridization with complementary DNA or RNA molecules. The identification of these accessible sites is a critical first step in identifying antisense-mediated gene suppression sites, as well as in a variety of other RNA-based analysis methods. Here, we present a rapid, hybridization-based, label-free method of identifying RNA accessible sites with surface plasmon resonance imaging (SPRi) on in situ synthesized oligonucleotide arrays prepared on carbon-on-metal substrates. The accessible sites of three pre-miRNAs, miRNA precursors of ~75 nt in length, were determined by hybridizing the RNA molecules to RNA-specific tiling arrays. An array comprised of all possible 6mer oligonucleotide sequences was also utilized in this work, offering a universal platform capable of studying RNA molecules in a high throughput manner. PMID:19874056

  10. Requirements for extravehicular activities on the lunar and Martian surfaces

    NASA Technical Reports Server (NTRS)

    Brown, Mariann F.; Schentrup, Susan M.

    1990-01-01

    Basic design reference requirements pertinent to EVA equipment on lunar and martian surfaces are provided. Environmental factors affecting surface EVA are analyzed including gravity, dust, atmospheric conditions, thermal gradients, lightning conditions, and radiation effects, and activities associated with surface EVA are outlined. Environmental and activity effects on EVA equipment are assessed, and emphasis is placed on planetary surface portable life support systems (PLSS), suit development, protection from micrometeoroids, dust, and radiation, food and water supplies, and the extravehicular mobility-unit thermal-control system. Environmental and activity impacts on PLSS design are studied, with focus on base self-sufficiency and reduction in resupply logistics.

  11. Active Sites Environmental Monitoring Program: Program plan. Revision 1

    SciTech Connect

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

    1992-02-01

    The Active Sites Environmental Monitoring Program (ASEMP), initiated in 1989, provides early detection and performance monitoring of transuranic (TRU) waste and active low-level waste (LLW) facilities at Oak Ridge National Laboratory (ORNL) in accordance with US Department of Energy (DOE) Order 5820.2A. Active LLW facilities in Solid Waste Storage Area (SWSA) 6 include Tumulus I and Tumulus II, the Interim Waste Management Facility (IWMF), LLW silos, high-range wells, asbestos silos, and fissile wells. The tumulus pads and IWMF are aboveground, high-strength concrete pads on which concrete vaults containing metal boxes of LLW are placed; the void space between the boxes and vaults is filled with grout. Eventually, these pads and vaults will be covered by an engineered multilayered cap. All other LLW facilities in SWSA 6 are below ground. In addition, this plan includes monitoring of the Hillcut Disposal Test Facility (HDTF) in SWSA 6, even though this facility was completed prior to the data of the DOE order. In SWSA 5 North, the TRU facilities include below-grade engineered caves, high-range wells, and unlined trenches. All samples from SWSA 6 are screened for alpha and beta activity, counted for gamma-emitting isotopes, and analyzed for tritium. In addition to these analytes, samples from SWSA 5 North are analyzed for specific transuranic elements.

  12. Passive and active EO sensing of small surface vessels

    NASA Astrophysics Data System (ADS)

    Steinvall, Ove; Berglund, Folke; Allard, Lars; Öhgren, Johan; Larsson, Hâkan; Amselem, Elias; Gustafsson, Frank; Repasi, Endre; Lutzmann, Peter; Göhler, Benjamin; Hammer, Marcus; McEwen, Kennedy; McEwan, Ken

    2015-10-01

    The detection and classification of small surface targets at long ranges is a growing need for naval security. This paper will present an overview of a measurement campaign which took place in the Baltic Sea in November 2014. The purpose was to test active and passive EO sensors (10 different types) for the detection, tracking and identification of small sea targets. The passive sensors were covering the visual, SWIR, MWIR and LWIR regions. Active sensors operating at 1.5 μm collected data in 1D, 2D and 3D modes. Supplementary sensors included a weather station, a scintillometer, as well as sensors for positioning and attitude determination of the boats. Three boats in the class 4-9 meters were used as targets. After registration of the boats at close range they were sent out to 5-7 km distance from the sensor site. At the different ranges the target boats were directed to have different aspect angles relative to the direction of observation. Staff from IOSB Fraunhofer in Germany and from Selex (through DSTL) in UK took part in the tests beside FOI who was arranging the trials. A summary of the trial and examples of data and imagery will be presented.

  13. Evaluation of surface waters associated with animal feeding operations for estrogenic chemicals and activity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Estrogens and estrogenic activity (EA) were evaluated in surface waters associated with animal feeding operations. Water was sampled at 19 sites in 12 states using discrete (n=41) and POCIS (n=19) sampling methods. Estrogenic chemicals measured in unfiltered water by GC/MS2 included: estrone (E1),17...

  14. Synthesis of supported bimetallic nanoparticles with controlled size and composition distributions for active site elucidation

    SciTech Connect

    Hakim, Sikander H.; Sener, Canan; Alba Rubio, Ana C.; Gostanian, Thomas M.; O'neill, Brandon J; Ribeiro, Fabio H.; Miller, Jeffrey T.; Dumesic, James A

    2015-08-01

    Elucidation of active sites in supported bimetallic catalysts is complicated by the high level of dispersity in the nanoparticle size and composition that is inherent in conventional methods of catalyst preparation. We present a synthesis strategy that leads to highly dispersed, bimetallic nanoparticles with uniform particle size and composition by means of controlled surface reactions. We demonstrate the synthesis of three systems, RhMo, PtMo, and RhRe, consisting of a highly reducible metal with an oxophilic promoter. These catalysts are characterized by FTIR, CO chemisorption, STEM/EDS, TPR, and XAS analysis. The catalytic properties of these bimetallic nanoparticles were probed for the selective CO hydrogenolysis of (hydroxymethyl)tetrahydropyran to produce 1,6 hexanediol. Based on the characterization results and reactivity trends, the active sites in the hydrogenolysis reaction are identified to be small ensembles of the more noble metal (Rh, Pt) adjacent to highly reduced moieties of the more oxophilic metal (Mo, Re).

  15. Active Site and Laminarin Binding in Glycoside Hydrolase Family 55*

    PubMed Central

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

    2015-01-01

    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

  16. Discovery and Characterization of Non-ATP Site Inhibitors of the Mitogen Activated Protein (MAP) Kinases

    SciTech Connect

    Comess, Kenneth M.; Sun, Chaohong; Abad-Zapatero, Cele; Goedken, Eric R.; Gum, Rebecca J.; Borhani, David W.; Argiriadi, Maria; Groebe, Duncan R.; Jia, Yong; Clampit, Jill E.; Haasch, Deanna L.; Smith, Harriet T.; Wang, Sanyi; Song, Danying; Coen, Michael L.; Cloutier, Timothy E.; Tang, Hua; Cheng, Xueheng; Quinn, Christopher; Liu, Bo; Xin, Zhili; Liu, Gang; Fry, Elizabeth H.; Stoll, Vincent; Ng, Teresa I.; Banach, David; Marcotte, Doug; Burns, David J.; Calderwood, David J.; Hajduk, Philip J.

    2012-03-02

    Inhibition of protein kinases has validated therapeutic utility for cancer, with at least seven kinase inhibitor drugs on the market. Protein kinase inhibition also has significant potential for a variety of other diseases, including diabetes, pain, cognition, and chronic inflammatory and immunologic diseases. However, as the vast majority of current approaches to kinase inhibition target the highly conserved ATP-binding site, the use of kinase inhibitors in treating nononcology diseases may require great selectivity for the target kinase. As protein kinases are signal transducers that are involved in binding to a variety of other proteins, targeting alternative, less conserved sites on the protein may provide an avenue for greater selectivity. Here we report an affinity-based, high-throughput screening technique that allows nonbiased interrogation of small molecule libraries for binding to all exposed sites on a protein surface. This approach was used to screen both the c-Jun N-terminal protein kinase Jnk-1 (involved in insulin signaling) and p38{alpha} (involved in the formation of TNF{alpha} and other cytokines). In addition to canonical ATP-site ligands, compounds were identified that bind to novel allosteric sites. The nature, biological relevance, and mode of binding of these ligands were extensively characterized using two-dimensional {sup 1}H/{sup 13}C NMR spectroscopy, protein X-ray crystallography, surface plasmon resonance, and direct enzymatic activity and activation cascade assays. Jnk-1 and p38{alpha} both belong to the MAP kinase family, and the allosteric ligands for both targets bind similarly on a ledge of the protein surface exposed by the MAP insertion present in the CMGC family of protein kinases and distant from the active site. Medicinal chemistry studies resulted in an improved Jnk-1 ligand able to increase adiponectin secretion in human adipocytes and increase insulin-induced protein kinase PKB phosphorylation in human hepatocytes, in

  17. Molecular Study of the Effects of Chemical Processing on Heterogeneous Ice Nucleation: Role of Active Sites and Product Formation

    NASA Astrophysics Data System (ADS)

    Sihvonen, S.; Schill, G. P.; Murphy, K. A.; Mueller, K.; Tolbert, M. A.; Freedman, M. A.

    2014-12-01

    Mineral dust aerosol is the largest global source of ice nuclei, but the identity of the active sites for nucleation is unknown. During atmospheric transport, mineral dust aerosol can encounter and react with sulfuric acid, which affects the ice nucleation activity either due to changes to reactive surface sites or product formation. In this study, we reacted two types of clays found in mineral dust, kaolinite and montmorillonite, with sulfuric acid. Variation in the mineral due to acid treatment was separated from product formation through rinsing techniques. The samples were subsequently reacted with a probe molecule, (3,3,3-trifluoropropyl)dimethylchlorosilane, that selectively binds to edge hydroxyl groups that are bonded to a silicon atom with three bridging oxygens. Hydroxyl groups are considered potential active sites, because they can hydrogen bond with water and facilitate ice nucleation. Attachment to these sites was quantified by 19F magic angle spinning nuclear magnetic resonance (MAS NMR) of the 19F atoms on the probe molecule, which provided a direct correlation of the number of hydroxyl groups. Our results indicate that the number of edge-site hydroxyl groups increases with exposure to acid. Ice nucleation measurements indicate that the sulfuric acid-treated mineral is less ice active than the untreated mineral. Surprisingly, no difference between the nucleation activity of the untreated mineral and acid-treated, rinsed mineral is observed. As a result, we hypothesize that once a critical density of active sites is reached for ice nucleation, there is no further change in nucleation activity despite a continued increase in active sites. We additionally propose that the reduced activity of the acid-treated mineral is due to product formation that blocks active sites on the mineral, rather than changes to active sites.

  18. Final report: survey and removal of radioactive surface contamination at environmental restoration sites, Sandia National Laboratories/New Mexico. Volume 1

    SciTech Connect

    Lambert, K.A.; Mitchell, M.M.; Jean, D.; Byrd, C.S.

    1997-09-01

    This report describes the survey and removal of radioactive surface contamination at Sandia`s Environmental Restoration (ER) sites. Radiological characterization was performed as a prerequisite to beginning the Resource Conservation and Recovery Act (RCRA) corrective action process. The removal of radioactive surface contamination was performed in order to reduce potential impacts to human health and the environment. The predominant radiological contaminant of concern was depleted uranium (DU). Between October 1993 and November 1996 scanning surface radiation surveys, using gamma scintillometers, were conducted at 65 sites covering approximately 908 acres. A total of 9,518 radiation anomalies were detected at 38 sites. Cleanup activities were conducted between October 1994 and November 1996. A total of 9,122 anomalies were removed and 2,072 waste drums were generated. The majority of anomalies not removed were associated with a site that has subsurface contamination beyond the scope of this project. Verification soil samples (1,008 total samples) were collected from anomalies during cleanup activities and confirm that the soil concentration achieved in the field were far below the target cleanup level of 230 pCi/g of U-238 (the primary constituent of DU) in the soil. Cleanup was completed at 21 sites and no further radiological action is required. Seventeen sites were not completed since cleanup activities wee precluded by ongoing site activity or were beyond the original project scope.

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

    PubMed

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

    2015-01-01

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

  20. Active Site Loop Conformation Regulates Promiscuous Activity in a Lactonase from Geobacillus kaustophilus HTA426

    PubMed Central

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

    2015-01-01

    Enzyme promiscuity is a prerequisite for fast divergent evolution of biocatalysts. A phosphotriesterase-like lactonase (PLL) from Geobacillus kaustophilus HTA426 (GkaP) exhibits main lactonase and promiscuous phosphotriesterase activities. To understand its catalytic and evolutionary mechanisms, we investigated a “hot spot” in the active site by saturation mutagenesis as well as X-ray crystallographic analyses. We found that position 99 in the active site was involved in substrate discrimination. One mutant, Y99L, exhibited 11-fold improvement over wild-type in reactivity (kcat/Km) toward the phosphotriesterase substrate ethyl-paraoxon, but showed 15-fold decrease toward the lactonase substrate δ-decanolactone, resulting in a 157-fold inversion of the substrate specificity. Structural analysis of Y99L revealed that the mutation causes a ∼6.6 Å outward shift of adjacent loop 7, which may cause increased flexibility of the active site and facilitate accommodation and/or catalysis of organophosphate substrate. This study provides for the PLL family an example of how the evolutionary route from promiscuity to specificity can derive from very few mutations, which promotes alteration in the conformational adjustment of the active site loops, in turn draws the capacity of substrate binding and activity. PMID:25706379

  1. Extensive site-directed mutagenesis reveals interconnected functional units in the alkaline phosphatase active site.

    PubMed

    Sunden, Fanny; Peck, Ariana; Salzman, Julia; Ressl, Susanne; Herschlag, Daniel

    2015-01-01

    Enzymes enable life by accelerating reaction rates to biological timescales. Conventional studies have focused on identifying the residues that have a direct involvement in an enzymatic reaction, but these so-called 'catalytic residues' are embedded in extensive interaction networks. Although fundamental to our understanding of enzyme function, evolution, and engineering, the properties of these networks have yet to be quantitatively and systematically explored. We dissected an interaction network of five residues in the active site of Escherichia coli alkaline phosphatase. Analysis of the complex catalytic interdependence of specific residues identified three energetically independent but structurally interconnected functional units with distinct modes of cooperativity. From an evolutionary perspective, this network is orders of magnitude more probable to arise than a fully cooperative network. From a functional perspective, new catalytic insights emerge. Further, such comprehensive energetic characterization will be necessary to benchmark the algorithms required to rationally engineer highly efficient enzymes. PMID:25902402

  2. Extensive site-directed mutagenesis reveals interconnected functional units in the alkaline phosphatase active site.

    PubMed

    Sunden, Fanny; Peck, Ariana; Salzman, Julia; Ressl, Susanne; Herschlag, Daniel

    2015-01-01

    Enzymes enable life by accelerating reaction rates to biological timescales. Conventional studies have focused on identifying the residues that have a direct involvement in an enzymatic reaction, but these so-called 'catalytic residues' are embedded in extensive interaction networks. Although fundamental to our understanding of enzyme function, evolution, and engineering, the properties of these networks have yet to be quantitatively and systematically explored. We dissected an interaction network of five residues in the active site of Escherichia coli alkaline phosphatase. Analysis of the complex catalytic interdependence of specific residues identified three energetically independent but structurally interconnected functional units with distinct modes of cooperativity. From an evolutionary perspective, this network is orders of magnitude more probable to arise than a fully cooperative network. From a functional perspective, new catalytic insights emerge. Further, such comprehensive energetic characterization will be necessary to benchmark the algorithms required to rationally engineer highly efficient enzymes.

  3. Interaction of mining activities and aquatic environment: A review from Greek mine sites.

    NASA Astrophysics Data System (ADS)

    Vasileiou, Eleni; Kallioras, Andreas

    2016-04-01

    In Greece a significant amount of mineral and ore deposits have been recorded accompanied by large industrial interest and a long mining history. Today many active and/or abandoned mine sites are scattered within the country; while mining activities take place in different sites for exploiting various deposits (clay, limestone, slate, gypsum, kaolin, mixed sulphide ores (lead, zinc, olivine, pozzolan, quartz lignite, nickel, magnesite, aluminum, bauxite, gold, marbles etc). The most prominent recent ones are: (i) the lignite exploitation that is extended in the area of Ptolemais (Western Macedonia) and Megalopolis (Central Peloponnese); and (ii) the major bauxite deposits located in central Greece within the Parnassos-Ghiona geotectonic zone and on Euboea Island. In the latter area, significant ores of magnesite were exploited and mixed sulphide ores. Centuries of intensive mining exploitation and metallurgical treatment of lead-silver deposits in Greece, have also resulted in significant abandoned sites, such as the one in Lavrion. Mining activities in Lavrio, were initiated in ancient times and continued until the 1980s, resulting in the production of significant waste stockpiles deposited in the area, crucial for the local water resources. Ιn many mining sites, environmental pressures are also recorded after the mine closure to the aquatic environment, as the surface waters flow through waste dump areas and contaminated soils. This paper aims to the geospatial visualization of the mining activities in Greece, in connection to their negative (surface- and/or ground-water pollution; overpumping due to extensive dewatering practices) or positive (enhanced groundwater recharge; pit lakes, improvement of water budget in the catchment scale) impacts on local water resources.

  4. Importance of surface carbide formation on the activity and selectivity of Pd surfaces in the selective hydrogenation of acetylene

    NASA Astrophysics Data System (ADS)

    Yang, Bo; Burch, Robbie; Hardacre, Christopher; Hu, P.; Hughes, Philip

    2016-04-01

    A recent experimental investigation (Kim et al. J. Catal. 306 (2013) 146-154) on the selective hydrogenation of acetylene over Pd nanoparticles with different shapes concluded that Pd(100) showed higher activity and selectivity than Pd(111) for acetylene hydrogenation. However, our recent density functional calculations (Yang et al. J. Catal. 305 (2013) 264-276) observed that the clean Pd(111) surface should result in higher activity and ethylene selectivity compared with the clean Pd(100) surface for acetylene hydrogenation. In the current work, using density functional theory calculations, we find that Pd(100) in the carbide form gives rise to higher activity and selectivity than Pd(111) carbide. These results indicate that the catalyst surface is most likely in the carbide form under the experimental reaction conditions. Furthermore, the adsorption energies of hydrogen atoms as a function of the hydrogen coverage at the surface and subsurface sites over Pd(100) are compared with those over Pd(111), and it is found that the adsorption of hydrogen atoms is always less favoured on Pd(100) over the whole coverage range. This suggests that the Pd(100) hydride surface will be less stable than the Pd(111) hydride surface, which is also in accordance with the experimental results reported.

  5. Crystallographic Analysis of Active Site Contributions to Regiospecificity in the Diiron Enzyme Toluene 4-Monooxygenase

    SciTech Connect

    Bailey, Lucas J.; Acheson, Justin F.; McCoy, Jason G.; Elsen, Nathaniel L.; Phillips, Jr., George N.; Fox, Brian G.

    2014-10-02

    Crystal structures of toluene 4-monooxygenase hydroxylase in complex with reaction products and effector protein reveal active site interactions leading to regiospecificity. Complexes with phenolic products yield an asymmetric {mu}-phenoxo-bridged diiron center and a shift of diiron ligand E231 into a hydrogen bonding position with conserved T201. In contrast, complexes with inhibitors p-NH{sub 2}-benzoate and p-Br-benzoate showed a {mu}-1,1 coordination of carboxylate oxygen between the iron atoms and only a partial shift in the position of E231. Among active site residues, F176 trapped the aromatic ring of products against a surface of the active site cavity formed by G103, E104 and A107, while F196 positioned the aromatic ring against this surface via a {pi}-stacking interaction. The proximity of G103 and F176 to the para substituent of the substrate aromatic ring and the structure of G103L T4moHD suggest how changes in regiospecificity arise from mutations at G103. Although effector protein binding produced significant shifts in the positions of residues along the outer portion of the active site (T201, N202, and Q228) and in some iron ligands (E231 and E197), surprisingly minor shifts (<1 {angstrom}) were produced in F176, F196, and other interior residues of the active site. Likewise, products bound to the diiron center in either the presence or absence of effector protein did not significantly shift the position of the interior residues, suggesting that positioning of the cognate substrates will not be strongly influenced by effector protein binding. Thus, changes in product distributions in the absence of the effector protein are proposed to arise from differences in rates of chemical steps of the reaction relative to motion of substrates within the active site channel of the uncomplexed, less efficient enzyme, while structural changes in diiron ligand geometry associated with cycling between diferrous and diferric states are discussed for their potential

  6. APOLLO 10: Training for Lunar Surface Activities

    NASA Technical Reports Server (NTRS)

    1974-01-01

    Astronauts train on a mock-up lunar surface, practicing the procedures they will follow on the real thing, and adjusting to the demands of the workload. From the film documentary 'APOLLO 10: 'Green Light for a Lunar Landing''. Part of a documentary series made in the early 70's on the APOLLO missions, and narrated by Burgess Meredith. (Actual date created is not known at this time) APOLLO 10: Manned lunar orbital flight with Thomas P Stafford, John W. Young, and Eugene A. Cernan to test all aspects of an actual manned lunar landing except the landing. Mission Duration 192hrs 3mins 23 sec

  7. Ubiquitin vinyl methyl ester binding orients the misaligned active site of the ubiquitin hydrolase UCHL1 into productive conformation

    SciTech Connect

    Boudreaux, David A.; Maiti, Tushar K.; Davies, Christopher W.; Das, Chittaranjan

    2010-07-06

    Ubiquitin carboxy-terminal hydrolase L1 (UCHL1) is a Parkinson disease-associated, putative cysteine protease found abundantly and selectively expressed in neurons. The crystal structure of apo UCHL1 showed that the active-site residues are not aligned in a canonical form, with the nucleophilic cysteine being 7.7 {angstrom} from the general base histidine, an arrangement consistent with an inactive form of the enzyme. Here we report the crystal structures of the wild type and two Parkinson disease-associated variants of the enzyme, S18Y and I93M, bound to a ubiquitin-based suicide substrate, ubiquitin vinyl methyl ester. These structures reveal that ubiquitin vinyl methyl ester binds primarily at two sites on the enzyme, with its carboxy terminus at the active site and with its amino-terminal {beta}-hairpin at the distal site - a surface-exposed hydrophobic crevice 17 {angstrom} away from the active site. Binding at the distal site initiates a cascade of side-chain movements in the enzyme that starts at a highly conserved, surface-exposed phenylalanine and is relayed to the active site resulting in the reorientation and proximal placement of the general base within 4 {angstrom} of the catalytic cysteine, an arrangement found in productive cysteine proteases. Mutation of the distal-site, surface-exposed phenylalanine to alanine reduces ubiquitin binding and severely impairs the catalytic activity of the enzyme. These results suggest that the activity of UCHL1 may be regulated by its own substrate.

  8. Preferential site occupancy of krypton atoms on free argon-cluster surfaces.

    PubMed

    Lundwall, M; Lindblad, A; Bergersen, H; Rander, T; Ohrwall, G; Tchaplyguine, M; Svensson, S; Björneholm, O

    2006-07-01

    Argon clusters have been doped with krypton atoms in a pick-up setup and investigated by means of ultraviolet and x-ray photoelectron spectroscopy (UPS and XPS). The width of the krypton surface feature in the XPS spectra from mixed krypton/argon clusters has been studied and found to be narrower than in the case of homogeneous krypton clusters. By considering known spectral broadening mechanisms of the cluster features and the electron binding energy shift of the cluster surface feature relative to the atomic signal, we conclude that krypton ad-atoms preferentially occupy high-coordination surface sites on the argon host-cluster.

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

    PubMed

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

    2016-09-12

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

  10. May 2011 Groundwater and Surface Water Sampling at the Rio Blanco, Colorado, Site (Data Validation Package)

    SciTech Connect

    2011-12-01

    Annual sampling was conducted at the Rio Blanco, Colorado, site for the Long-Term Hydrologic Monitoring Program May 16-17, 2011, to monitor groundwater and surface water for potential radionuclide contamination. Sampling and analyses were conducted as specified in Sampling and Analysis Plan for the U.S. Department of Energy Office of Legacy Management Sites (LMS/PRO/S04351, continually updated). A duplicate sample was collected from location Johnson Artesian WL. Samples were analyzed by the U.S. Environmental Protection Agency (EPA) Radiation&Indoor Environments National Laboratory in Las Vegas, Nevada. Samples were analyzed for gamma-emitting radionuclides by high-resolution gamma spectrometry, and for tritium using the conventional method. Tritium was not measured using the enrichment method because the EPA laboratory no longer offers that service. Results of this monitoring at the Rio Blanco site demonstrate that groundwater and surface water outside the boundaries have not been affected by project-related contaminants.

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

    PubMed

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

    2015-08-01

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

  12. New developments for the site-specific attachment of protein to surfaces

    SciTech Connect

    Camarero, J A

    2005-05-12

    Protein immobilization on surfaces is of great importance in numerous applications in biology and biophysics. The key for the success of all these applications relies on the immobilization technique employed to attach the protein to the corresponding surface. Protein immobilization can be based on covalent or noncovalent interaction of the molecule with the surface. Noncovalent interactions include hydrophobic interactions, hydrogen bonding, van der Waals forces, electrostatic forces, or physical adsorption. However, since these interactions are weak, the molecules can get denatured or dislodged, thus causing loss of signal. They also result in random attachment of the protein to the surface. Site-specific covalent attachment of proteins onto surfaces, on the other hand, leads to molecules being arranged in a definite, orderly fashion and uses spacers and linkers to help minimize steric hindrances between the protein surface. This work reviews in detail some of the methods most commonly used as well as the latest developments for the site-specific covalent attachment of protein to solid surfaces.

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

  14. Post-Shot Surface Damage Detected with LIDAR at the Source Physics Experiment Site (Invited)

    NASA Astrophysics Data System (ADS)

    Schultz-Fellenz, E. S.; Sussman, A. J.; Kelley, R. E.; Cooper, D. I.

    2013-12-01

    Designed to improve long-range treaty monitoring capabilities, the Source Physics Experiment series is being conducted at a location in Nevada and provides an opportunity to advance near-field monitoring and field-based investigations of suspected underground test locations. In particular, features associated with underground testing can be evaluated using Source Physics Experiment activities as analogs, linking on-site inspections with remote sensing technologies. Following a calibration shot (SPE 1), SPE 2 (10/2011) and SPE 3 (07/2012) were performed in the same emplacement hole with 1.0 ton of explosives at 150 ft depth. A fourth shot (SPE 4) is planned for August 2013 as a 220 lb (100 kg) TNT equivalent shot at a depth of 315 ft (96 m). Because one of the goals of the Source Physics Experiments is to determine damage effects on seismic wave propagation and improve modeling capabilities, a key component in the predictive component and ultimate validation of the models is a full understanding of the intervening geology between the source and instrumented bore holes. Ground-based LIDAR and fracture mapping, mechanical properties determined via laboratory testing of rock core, discontinuity analysis and optical microscopy of the core rocks were performed prior to and following each experiment. Results of the LIDAR collects from both SPE 2 and 3 indicate a permanent ground displacement of up to several centimeters aligning along the projected surface traces of two faults observed in the core and fractures mapped at the surface. Work by Los Alamos National Laboratory was sponsored by the National Nuclear Security Administration Award No. DE-AC52-06NA25946.

  15. Radiological impact of surface water and sediment near uranium mining sites.

    PubMed

    Ivanova, K; Stojanovska, Z; Badulin, V; Kunovska, B; Yovcheva, M

    2015-12-01

    The aim of this study is to assess the radiological impact of surface water and sediment around uranium mining sites 20 years after their closing. The areas under observations are 31 former classical underground uranium mining and exploratory sites in Bulgaria, named as objects. The extraction and processing of uranium ores in the Republic of Bulgaria were ended in 1992. To assess the radiological impact of radionuclides field expeditions were performed to sample water and bottom sediment. The migration of uranium through surface water was examined as one of the major pathways for contamination spread. The range of uranium concentration in water flowing from the mining sites was from 0.012 to 6.8 mgU l(-1) with a geometric mean of 0.192 mgU l(-1). The uranium concentrations in water downstream the mining sites were approximately 3 times higher than the background value (upstream). The concentrations of Unat, (226)Ra, (210)Pb, and (232)Th in the sediment of downstream river were higher than those upstream by 3.4, 2.6, 2, and 1.7 times, respectively. The distribution coefficient of uranium reflects its high mobility in most of the sites. In order to evaluate the impact on people as well as site prioritization for more detailed assessment and water management, screening dose assessments were done.

  16. Radiological impact of surface water and sediment near uranium mining sites.

    PubMed

    Ivanova, K; Stojanovska, Z; Badulin, V; Kunovska, B; Yovcheva, M

    2015-12-01

    The aim of this study is to assess the radiological impact of surface water and sediment around uranium mining sites 20 years after their closing. The areas under observations are 31 former classical underground uranium mining and exploratory sites in Bulgaria, named as objects. The extraction and processing of uranium ores in the Republic of Bulgaria were ended in 1992. To assess the radiological impact of radionuclides field expeditions were performed to sample water and bottom sediment. The migration of uranium through surface water was examined as one of the major pathways for contamination spread. The range of uranium concentration in water flowing from the mining sites was from 0.012 to 6.8 mgU l(-1) with a geometric mean of 0.192 mgU l(-1). The uranium concentrations in water downstream the mining sites were approximately 3 times higher than the background value (upstream). The concentrations of Unat, (226)Ra, (210)Pb, and (232)Th in the sediment of downstream river were higher than those upstream by 3.4, 2.6, 2, and 1.7 times, respectively. The distribution coefficient of uranium reflects its high mobility in most of the sites. In order to evaluate the impact on people as well as site prioritization for more detailed assessment and water management, screening dose assessments were done. PMID:26505204

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

    PubMed

    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

  18. Zymogen Activation and Subcellular Activity of Subtilisin Kexin Isozyme 1/Site 1 Protease*

    PubMed Central

    da Palma, Joel Ramos; Burri, Dominique Julien; Oppliger, Joël; Salamina, Marco; Cendron, Laura; de Laureto, Patrizia Polverino; Seidah, Nabil Georges; Kunz, Stefan; Pasquato, Antonella

    2014-01-01

    The proprotein convertase subtilisin kexin isozyme 1 (SKI-1)/site 1 protease (S1P) plays crucial roles in cellular homeostatic functions and is hijacked by pathogenic viruses for the processing of their envelope glycoproteins. Zymogen activation of SKI-1/S1P involves sequential autocatalytic processing of its N-terminal prodomain at sites B′/B followed by the herein newly identified C′/C sites. We found that SKI-1/S1P autoprocessing results in intermediates whose catalytic domain remains associated with prodomain fragments of different lengths. In contrast to other zymogen proprotein convertases, all incompletely matured intermediates of SKI-1/S1P showed full catalytic activity toward cellular substrates, whereas optimal cleavage of viral glycoproteins depended on B′/B processing. Incompletely matured forms of SKI-1/S1P further process cellular and viral substrates in distinct subcellular compartments. Using a cell-based sensor for SKI-1/S1P activity, we found that 9 amino acid residues at the cleavage site (P1–P8) and P1′ are necessary and sufficient to define the subcellular location of processing and to determine to what extent processing of a substrate depends on SKI-1/S1P maturation. In sum, our study reveals novel and unexpected features of SKI-1/S1P zymogen activation and subcellular specificity of activity toward cellular and pathogen-derived substrates. PMID:25378398

  19. [Ultrastructural investigations on anionic surface sites of Brucella canis (author's transl)].

    PubMed

    Weber, A; Schiefer, H G; Krauss, H

    1977-11-01

    Anionic sites on the surface of Brucella canis were visualized in the electron microscope by staining with positively charged ferric oxide hydrosols in acetic acid (AI-reagent), or propanoic acid (PI-reagent), and with a polycationic ferritin derivative. With the AI-reagent, single or small aggregates of ferric oxide particles were bound to the cell surface of Br. canis, whereas, with the lipophilic PI-reagent, the microorganisms were heavily stained with focal aggregates of iron granules. The polycationic ferritin label was uniformly distributed over the entire cell surface of Br. canis. The ferritin label was not bound on the surface of the organisms after prior treatment with trichloroacetic acid or methanolic hydrochloric acid. Treatment with aqueous acetone, chloroform/methanol, diethyl ether, sodium deoxycholate, pronase, lysozyme, hyaluronidase, and sodium periodate neither influenced the morphology of the Brucella nor diminished their ionic binding sites. Our results indicate that the anionic sites on the cell surface of Br. canis may be carboxyl and phosphate groups of lipopolysaccharides.

  20. Preliminary Correlation Map of Geomorphic Surfaces in North-Central Frenchman Flat, Nevada Test Site

    SciTech Connect

    Bechtel Nevada

    2005-08-01

    This correlation map (scale = 1:12,000) presents the results of a mapping initiative that was part of the comprehensive site characterization required to operate the Area 5 Radioactive Waste Management Site, a low-level radioactive waste disposal facility located in northern Frenchman Flat at the Nevada Test Site. Eight primary map units are recognized for Quaternary surfaces: remnants of six alluvial fan or terrace surfaces, one unit that includes colluvial aprons associated with hill slopes, and one unit for anthropogenically disturbed surfaces. This surficial geology map provides fundamental data on natural processes for reconstruction of the Quaternary history of northern Frenchman Flat, which in turn will aid in the understanding of the natural processes that act to develop the landscape, and the time-frames involved in landscape development. The mapping was conducted using color and color-infrared aerial photographs and field verification of map unit composition and boundaries. Criteria for defining the map unit composition of geomorphic surface units are based on relative geomorphic position, landform morphology, and degree of preservation of surface morphology. The bedrock units identified on this map were derived from previous published mapping efforts and are included for completeness.

  1. Site-specific immobilization of protein layers on gold surfaces via orthogonal sortases.

    PubMed

    Raeeszadeh-Sarmazdeh, Maryam; Parthasarathy, Ranganath; Boder, Eric T

    2015-04-01

    We report a site-specific, sortase-mediated ligation to immobilize proteins layer-by-layer on a gold surface. Recombinant fluorescent proteins with a Sortase A recognition tag at the C-terminus were immobilized on peptide-modified gold surfaces. We used two sortases with different substrate specificities (Streptococcus pyogenes Sortase A and Staphylococcus aureus Sortase A) to immobilize layers of GFP and mCherry site-specifically on the gold surface. Surfaces were characterized using fluorescence and atomic force microscopy after immobilizing each layer of protein. Fluorescent micrographs showed that both protein immobilization on the modified gold surface and protein oligomerization are sortase-dependent. AFM images showed that either homogenous protein monolayers or layers of protein oligomers can be generated using appropriately tagged substrate proteins. Using Sortase A variants with orthogonal peptide substrate specificities, site-specific immobilization of appropriately tagged GFP onto a layer of immobilized mCherry was achieved without disruption of the underlying protein layer.

  2. Orthogonal electrode catheter array for mapping of endocardial focal site of ventricular activation

    SciTech Connect

    Desai, J.M.; Nyo, H.; Vera, Z.; Seibert, J.A.; Vogelsang, P.J. )

    1991-04-01

    Precise location of the endocardial site of origin of ventricular tachycardia may facilitate surgical and catheter ablation of this arrhythmia. The endocardial catheter mapping technique can locate the site of ventricular tachycardia within 4-8 cm2 of the earliest site recorded by the catheter. This report describes an orthogonal electrode catheter array (OECA) for mapping and radiofrequency ablation (RFA) of endocardial focal site of origin of a plunge electrode paced model of ventricular activation in dogs. The OECA is an 8 F five pole catheter with four peripheral electrodes and one central electrode (total surface area 0.8 cm{sup 2}). In eight mongrel dogs, mapping was performed by arbitrarily dividing the left ventricle (LV) into four segments. Each segment was mapped with OECA to find the earliest segment. Bipolar and unipolar electrograms were obtained. The plunge electrode (not visible on fluoroscopy) site was identified by the earliest wave front arrival times of -30 msec or earlier at two or more electrodes (unipolar electrograms) with reference to the earliest recorded surface ECG (I, AVF, and V1). Validation of the proximity of the five electrodes of the OECA to the plunge electrode was performed by digital radiography and RFA. Pathological examination was performed to document the proximity of the OECA to the plunge electrode and also for the width, depth, and microscopic changes of the ablation. To find the segment with the earliest LV activation a total of 10 {plus minus} 3 (mean {plus minus} SD) positions were mapped. Mean arrival times at the two earlier electrodes were -39 {plus minus} 4 msec and -35 {plus minus} 3 msec. Digital radiography showed the plunge electrode to be within the area covered by all five electrodes in all eight dogs. The plunge electrode was within 1 cm2 area of the region of RFA in all eight dogs.

  3. Clear-sky shortwave radiative closure for the Cabauw Baseline Surface Radiation Network site, the Netherlands

    NASA Astrophysics Data System (ADS)

    Wang, P.; Knap, W. H.; Kuipers Munneke, P.; Stammes, P.

    2009-04-01

    During the last two decades, several attempts have been made to achieve agreement between clear-sky shortwave broadband irradiance models and surface measurements of direct and diffuse irradiance. In general, models and measurements agreed well for the direct component but closing the gap for diffuse irradiances remained problematic. The number of studies reporting a satisfactory degree of closure for both direct and diffuse irradiance is still limited, which motivated us to perform the study presented here. In this paper a clear-sky shortwave closure analysis is presented for the Baseline Surface Radiation Network (BSRN) site of Cabauw, the Netherlands (51.97 °N, 4.93 °E). The analysis is based on an exceptional period of fine weather in the first half of May 2008 during the Intensive Measurement Period At the Cabauw Tower (IMPACT), an activity of the European Integrated project on Aerosol Cloud Climate and Air Quality Interactions (EUCAARI). Although IMPACT produced a wealth of data, it was decided to conduct the closure analysis using routine measurements only, provided by BSRN and the Aerosol Robotic Network (AERONET), completed with radiosonde obervations. The rationale for this pragmatic approach is the possibility of applying the method presented here to other periods and (BSRN) sites, where routine measurements are readily available, without having to deal with the investments and restrictions of an intensive observation period. The analysis is based on a selection of 72 comparisons on 6 days between BSRN measurements and Doubling Adding KNMI (DAK) model simulations of direct, diffuse, and global irradiance. The data span a wide range of aerosol properties, water vapour columns, and solar zenith angles. The model input consisted of operational Aerosol Robotic Network (AERONET) aerosol products and radiosonde data. On the basis of these data excellent closure was obtained: the mean differences between model and measurements are 2 W/m2 (+0.2%) for direct

  4. Chloride in ground water and surface water in the vicinity of selected surface-water sampling sites of the beneficial use monitoring program of Oklahoma, 2003

    USGS Publications Warehouse

    Mashburn, Shana L.; Sughru, Michael P.

    2004-01-01

    The Oklahoma Water Resources Board Beneficial Use Monitoring Program reported exceedances of beneficial-use standards for chloride at 11 surface-water sampling sites from January to October 2002. The U.S. Geological Survey, in cooperation with the Oklahoma Department of Environmental Quality, conducted a study to determine the chloride concentrations in ground water in the vicinity of Beneficial Use Monitoring Program surface-water sampling sites not meeting beneficial use standards for chloride and compare chloride concentrations in ground water and surface water. The chloride-impaired Beneficial Use Monitoring Program surface-water sampling sites are located in the western and southern regions of Oklahoma. The ground-water sampling sites were placed in proximity to the 11 surface-water sampling sites designated impaired by chloride by the Oklahoma Water Resources Board. Two surface-water sampling sites were located on the Beaver River (headwaters of the North Canadian River), three sites on the Cimarron River, one site on Sandy Creek, one site on North Fork Red River, and four sites on the Red River. Six ground-water samples were collected, when possible, from two test holes located upstream from each of the 11 Beneficial Use Monitoring Program surface-water sampling sites. One test hole was placed on the left bank and right bank, when possible, of each Beneficial Use Monitoring Program surfacewater sampling site. All test holes were located on alluvial deposits adjacent to the Beneficial Use Monitoring Program surface-water sampling sites within 0.5 mile of the stream. Top, middle, and bottom ground-water samples were collected from the alluvium at each test hole, when possible. Water properties of specific conductance, pH, water temperature, and dissolved oxygen were recorded in the field before sampling for chloride. The ground-water median chloride concentrations at 8 of the 11 Beneficial Use Monitoring Program sites were less than the surface-water median

  5. Surfaces of Fluorinated Pyridinium Block Copolymers with Enhanced Antibacterial Activity

    SciTech Connect

    Krishnan,S.; Ward, R.; Hexemer, A.; Sohn, K.; Lee, K.; Angert, E.; Fischer, D.; Kramer, E.; Ober, C.

    2006-01-01

    Polystyrene-b-poly(4-vinylpyridine) copolymers were quaternized with 1-bromohexane and 6-perfluorooctyl-1-bromohexane. Surfaces prepared from these polymers were characterized by contact angle measurements, near-edge X-ray absorption fine structure spectroscopy and X-ray photoelectron spectroscopy. The fluorinated pyridinium surfaces showed enhanced antibacterial activity compared to their nonfluorinated counterparts. Even a polymer with a relatively low molecular weight pyridinium block showed high antimicrobial activity. The bactericidal effect was found to be related to the molecular composition and organization in the top 2-3 nm of the surface and increased with increasing hydrophilicity and pyridinium concentration of the surface.

  6. Surface diffusion activation energy determination using ion beam microtexturing

    NASA Technical Reports Server (NTRS)

    Rossnagel, S. M.; Robinson, R. S.

    1982-01-01

    The activation energy for impurity atom (adatom) surface diffusion can be determined from the temperature dependence of the spacing of sputter cones. These cones are formed on the surface during sputtering while simultaneously adding impurities. The impurities form clusters by means of surface diffusion, and these clusters in turn initiate cone formation. Values are given for the surface diffusion activation energies for various materials on polycrystalline Cu, Al, Pb, Au, and Ni. The values for different impurity species on each of these substrates are approximately independent of impurity species within the experimental uncertainty, suggesting the absence of strong chemical bonding effects on the diffusion.

  7. Pollution distribution of heavy metals in surface soil at an informal electronic-waste recycling site.

    PubMed

    Fujimori, Takashi; Takigami, Hidetaka

    2014-02-01

    We studied distribution of heavy metals [lead (Pb), copper (Cu) and zinc (Zn)] in surface soil at an electronic-waste (e-waste) recycling workshop near Metro Manila in the Philippines to evaluate the pollution size (spot size, small area or the entire workshop), as well as to assess heavy metal transport into the surrounding soil environment. On-site length-of-stride-scale (~70 cm) measurements were performed at each surface soil point using field-portable X-ray fluorescence (FP-XRF). The surface soil at the e-waste recycling workshop was polluted with Cu, Zn and Pb, which were distributed discretely in surface soil. The site was divided into five areas based on the distance from an entrance gate (y-axis) of the e-waste recycling workshop. The three heavy metals showed similar concentration gradients in the y-axis direction. Zn, Pb and Cu concentrations were estimated to decrease to half of their maximum concentrations at ~3, 7 and 7 m from the pollution spot, respectively, inside the informal e-waste recycling workshop. Distance from an entrance may play an important role in heavy metal transport at the soil surface. Using on-site FP-XRF, we evaluated the metal ratio to characterise pollution features of the solid surface. Variability analysis of heavy metals revealed vanishing surficial autocorrelation over metre ranges. Also, the possibility of concentration prediction at unmeasured points using geostatistical kriging was evaluated, and heavy metals had a relative "small" pollution scales and remained inside the original workshop compared with toxic organohalogen compounds. Thus, exposure to heavy metals may directly influence the health of e-waste workers at the original site rather than the surrounding habitat and environmental media. PMID:23645478

  8. Pollution distribution of heavy metals in surface soil at an informal electronic-waste recycling site.

    PubMed

    Fujimori, Takashi; Takigami, Hidetaka

    2014-02-01

    We studied distribution of heavy metals [lead (Pb), copper (Cu) and zinc (Zn)] in surface soil at an electronic-waste (e-waste) recycling workshop near Metro Manila in the Philippines to evaluate the pollution size (spot size, small area or the entire workshop), as well as to assess heavy metal transport into the surrounding soil environment. On-site length-of-stride-scale (~70 cm) measurements were performed at each surface soil point using field-portable X-ray fluorescence (FP-XRF). The surface soil at the e-waste recycling workshop was polluted with Cu, Zn and Pb, which were distributed discretely in surface soil. The site was divided into five areas based on the distance from an entrance gate (y-axis) of the e-waste recycling workshop. The three heavy metals showed similar concentration gradients in the y-axis direction. Zn, Pb and Cu concentrations were estimated to decrease to half of their maximum concentrations at ~3, 7 and 7 m from the pollution spot, respectively, inside the informal e-waste recycling workshop. Distance from an entrance may play an important role in heavy metal transport at the soil surface. Using on-site FP-XRF, we evaluated the metal ratio to characterise pollution features of the solid surface. Variability analysis of heavy metals revealed vanishing surficial autocorrelation over metre ranges. Also, the possibility of concentration prediction at unmeasured points using geostatistical kriging was evaluated, and heavy metals had a relative "small" pollution scales and remained inside the original workshop compared with toxic organohalogen compounds. Thus, exposure to heavy metals may directly influence the health of e-waste workers at the original site rather than the surrounding habitat and environmental media.

  9. Adsorption sites on icosahedral quasicrystal surfaces: Dark stars and white flowers

    SciTech Connect

    Unal, B.; Jenks, C.J.; Thiel, P.A.

    2009-01-12

    From other work, two preferred sites have been suggested for metals and semimetals adsorbed on the fivefold surfaces of icosahedral, Al-based quasicrystals. Because of their appearance in scanning tunneling microscopy (STM) images, these sites are known as dark stars and white flowers. In this paper, we analyze four bulk structural models in physical space to determine the types, chemical decorations, and densities of the dark star - and, to a lesser extent, the white flower - adsorption sites for the fivefold planes of icosahedral Al-Pd-Mn. We find that the chemical decorations of these sites are heterogeneous, even within a single model. Both features are also structurally heterogeneous, according to STM measurements, and the structural variation is consistent with the bulk structure models. Finally, from the models, the density of dark stars in the planes correlates with the step height. This may explain previous experimental observations of different properties for different terraces.

  10. Estimations of the extent of migration of surficially applied water for various surface conditions near the potential repository perimeter; Yucca Mountain Site Characterization Project

    SciTech Connect

    Sobolik, S.R.; Fewell, M.E.

    1993-12-01

    The Yucca Mountain Site Characterization Project is studying Yucca Mountain in southwestern Nevada as a potential site for a high-level nuclear waste repository. Site characterization includes surface-based and underground testing. Analyses have been performed to support the design of site characterization activities so to have minimal impact on the ability of the site to isolate waste, and on tests performed as part of the characterization process. Two examples of site characterization activities are the construction of an Exploratory Studies Facility, which may include underground shafts, drifts, and ramps, and surface-based testing activities, which may require borehole drilling, excavation of test pits, and road watering for dust control. The information in this report pertains to two-dimensional numerical calculations modeling the movement of surficially applied water and the potential effects of that water on repository performance and underground experiments. This document contains information that has been used in preparing recommendations for two Yucca Mountain Site Characterization Project documents: Appendix I of the Exploratory Studies Facility Design Requirements document, and the Surface-Based Testing Field Requirements Document.

  11. Site-specific PEGylation of lidamycin and its antitumor activity.

    PubMed

    Li, Liang; Shang, Boyang; Hu, Lei; Shao, Rongguang; Zhen, Yongsu

    2015-05-01

    In this study, N-terminal site-specific mono-PEGylation of the recombinant lidamycin apoprotein (rLDP) of lidamycin (LDM) was prepared using a polyethyleneglycol (PEG) derivative (M w 20 kDa) through a reactive terminal aldehyde group under weak acidic conditions (pH 5.5). The biochemical properties of mPEG-rLDP-AE, an enediyne-integrated conjugate, were analyzed by SDS-PAGE, RP-HPLC, SEC-HPLC and MALDI-TOF. Meanwhile, in vitro and in vivo antitumor activity of mPEG-rLDP-AE was evaluated by MTT assays and in xenograft model. The results indicated that mPEG-rLDP-AE showed significant antitumor activity both in vitro and in vivo. After PEGylation, mPEG-rLDP still retained the binding capability to the enediyne AE and presented the physicochemical characteristics similar to that of native LDP. It is of interest that the PEGylation did not diminish the antitumor efficacy of LDM, implying the possibility that this derivative may function as a payload to deliver novel tumor-targeted drugs. PMID:26579455

  12. Urban Climate Station Site Selection Through Combined Digital Surface Model and Sun Angle Calculations

    NASA Technical Reports Server (NTRS)

    Kidd, Chris; Chapman, Lee

    2012-01-01

    Meteorological measurements within urban areas are becoming increasingly important due to the accentuating effects of climate change upon the Urban Heat Island (UHI). However, ensuring that such measurements are representative of the local area is often difficult due to the diversity of the urban environment. The evaluation of sites is important for both new sites and for the relocation of established sites to ensure that long term changes in the meteorological and climatological conditions continue to be faithfully recorded. Site selection is traditionally carried out in the field using both local knowledge and visual inspection. This paper exploits and assesses the use of lidar-derived digital surface models (DSMs) to quantitatively aid the site selection process. This is acheived by combining the DSM with a solar model, first to generate spatial maps of sky view factors and sun-hour potential and second, to generate site-specific views of the horizon. The results show that such a technique is a useful first-step approach to identify key sites that may be further evaluated for the location of meteorological stations within urban areas.

  13. Site study plan for Exploratory shaft facilities design foundation boreholes (shaft surface facility foundation borings), Deaf Smith County Site, Texas: Surface-based geotechnical field program: Preliminary draft

    SciTech Connect

    Not Available

    1987-12-01

    This site study plan describes the Exploratory Shaft Facilities (ESF) Design Foundation Boreholes field activities to be conducted during early stages of Site Characterization at the Deaf Smith County, Texas, site. The field program has been designed to provide data useful in addressing information/data needs resulting from federal/state/local regulations, and repository program requirements. Approximately 50 foundation boreholes will be drilled within the ESP location to provide data necessary for design of the ESF and to satisfy applicable shaft permitting requirements. Soils and subsurface rock will be sampled as the foundation boreholes are advanced. Soil samples or rock core will be taken through the Blackwater Draw and Ogallala Formations and the Dockum Group. Hydrologic testing will be performed in boreholes that penetrates the water table. In-situ elastic properties will be determined from both the soil strata and rock units along the length of the boreholes. Field methods/tests are chosen that provide the best or only means of obtaining the required data. The Salt Repository Project (SRP) Networks specify the schedule under which the program will operate. Drilling will not begin until after site ground water baseline conditions have been established. The Technical Field Services Contractor is responsible for conducting the field program of drilling and testing. Samples and data will be handled and reported in accordance with established SRP procedures. A quality assurance program will be utilized to assure that activities affecting quality are performed correctly and that the appropriate documentation is maintained. 25 refs., 10 figs., 6 tabs.

  14. Influence of Clouds On The Surface Radiative Balance For Two Mediterranean Sites

    NASA Astrophysics Data System (ADS)

    Bortoli, D.; Costa, M. J.; Nardino, M.

    Clouds strongly affect the Earth's climate influencing the surface radiative balance by reducing the incident solar radiation and increasing the downward longwave flux. Al- though the quantitative impact of clouds on the surface radiative balance is necessarily associated with great uncertainties due to the complexity and variation of the under- lying parameters, cloud radiative forcing is one of the main regulating factors of the Earth's climate. The present work aims at determining the effect of cloud coverage on the surface radiative balance, in order to contribute for a better understanding of local variations in the Mediterranean climate. Measurements of the cloud cover index (CCI) require the presence of an observer capable of quantifying cloud amounts in the sky in sight above the measurements' site. Since such measurements are not always available the cloud cover index is re- trieved using two different methodologies. On one hand the CCI is computed from the surface radiometer measurements throughout a parameterisation. On the other it is retrieved using a bi-spectral algorithm based on the METEOSAT satellite measure- ments from the visible and infrared spectral regions. Results of the CCI are compared with co-located observations to perform a general check against the available "ground truth". At the same time the CCI values obtained from both methodologies are inter- compared. Results of the CCI and their implications on the surface radiative balance are presented for the two Mediterranean sites selected, one located in Italy and the other in the south of Portugal. The cloud radiative forcing calculations show a cooling effect of the surface in presence of clouds for both sites. Moreover, a seasonal dependence is obtained, with a stronger cooling effect during summer. Acknowledgements: The work was supported by Instituto de Cooperação Científica e Tecnológica Internacional (ICCTI) - Portugal and Consiglio Nazionale delle Ricerche (CNR) - Italy

  15. Surface complexation modeling of uranyl adsorption on corrensite from the Waste Isolation Pilot Plant Site

    SciTech Connect

    Park, Sang-Won; Leckie, J.O.; Siegel, M.D.

    1995-09-01

    Corrensite is the dominant clay mineral in the Culebra Dolomite at the Waste Isolation Pilot Plant. The surface characteristics of corrensite, a mixed chlorite/smectite clay mineral, have been studied. Zeta potential measurements and titration experiments suggest that the corrensite surface contains a mixture of permanent charge sites on the basal plane and SiOH and AlOH sites with a net pH-dependent charge at the edge of the clay platelets. Triple-layer model parameters were determined by the double extrapolation technique for use in chemical speciation calculations of adsorption reactions using the computer program HYDRAQL. Batch adsorption studies showed that corrensite is an effective adsorbent for uranyl. The pH-dependent adsorption behavior indicates that adsorption occurs at the edge sites. Adsorption studies were also conducted in the presence of competing cations and complexing ligands. The cations did not affect uranyl adsorption in the range studied. This observation lends support to the hypothesis that uranyl adsorption occurs at the edge sites. Uranyl adsorption was significantly hindered by carbonate. It is proposed that the formation of carbonate uranyl complexes inhibits uranyl adsorption and that only the carbonate-free species adsorb to the corrensite surface. The presence of the organic complexing agents EDTA and oxine also inhibits uranyl sorption.

  16. Alignment of Surface-Atmosphere Exchange Sensors at Sloped Sites: An Integrated Strategy

    NASA Astrophysics Data System (ADS)

    Metzger, S.; Ayres, E.; Clement, R.; Durden, D.; Foken, T.; Kowalski, A. S.; Luo, H.; McCaughey, J. H.; Durden, N. P.; Serrano-Ortiz, P.; Sun, J.

    2015-12-01

    Closure of the energy balance on the earth's surface is regarded as an indicator that the measurements of radiative, turbulent, diffusive and storage fluxes fulfill fundamental methodological assumptions. However, for sloped measurement sites the different terms contributing to the energy balance are not aligned along the axes of a single reference coordinate system. Consequently, a measurement and data processing strategy is needed that enables consistently quantifying each contributing term. The National Ecological Observatory Network (NEON) is currently deploying surface-atmosphere exchange sensors at several dozen measurement sites, 50% of which are located on slopes up to 20 degrees. To enable unbiased observations across sites, the incident angle between a flux and its measurement should be minimized, and instrument limitations and spatial representativeness need to be considered. Here, we present a strategy that combines site-adaptive instrument alignment with real-time attitude tracking and a set of trigonometric, radiative and source area conversions. This allows obeying the physical limitations underlying radiation, turbulence, profile and soil heat flux sensors, while providing observations in a consistent frame of reference. The strategy is evaluated against initial findings from the first months of surface-atmosphere exchange sensor deployments at NEON.

  17. Saline Snow Surfaces and Arctic Bromine Activation

    NASA Astrophysics Data System (ADS)

    Pratt, K. A.; Custard, K. D.; Shepson, P.; Douglas, T. A.; Pöhler, D.; General, S.; Zielcke, J.; Platt, U.; Carlsen, M. S.; Tanner, D.; Huey, L. G.; Stirm, B.

    2012-12-01

    Following polar sunrise, tropospheric ozone levels often decrease rapidly to near zero, concurrent with mercury depletion and deposition. Despite our increasing understanding of the spatial variability of BrO and possible mechanisms based on laboratory studies, important questions remain regarding the most efficient sources of and mechanisms for Arctic halogen activation, leading to tropospheric ozone depletion. Rapid sea ice decline in the Arctic is expected to influence halogen activation and corresponding ozone and mercury depletion events. Therefore, an improved understanding of halogen activation is necessary to predict future changes in atmospheric chemical composition. During the March-April 2012 BRomine, Ozone, and Mercury EXperiment (BROMEX) in Barrow, Alaska, outdoor chamber experiments with snow and ice samples were conducted. Ozone was added as the precursor oxidant, and the samples were investigated with and without ambient sunlight. Samples included first-year sea ice, brine icicles, several layers of snow above first-year sea ice, and seasonal snow above the tundra. Chemical ionization mass spectrometry was utilized to monitor Br2 production, and ion chromatography was utilized to measure the bromide, chloride, nitrate, and sulfate content of the melted snow/ice samples. Surprisingly, tundra snow and drifting snow above sea ice produced the most Br2, with no production resulting from sea ice and basal snow directly above sea ice, suggesting more efficient production from samples characterized by greater acidity and lower chloride/bromide ratios. In addition, Br2 was only observed in the presence of sunlight, indicating the role of snowpack photolysis and the hydroxyl radical in its production. The observed trends in Br2 production may also help explain observations of inland hotspots in measured BrO by aircraft-based nadir MAX-DOAS (Multi Axis-Differential Optical Absorption Spectroscopy) measurements, conducted during the same field campaign. The

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

    PubMed

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

    2015-02-24

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

  19. Geologic surface effects of underground nuclear testing, Yucca Flat, Nevada Test Site, Nevada

    SciTech Connect

    Grasso, D.N.

    2000-05-31

    This report presents a new Geographic Information System composite map of the geologic surface effects caused by underground nuclear testing in the Yucca Flat Physiographic Area of the Nevada Test Site, Nye County, Nevada. The Nevada Test Site (NTS) was established in 1951 as a continental location for testing nuclear devices (Allen and others, 1997, p.3). Originally known as the ''Nevada Proving Ground'', the NTS hosted a total of 928 nuclear detonations, of which 828 were conducted underground (U.S. Department of Energy, 1994). Three principal testing areas of the NTS were used: (1) Yucca Flat, (2) Pahute Mesa, and (3) Rainier Mesa including Aqueduct Mesa. Underground detonations at Yucca Flat and Pahute Mesa were typically emplaced in vertical drill holes, while others were tunnel emplacements. Of the three testing areas, Yucca Flat was the most extensively used, hosting 658 underground tests (747 detonations) located at 719 individual sites (Allen and others, 1997, p.3-4). Figure 1 shows the location of Yucca Flat and other testing areas of the NTS. Figure 2 shows the locations of underground nuclear detonation sites at Yucca Flat. Table 1 lists the number of underground nuclear detonations conducted, the number of borehole sites utilized, and the number of detonations mapped for surface effects at Yucca Flat by NTS Operational Area.

  20. Optimization of Sample Site Selection Imaging for OSIRIS-REx Using Asteroid Surface Analog Images

    NASA Astrophysics Data System (ADS)

    Tanquary, Hannah E.; Sahr, Eric; Habib, Namrah; Hawley, Christopher; Weber, Nathan; Boynton, William V.; Kinney-Spano, Ellyne; Lauretta, Dante

    2014-11-01

    OSIRIS-REx will return a sample of regolith from the surface of asteroid 101955 Bennu. The mission will obtain high resolution images of the asteroid in order to create detailed maps which will satisfy multiple mission objectives. To select a site, we must (i) identify hazards to the spacecraft and (ii) characterize a number of candidate sites to determine the optimal location for sampling. To further characterize the site, a long-term science campaign will be undertaken to constrain the geologic properties. To satisfy these objectives, the distribution and size of blocks at the sample site and backup sample site must be determined. This will be accomplished through the creation of rock size frequency distribution maps. The primary goal of this study is to optimize the creation of these map products by assessing techniques for counting blocks on small bodies, and assessing the methods of analysis of the resulting data. We have produced a series of simulated surfaces of Bennu which have been imaged, and the images processed to simulate Polycam images during the Reconnaissance phase. These surface analog images allow us to explore a wide range of imaging conditions, both ideal and non-ideal. The images have been “degraded”, and are displayed as thumbnails representing the limits of Polycam resolution from an altitude of 225 meters. Specifically, this study addresses the mission requirement that the rock size frequency distribution of regolith grains < 2cm in longest dimension must be determined for the sample sites during Reconnaissance. To address this requirement, we focus on the range of available lighting angles. Varying illumination and phase angles in the simulated images, we can compare the size-frequency distributions calculated from the degraded images with the known size frequency distributions of the Bennu simulant material, and thus determine the optimum lighting conditions for satisfying the 2 cm requirement.

  1. Surface and downhole shear wave seismic methods for thick soil site investigations

    USGS Publications Warehouse

    Hunter, J.A.; Benjumea, B.; Harris, J.B.; Miller, R.D.; Pullan, S.E.; Burns, R.A.; Good, R.L.

    2002-01-01

    Shear wave velocity-depth information is required for predicting the ground motion response to earthquakes in areas where significant soil cover exists over firm bedrock. Rather than estimating this critical parameter, it can be reliably measured using a suite of surface (non-invasive) and downhole (invasive) seismic methods. Shear wave velocities from surface measurements can be obtained using SH refraction techniques. Array lengths as large as 1000 m and depth of penetration to 250 m have been achieved in some areas. High resolution shear wave reflection techniques utilizing the common midpoint method can delineate the overburden-bedrock surface as well as reflecting boundaries within the overburden. Reflection data can also be used to obtain direct estimates of fundamental site periods from shear wave reflections without the requirement of measuring average shear wave velocity and total thickness of unconsolidated overburden above the bedrock surface. Accurate measurements of vertical shear wave velocities can be obtained using a seismic cone penetrometer in soft sediments, or with a well-locked geophone array in a borehole. Examples from thick soil sites in Canada demonstrate the type of shear wave velocity information that can be obtained with these geophysical techniques, and show how these data can be used to provide a first look at predicted ground motion response for thick soil sites. ?? 2002 Published by Elsevier Science Ltd.

  2. Chemosynthetic microbial activity at Mid-Atlantic Ridge hydrothermal vent sites

    NASA Astrophysics Data System (ADS)

    Wirsen, Carl O.; Jannasch, Holger W.; Molyneaux, Stephen J.

    1993-06-01

    Chemosynthetic production of microbial biomass, determined by 14CO2 fixation and enzymatic (RuBisCo) activity, at the Mid-Atlantic Ridge (MAR) 23° and 26°N vent sites was found in various niches: warm water emissions, loosely rock-attached flocculent material, dense morphologically diverse bacterial mats covering the surfaces of polymetal sulfide deposits, and filamentous microbes on the carapaces of shrimp (Rimicaris exoculata). The bacterial mats on polymetal sulfide surfaces contained unicellular and filamentous bacteria which appeared to use as their chemolithotrophic electron or energy source either dissolved reduced minerals from vent emissions, mainly sulfur compounds, or solid metal sulfide deposits, mainly pyrite. Moderately thermophilic Chemosynthetic activity was observed in carbon dioxide fixation experiments and in enrichments, but no thermophilic aerobic sulfur oxidizers could be isolated. Both obligate and facultative chemoautotrophs growing at mesophilic temperatures were isolated from all chemosynthetically active surface scrapings. The obligate autotrophs could oxidize sterilized MAR natural sulfide deposits as well as technical pyrite at near neutral pH, in addition to dissolved reduced sulfur compounds. While the grazing by shrimp on the surface mats of MAR metal sulfide deposits was observed and deemed important, the animals' primary occurrence in dense swarms near vent emissions suggests that they were feeding at these sites, where conditions for Chemosynthetic growth of their filamentous microbial epiflora were optimal. The data show that the transformation of geothermal energy at the massive polymetal sulfide deposits of the MAR is based on the lithoautotrophic oxidation of soluble sulfides and pyrites into microbial biomass.

  3. Evaluation of Cavity Collapse and Surface Crater Formation at the Norbo Underground Nuclear Test in U8c, Nevada Nuclear Security Site, and the Impact on Stability of the Ground Surface

    SciTech Connect

    Pawloski, G A

    2012-06-18

    Lawrence Livermore National Laboratory (LLNL) Containment Program performed a review of nuclear test-related data for the Norbo underground nuclear test in U8c to assist in evaluating this legacy site as a test bed for application technologies for use in On-Site Inspections (OSI) under the Comprehensive Nuclear Test Ban Treaty. This request is similar to one made for the Salut site in U8c (Pawloski, 2012b). Review of the Norbo site is complicated because the test first exhibited subsurface collapse, which was not unusual, but it then collapsed to the surface over one year later, which was unusual. Of particular interest is the stability of the ground surface above the Norbo detonation point. Proposed methods for on-site verification include radiological signatures, artifacts from nuclear testing activities, and imaging to identify alteration to the subsurface hydrogeology due to the nuclear detonation. Aviva Sussman from the Los Alamos National Laboratory (LANL) has also proposed work at this site. Both proposals require physical access at or near the ground surface of specific underground nuclear test locations at the Nevada Nuclear Security Site (NNSS), formerly the Nevada Test Site (NTS), and focus on possible activities such as visual observation, multispectral measurements, and shallow and deep geophysical surveys.

  4. Formation of metal nanoclusters on specific surface sites of protein molecules.

    PubMed

    Braun, Nathalie; Meining, Winfried; Hars, Ulrike; Fischer, Markus; Ladenstein, Rudolf; Huber, Robert; Bacher, Adelbert; Weinkauf, Sevil; Bachmann, Luis

    2002-08-01

    During vacuum condensation of metals on frozen proteins, nanoclusters are preferentially formed at specific surface sites (decoration). Understanding the nature of metal/protein interaction is of interest for structure analysis and is also important in the fields of biocompatibility and sensor development. Studies on the interaction between metal and distinct areas on the protein which enhance or impede the probability for cluster formation require information on the structural details of the protein's surface underlying the metal clusters. On three enzyme complexes, lumazine synthase from Bacillus subtilis, proteasome from Thermoplasma acidophilum and GTP cyclohydrolase I from Escherichia coli, the decoration sites as determined by electron microscopy (EM) were correlated with their atomic surface structures as obtained by X-ray crystallography. In all three cases, decoration of the same protein results in different cluster distributions for gold and silver. Gold decorates surface areas consisting of polar but uncharged residues and with rough relief whereas silver clusters are preferentially formed on top of protein pores outlined by charged and hydrophilic residues and filled with frozen buffer under the experimental conditions. A common quality of both metals is that they strictly avoid condensation on hydrophobic sites lacking polar and charged residues. The results open ways to analyse the binding mechanism of nanoclusters to small specific sites on the surface of hydrated biomacromolecules by non-microscopic, physical-chemical methods. Understanding the mechanism may lead to advanced decoration techniques resulting in fewer background clusters. This would improve the analysis of single molecules with regard to their symmetries and their orientation in the adsorbed state and in precrystalline assemblies as well as facilitate the detection of point defects in crystals caused by misorientation or by impurities. PMID:12144790

  5. May 2013 Groundwater and Surface Water Sampling at the Rio Blanco, Colorado, Site (Data Validation Package)

    SciTech Connect

    2013-10-01

    Annual sampling was conducted at the Rio Blanco, Colorado, site for the Long-Term Hydrologic Monitoring Program May 14-16, 2013, to monitor groundwater and surface water for potential radionuclide contamination. Sampling and analyses were conducted as specified in Sampling and Analysis Plan for the U.S. Department of Energy Office of Legacy Management Sites (LMS/PRO/S04351, continually updated). A duplicate sample was collected from location CER #1 Black Sulphur. Samples were analyzed for gamma-emitting radionuclides by high-resolution gamma spectrometry and for tritium using the conventional and enrichment methods.

  6. Fluoride Adsorption on Goethite in Relation to Different Types of Surface Sites.

    PubMed

    Hiemstra; Van Riemsdijk WH

    2000-05-01

    Metal (hydr)oxides have different types of surface groups. Fluoride ions have been used as a probe to assess the number of surface sites. We have studied the F(-) adsorption on goethite by measuring the F(-) and H(+) interaction and F(-) adsorption isotherms. Fluoride ions exchange against singly coordinated surface hydroxyls at low F(-) concentrations. At higher concentrations also the doubly coordinated OH groups are involved. The replacement of a surface OH(-) by F(-) suggests that all F charge (-1) is located at the surface in contrast to oxyanions which have a charge distribution in the interface due to the binding structure in which the anion only partially coordinates with the surface. Analysis of our F(-) data with the CD-MUSIC approach shows that the formation of the fluoride surface complex is accompanied by a redistribution of charge. This is supposed to be due to a net switch in the H bonding as a result of the change of the type of surface complex from donating (FeOH, FeOH(2)) to proton accepting (FeF). The modeled redistribution of charge is approximately equivalent with the change of a donating H bond into an accepting H bond. At high F(-) concentrations precipitation of F(-), as for instance FeF(3)(s), may occur. The rate of formation is catalyzed by the presence of high electrolyte concentrations. Copyright 2000 Academic Press. PMID:10767149

  7. The abandoned surface mining sites in the Czech Republic: mapping and creating a database with a GIS web application

    NASA Astrophysics Data System (ADS)

    Pokorný, Richard; Tereza Peterková, Marie

    2016-05-01

    Based on the vectorization of the 55-volume book series the Quarry Inventories of the Czechoslovak Republic/Czechoslovak Socialist Republic, published in the years 1932-1961, a new comprehensive database was built comprising 9958 surface mining sites of raw materials, which were active in the first half of the 20th century. The mapped area covers 40.9 % of the territory of the Czech Republic. For the purposes of visualization, a map application, the Quarry Inventories Online, was created that enables the data visualization.

  8. Decomposition degree of chlorofluorocarbon (CFC) and CFC replacements during recovery with surface-modified activated carbon

    SciTech Connect

    Tanada, Seiki; Kawasaki, Naohito; Nakamura, Takeo; Abe, Ikuo

    1996-02-10

    The recovery efficiency of 1,1,2-trichloro-1,2,2-trifluoroethane (CFC113) and three CFC replacements (1,1-dichloro-1-fluoroethane, HCFC141b; 1,3-dichloro-1,1,2,2,3-pentafluoro-propane, HCFC225cb; and 2,2,3,3,3-pentafluoro-1-propanol, 5FP) were investigated on the basis of their degree of decomposition and adsorption isotherms. The authors prepared activated carbons with various surface polarities to elucidate the recovery efficiency, the amount adsorbed, and the degree of decomposition. The amount of CFC113 adsorbed onto untreated activated carbon was the largest of all. That of HCFC225cb adsorbed onto activated carbon treated with hydrogen gas was larger than that adsorbed onto untreated activated carbon and activated carbon treated with 6 N nitric acid. The amount of 5FP and HCFC141b adsorbed on the various activated carbons was not substantial. The degree of decomposition of CFC replacements using the untreated activated carbon except for HCFC225cb was the largest of all. In the case without the activated carbon, that of CFC and the CFC replacements increased in the order 5FP, CFC113 or HCFC225cb, and HCFC141b. It is concluded that the recovery of CFC replacements was possible using the surface-modified activated carbons rather than the untreated activated carbon. The degree of decomposition of the CFC replacements during recovery using the activated carbon depends on the relationship between the adsorption site of the surface of the activated carbon and the polarity, hydrophilic site, or hydrophobic site of the CFC replacement molecule.

  9. Characterization of surface active materials derived from farm products

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Surface active materials obtained by chemical modification of plant protein isolates (lupin, barley, oat), corn starches (dextrin, normal, high amylose, and waxy) and soybean oil (soybean oil based polysoaps, SOPS) were investigated for their surface and interfacial properties using axisymmetric dro...

  10. Surface-active properties of humic and sulfochlorohumic acids

    SciTech Connect

    Ryabova, I.N.; Mustafina, G.A.; Akkulova, Z.G.; Satymbaeva, A.S.

    2009-10-15

    The surface tension of alkaline solutions of humic acids and their sulfochloroderivatives, which are synthesized by sulfonation of chlorohumic acids isolated from coal chlorinated by the electrochemical method, is investigated. It is established that humic compounds possess weak surface activity. Basic adsorption parameters are calculated.

  11. Soil surface disturbances in cold deserts: Effects on nitrogenase activity in cyanobacterial-lichen soil crusts

    USGS Publications Warehouse

    Belnap, Jayne

    1996-01-01

    CyanobacteriaMichen soil crusts can be a dominant source of nitrogen for cold-desert ecosystems. Effects of surface disturbance from footprints, bike and vehicle tracks on the nitrogenase activity in these crusts was investigated. Surface disturbances reduced nitrogenase activity by 30-100%. Crusts dominated by the cyanobacterium Microcoleus vaginatus on sandy soils were the most susceptible to disruption; crusts on gypsiferous soils were the least susceptible. Crusts where the soil lichen Collema tenax was present showed less immediate effects; however, nitrogenase activity still declined over time. Levels of nitrogenase activity reduction were affected by the degree of soil disruption and whether sites were dominated by cyanobacteria with or without heterocysts. Consequently, anthropogenic surface disturbances may have serious implications for nitrogen budgets in these ecosystems.

  12. Surface modification of active material structures in battery electrodes

    DOEpatents

    Erickson, Michael; Tikhonov, Konstantin

    2016-02-02

    Provided herein are methods of processing electrode active material structures for use in electrochemical cells or, more specifically, methods of forming surface layers on these structures. The structures are combined with a liquid to form a mixture. The mixture includes a surface reagent that chemically reacts and forms a surface layer covalently bound to the structures. The surface reagent may be a part of the initial liquid or added to the mixture after the liquid is combined with the structures. In some embodiments, the mixture may be processed to form a powder containing the structures with the surface layer thereon. Alternatively, the mixture may be deposited onto a current collecting substrate and dried to form an electrode layer. Furthermore, the liquid may be an electrolyte containing the surface reagent and a salt. The liquid soaks the previously arranged electrodes in order to contact the structures with the surface reagent.

  13. Analysis of multi-temporal landsat satellite images for monitoring land surface temperature of municipal solid waste disposal sites.

    PubMed

    Yan, Wai Yeung; Mahendrarajah, Prathees; Shaker, Ahmed; Faisal, Kamil; Luong, Robin; Al-Ahmad, Mohamed

    2014-12-01

    This studypresents a remote sensing application of using time series Landsat satellite images for monitoring the Trail Road and Nepean municipal solid waste (MSW) disposal sites in Ottawa, Ontario, Canada. Currently, the Trail Road landfill is in operation; however, during the 1960s and 1980s, the city relied heavily on the Nepean landfill. More than 400 Landsat satellite images were acquired from the US Geological Survey (USGS) data archive between 1984 and 2011. Atmospheric correction was conducted on the Landsat images in order to derive the landfill sites' land surface temperature (LST). The findings unveil that the average LST of the landfill was always higher than the immediate surrounding vegetation and air temperature by 4 to 10 °C and 5 to 11.5 °C, respectively. During the summer, higher differences of LST between the landfill and its immediate surrounding vegetation were apparent, while minima were mostly found in fall. Furthermore, there was no significant temperature difference between the Nepean landfill (closed) and the Trail Road landfill (active) from 1984 to 2007. Nevertheless, the LST of the Trail Road landfill was much higher than the Nepean by 15 to 20 °C after 2007. This is mainly due to the construction and dumping activities (which were found to be active within the past few years) associated with the expansion of the Trail Road landfill. The study demonstrates that the use of the Landsat data archive can provide additional and viable information for the aid of MSW disposal site monitoring.

  14. Combined Active and Passive Seismic Methods To Characterize Strongmotion Sites in Washington and Oregon, United States

    NASA Astrophysics Data System (ADS)

    Pileggi, D.; Cakir, R.; Lunedei, E.; Albarello, D.; Walsh, T. J.

    2011-12-01

    Knowledge of the shear-wave velocity profile at strongmotion station sites is important for calibrating accelerograms in terms of local site effects. Surface-wave seismic prospecting methods (both in active and passive configurations) provide an effective tool for an inexpensive and deep penetrating seismic characterization of subsoil. We used a combination of active (Multi-channel Analysis of Surface Waves, MASW) and passive (Extended Spectral AutoCorrelation, ESAC) array techniques along with the single-station ambient vibration measurements (Horizontal-to-Vertical Spectral Ratios - HVSR) to characterize strong-motion sites in Washington and Oregon. The MASW analysis was used to better constrain the shallowest part of the Vs profile, while effective dispersion curve provided by ESAC and HVSR data allow us to extend the survey downwards (up to hundred meters of depth). The combined use of these data in the frame of global-search inversion algorithms (Genetic Algorithms) allows us to manage the extreme non-linearity of the inverse problem and mitigate problems associated with the non-uniqueness of the solution. A strict synergy between geologic surveys, boreholes (when the latter was available) and seismic surveys allows a further reduction of relevant uncertainties. Preliminary results show that; i) this combined methodology is a practical, inexpensive, and fast way to characterize multiple strong motion sites; ii) local geology and/or borehole information was combined to better constrain the inversion and to reduce the uncertainty in velocity profiles; and, iii) this combined methodology gives additional information of shear-wave velocities at greater depths.

  15. Relating subsurface temperature changes to microbial activity at a crude oil-contaminated site.

    PubMed

    Warren, Ean; Bekins, Barbara A

    2015-11-01

    Crude oil at a spill site near Bemidji, Minnesota has been undergoing aerobic and anaerobic biodegradation for over 30 years, creating a 150-200 m plume of primary and secondary contaminants. Microbial degradation generates heat that should be measurable under the right conditions. To measure this heat, thermistors were installed in wells in the saturated zone and in water-filled monitoring tubes in the unsaturated zone. In the saturated zone, a thermal groundwater plume originates near the residual oil body with temperatures ranging from 2.9°C above background near the oil to 1.2°C down gradient. Temperatures in the unsaturated zone above the oil body were up to 2.7°C more than background temperatures. Previous work at this site has shown that methane produced from biodegradation of the oil migrates upward and is oxidized in a methanotrophic zone midway between the water table and the surface. Enthalpy calculations and observations demonstrate that the temperature increases primarily result from aerobic methane oxidation in the unsaturated zone above the oil. Methane oxidation rates at the site independently estimated from surface CO2 efflux data are comparable to rates estimated from the observed temperature increases. The results indicate that temperature may be useful as a low-cost measure of activity but care is required to account for the correct heat-generating reactions, other heat sources and the effects of focused recharge.

  16. Relating subsurface temperature changes to microbial activity at a crude oil-contaminated site.

    PubMed

    Warren, Ean; Bekins, Barbara A

    2015-11-01

    Crude oil at a spill site near Bemidji, Minnesota has been undergoing aerobic and anaerobic biodegradation for over 30 years, creating a 150-200 m plume of primary and secondary contaminants. Microbial degradation generates heat that should be measurable under the right conditions. To measure this heat, thermistors were installed in wells in the saturated zone and in water-filled monitoring tubes in the unsaturated zone. In the saturated zone, a thermal groundwater plume originates near the residual oil body with temperatures ranging from 2.9°C above background near the oil to 1.2°C down gradient. Temperatures in the unsaturated zone above the oil body were up to 2.7°C more than background temperatures. Previous work at this site has shown that methane produced from biodegradation of the oil migrates upward and is oxidized in a methanotrophic zone midway between the water table and the surface. Enthalpy calculations and observations demonstrate that the temperature increases primarily result from aerobic methane oxidation in the unsaturated zone above the oil. Methane oxidation rates at the site independently estimated from surface CO2 efflux data are comparable to rates estimated from the observed temperature increases. The results indicate that temperature may be useful as a low-cost measure of activity but care is required to account for the correct heat-generating reactions, other heat sources and the effects of focused recharge. PMID:26409188

  17. Relating subsurface temperature changes to microbial activity at a crude oil-contaminated site

    NASA Astrophysics Data System (ADS)

    Warren, Ean; Bekins, Barbara A.

    2015-11-01

    Crude oil at a spill site near Bemidji, Minnesota has been undergoing aerobic and anaerobic biodegradation for over 30 years, creating a 150-200 m plume of primary and secondary contaminants. Microbial degradation generates heat that should be measurable under the right conditions. To measure this heat, thermistors were installed in wells in the saturated zone and in water-filled monitoring tubes in the unsaturated zone. In the saturated zone, a thermal groundwater plume originates near the residual oil body with temperatures ranging from 2.9 °C above background near the oil to 1.2 °C down gradient. Temperatures in the unsaturated zone above the oil body were up to 2.7 °C more than background temperatures. Previous work at this site has shown that methane produced from biodegradation of the oil migrates upward and is oxidized in a methanotrophic zone midway between the water table and the surface. Enthalpy calculations and observations demonstrate that the temperature increases primarily result from aerobic methane oxidation in the unsaturated zone above the oil. Methane oxidation rates at the site independently estimated from surface CO2 efflux data are comparable to rates estimated from the observed temperature increases. The results indicate that temperature may be useful as a low-cost measure of activity but care is required to account for the correct heat-generating reactions, other heat sources and the effects of focused recharge.

  18. Relating subsurface temperature changes to microbial activity at a crude oil-contaminated site

    USGS Publications Warehouse

    Warren, Ean; Bekins, Barbara A.

    2015-01-01

    Crude oil at a spill site near Bemidji, Minnesota has been undergoing aerobic and anaerobic biodegradation for over 30 years, creating a 150–200 m plume of primary and secondary contaminants. Microbial degradation generates heat that should be measurable under the right conditions. To measure this heat, thermistors were installed in wells in the saturated zone and in water-filled monitoring tubes in the unsaturated zone. In the saturated zone, a thermal groundwater plume originates near the residual oil body with temperatures ranging from 2.9 °C above background near the oil to 1.2 °C down gradient. Temperatures in the unsaturated zone above the oil body were up to 2.7 °C more than background temperatures. Previous work at this site has shown that methane produced from biodegradation of the oil migrates upward and is oxidized in a methanotrophic zone midway between the water table and the surface. Enthalpy calculations and observations demonstrate that the temperature increases primarily result from aerobic methane oxidation in the unsaturated zone above the oil. Methane oxidation rates at the site independently estimated from surface CO2 efflux data are comparable to rates estimated from the observed temperature increases. The results indicate that temperature may be useful as a low-cost measure of activity but care is required to account for the correct heat-generating reactions, other heat sources and the effects of focused recharge.

  19. Analysis of Hydrogen Tunneling in an Enzyme Active Site using von Neumann Measurements

    PubMed Central

    Sumner, Isaiah; Iyengar, Srinivasan S.

    2010-01-01

    We build on our earlier quantum wavepacket study of hydrogen transfer in the biological enzyme, soybean lipoxygenase-1, by using von Neumann quantum measurement theory to gain qualitative insights into the transfer event. We treat the enzyme active site as a measurement device which acts on the tunneling hydrogen nucleus via the potential it exerts at each configuration. A series of changing active site geometries during the tunneling process effects a sequential projection of the initial, reactant state onto the final, product state. We study this process using several different kinds of von Neumann measurements and show how a discrete sequence of such measurements not only progressively increases the projection of the hydrogen nuclear wavepacket onto the product side but also favors proton over deuteron transfer. Several qualitative features of the hydrogen tunneling problem found in wavepacket dynamics studies are also recovered here. These include the shift in the “transition state” towards the reactant as a result of nuclear quantization, greater participation of excited states in the case of deuterium, and presence of critical points along the reaction coordinate that facilitate hydrogen and deuterium transfer and coincide with surface crossings. To further “tailor” the dynamics, we construct a perturbation to the sequence of measurements, that is a perturbation to the dynamical sequence of active site geometry evolution, which leads us to insight on the existence of sensitive regions of the reaction profile where subtle changes to the dynamics of the active site can have an effect on the hydrogen and deuterium transfer process. PMID:22933858

  20. Crystal structures of human tissue kallikrein 4: activity modulation by a specific zinc binding site.

    PubMed

    Debela, Mekdes; Magdolen, Viktor; Grimminger, Valerie; Sommerhoff, Christian; Messerschmidt, Albrecht; Huber, Robert; Friedrich, Rainer; Bode, Wolfram; Goettig, Peter

    2006-10-01

    Human tissue kallikrein 4 (hK4) belongs to a 15-member family of closely related serine proteinases. hK4 is predominantly expressed in prostate, activates hK3/PSA, and is up-regulated in prostate and ovarian cancer. We have identified active monomers of recombinant hK4 besides inactive oligomers in solution. hK4 crystallised in the presence of zinc, nickel, and cobalt ions in three crystal forms containing cyclic tetramers and octamers. These structures display a novel metal site between His25 and Glu77 that links the 70-80 loop with the N-terminal segment. Micromolar zinc as present in prostatic fluid inhibits the enzymatic activity of hK4 against fluorogenic substrates. In our measurements, wild-type hK4 exhibited a zinc inhibition constant (IC50) of 16 microM including a permanent residual activity, in contrast to the zinc-independent mutants H25A and E77A. Since the Ile16 N terminus of wild-type hK4 becomes more accessible for acetylating agents in the presence of zinc, we propose that zinc affects the hK4 active site via the salt-bridge formed between the N terminus and Asp194 required for a functional active site. hK4 possesses an unusual 99-loop that creates a groove-like acidic S2 subsite. These findings explain the observed specificity of hK4 for the P1 to P4 substrate residues. Moreover, hK4 shows a negatively charged surface patch, which may represent an exosite for prime-side substrate recognition. PMID:16950394

  1. Goethite surface reactivity: III. Unifying arsenate adsorption behavior through a variable crystal face - Site density model

    NASA Astrophysics Data System (ADS)

    Salazar-Camacho, Carlos; Villalobos, Mario

    2010-04-01

    We developed a model that describes quantitatively the arsenate adsorption behavior for any goethite preparation as a function of pH and ionic strength, by using one basic surface arsenate stoichiometry, with two affinity constants. The model combines a face distribution-crystallographic site density model for goethite with tenets of the Triple Layer and CD-MUSIC surface complexation models, and is self-consistent with its adsorption behavior towards protons, electrolytes, and other ions investigated previously. Five different systems of published arsenate adsorption data were used to calibrate the model spanning a wide range of chemical conditions, which included adsorption isotherms at different pH values, and adsorption pH-edges at different As(V) loadings, both at different ionic strengths and background electrolytes. Four additional goethite-arsenate systems reported with limited characterization and adsorption data were accurately described by the model developed. The adsorption reaction proposed is: lbond2 FeOH +lbond2 SOH +AsO43-+H→lbond2 FeOAsO3[2-]…SOH+HO where lbond2 SOH is an adjacent surface site to lbond2 FeOH; with log K = 21.6 ± 0.7 when lbond2 SOH is another lbond2 FeOH, and log K = 18.75 ± 0.9, when lbond2 SOH is lbond2 Fe 2OH. An additional small contribution of a protonated complex was required to describe data at low pH and very high arsenate loadings. The model considered goethites above 80 m 2/g as ideally composed of 70% face (1 0 1) and 30% face (0 0 1), resulting in a site density for lbond2 FeOH and for lbond2 Fe 3OH of 3.125/nm 2 each. Below 80 m 2/g surface capacity increases progressively with decreasing area, which was modeled by considering a progressively increasing proportion of faces (0 1 0)/(1 0 1), because face (0 1 0) shows a much higher site density of lbond2 FeOH groups. Computation of the specific proportion of faces, and thus of the site densities for the three types of crystallographic surface groups present in

  2. Characterization of the active site of chloroperoxidase using physical techniques

    SciTech Connect

    Hall, K.S.

    1986-01-01

    Chloroperoxidase (CPO) and Cytochrome P-450, two very different hemeproteins, have been shown to have similar active sites by several techniques. Recent work has demonstrated thiolate ligation from a cysteine residue to the iron in P-450. A major portion of this research has been devoted to obtaining direct evidence that CPO also has a thiolate 5th ligand from a cysteine residue. This information will provide the framework for a detailed analysis of the structure-function relationships between peroxidases, catalase and cytochrome P-450 hemeproteins. To determine whether the 5th ligand is a cysteine, methionine or a unique amino acid, specific isotope enrichment experiments were used. Preliminary /sup 1/H-NMR studies show that the carbon monoxide-CPO complex has a peak in the upfield region corresponding to alpha-protons of a thiolate amino acid. C. fumago was grown on 95% D/sub 2/O media with a small amount of /sup 1/H-cysteine added. Under these conditions C. fumago slows down the biosynthesis of cysteine by at least 50% and utilizes the exogenous cysteine in the media. GC-MS was able to show that the methylene protons next to the sulfur atom in cysteine are 80-90% protonated while these positions in methionine are approximately 73% deuterated. Comparison of the /sup 1/H-NMR spectra of CO-CPO and CO-CPO indicate the presence of a cysteine ligand in chloroperoxidase.

  3. N6-Methyldeoxyadenosine Marks Active Transcription Start Sites in Chlamydomonas

    PubMed Central

    Chen, Kai; Deng, Xin; Yu, Miao; Han, Dali; Hao, Ziyang; Liu, Jianzhao; Lu, Xingyu; Dore, Louis C; Weng, Xiaocheng; Ji, Quanjiang; Mets, Laurens; He, Chuan

    2015-01-01

    SUMMARY N6-methyldeoxyadenosine (6mA or m6A) is a DNA modification preserved in prokaryotes to eukaryotes. It is widespread in bacteria, and functions in DNA mismatch repair, chromosome segregation, and virulence regulation. In contrast, the distribution and function of 6mA in eukaryotes have been unclear. Here we present a comprehensive analysis of the 6mA landscape in the genome of Chlamydomonas using new sequencing approaches. We identified the 6mA modification in 84% of genes in Chlamydomonas. We found that 6mA mainly locates at ApT dinucleotides around transcription start sites (TSS) with a bimodal distribution, and appears to mark active genes. A periodic pattern of 6mA deposition was also observed at base resolution, which is associated with nucleosome distribution near the TSS, suggesting a possible role in nucleosome positioning. The new genome-wide mapping of 6mA and its unique distribution in the Chlamydomonas genome suggest potential regulatory roles of 6mA in gene expression in eukaryotic organisms. PMID:25936837

  4. Disturbance opens recruitment sites for bacterial colonization in activated sludge.

    PubMed

    Vuono, David C; Munakata-Marr, Junko; Spear, John R; Drewes, Jörg E

    2016-01-01

    Little is known about the role of immigration in shaping bacterial communities or the factors that may dictate success or failure of colonization by bacteria from regional species pools. To address these knowledge gaps, the influence of bacterial colonization into an ecosystem (activated sludge bioreactor) was measured through a disturbance gradient (successive decreases in the parameter solids retention time) relative to stable operational conditions. Through a DNA sequencing approach, we show that the most abundant bacteria within the immigrant community have a greater probability of colonizing the receiving ecosystem, but mostly as low abundance community members. Only during the disturbance do some of these bacterial populations significantly increase in abundance beyond background levels and in few cases become dominant community members post-disturbance. Two mechanisms facilitate the enhanced enrichment of immigrant populations during disturbance: (i) the availability of resources left unconsumed by established species and (ii) the increased availability of niche space for colonizers to establish and displace resident populations. Thus, as a disturbance decreases local diversity, recruitment sites become available to promote colonization. This work advances our understanding of microbial resource management and diversity maintenance in complex ecosystems. PMID:25727891

  5. Active Site Characterization of Proteases Sequences from Different Species of Aspergillus.

    PubMed

    Morya, V K; Yadav, Virendra K; Yadav, Sangeeta; Yadav, Dinesh

    2016-09-01

    A total of 129 proteases sequences comprising 43 serine proteases, 36 aspartic proteases, 24 cysteine protease, 21 metalloproteases, and 05 neutral proteases from different Aspergillus species were analyzed for the catalytically active site residues using MEROPS database and various bioinformatics tools. Different proteases have predominance of variable active site residues. In case of 24 cysteine proteases of Aspergilli, the predominant active site residues observed were Gln193, Cys199, His364, Asn384 while for 43 serine proteases, the active site residues namely Asp164, His193, Asn284, Ser349 and Asp325, His357, Asn454, Ser519 were frequently observed. The analysis of 21 metalloproteases of Aspergilli revealed Glu298 and Glu388, Tyr476 as predominant active site residues. In general, Aspergilli species-specific active site residues were observed for different types of protease sequences analyzed. The phylogenetic analysis of these 129 proteases sequences revealed 14 different clans representing different types of proteases with diverse active site residues.

  6. Enhancements in nocturnal surface ozone at urban sites in the UK.

    PubMed

    Kulkarni, Pavan S; Bortoli, D; Silva, A M; Reeves, C E

    2015-12-01

    Analysis of diurnal patterns of surface ozone (O3) at multiple urban sites in the UK shows the occurrence of prominent nocturnal enhancements during the winter months (November-March). Whilst nocturnal surface ozone (NSO) enhancement events have been observed at other locations, this is the first time that such features have been demonstrated to occur in the UK and the second location globally. The observed NSO enhancement events in the UK were found to be so prevalent that they are clearly discernible in monthly diurnal cycles averaged over several years of data. Long-term (2000-2010) analysis of hourly surface ozone data from 18 urban background stations shows a bimodal diurnal variation during the winter months with a secondary nighttime peak around 0300 hours along with the primary daytime peak. For all but one site, the daily maxima NSO concentrations during the winter months exceeded 60 μg/m(3) on >20 % of the nights. The highest NSO value recorded was 118 μg/m(3). During the months of November, December, and January, the monthly averaged O3 concentrations observed at night (0300 h) even exceeded those observed in the daytime (1300 h). The analysis also shows that these NSO enhancements can last for several hours and were regional in scale, extending across several stations simultaneously. Interestingly, the urban sites in the north of the UK exhibited higher NSO than the sites in the south of the UK, despite their daily maxima being similar. In part, this seems to be related to the sites in the north typically having lower concentrations of nitrogen oxides.

  7. Environmental assessment of ground water compliance activities at the Uranium Mill Tailings Site, Spook, Wyoming. Revision 0

    SciTech Connect

    1996-03-01

    This document is an environmental assessment of the Spook, Wyoming, Uranium Mill Tailings Remedial Action (UMTRA) Project site. It analyzes the impacts of the U.S. Department of Energy (DOE) proposed action for ground water compliance. The proposed action is to comply with the U.S. Environmental Protection Agency (EPA) standards for the UMTRA Project sites (40 CFR Part 192) by meeting supplemental standards based on the limited use ground water at the Spook site. This proposed action would not require site activities, including ground water monitoring, characterization, or institutional controls. Ground water in the uppermost aquifer was contaminated by uranium processing activities at the Spook site, which is in Converse County, approximately 48 miles (mi) (77 kilometers [km]) northeast of Casper, Wyoming. Constituents from the site infiltrated and migrated into the uppermost aquifer, forming a plume that extends approximately 2500 feet (ft) (800 meters [m]) downgradient from the site. The principal site-related hazardous constituents in this plume are uranium, selenium, and nitrate. Background ground water in the uppermost aquifer at the site is considered limited use. It is neither a current nor a potential source of drinking water because of widespread, ambient contamination that cannot be cleaned up using treatment methods reasonably employed in public water supply systems (40 CFR {section} 192.11 (e)). Background ground water quality also is poor due to first, naturally occurring conditions (natural uranium mineralization associated with an alteration front), and second, the effects of widespread human activity not related to uranium milling operations (uranium exploration and mining activities). There are no known exposure pathways to humans, animals, or plants from the contaminated ground water in the uppermost aquifer because it does not discharge to lower aquifers, to the surface, or to surface water.

  8. Surface geophysics and porewater evaluation at the Lower Darby Creek Area Superfund Site, Philadelphia, Pennsylvania, 2013

    USGS Publications Warehouse

    Walker, Charles W.; Degnan, James R.; Brayton, Michael J.; Cruz, Roberto M.; Lorah, Michelle M.

    2015-01-01

    In cooperation with the U.S. Environmental Protection Agency (EPA), Region 3, the U.S. Geological Survey (USGS) is participating in an ongoing study to aid in the identification of subsurface heterogeneities that may act as preferential pathways for contaminant transport in and around the Lower Darby Creek Area (LDCA) Superfund Site, Philadelphia Pa. Lower Darby Creek, which flows into the Delaware River, borders the western part of the former landfill site. In 2013, the USGS conducted surface geophysics measurements and stream porewater sampling to provide additional data for EPA’s site characterization. This report contains data collected from field measurements of direct current (DC) resistivity, frequency-domain electromagnetic (FDEM) surveys, and stream porewater specific conductance (SC).

  9. Hanford Site Environmental data for Calendar Year 1990. Surface and Columbia River

    SciTech Connect

    Bisping, L.E.; Woodruff, R.K.

    1992-01-01

    Environmental monitoring at the Hanford Site, located in southeastern Washington State, is conducted by Battelle Memorial Institute, Pacific Northwest Division, as part of its contract to operate the Pacific Northwest Laboratory (PNL) for the US Department of Energy. The data collected provide a historical record of radionuclide and radiation levels attributable to natural causes, worldwide fallout, and Hanford operations. Data are also collected to monitor several chemicals. Pacific Northwest Laboratory publishes an annual environmental report for the Hanford Site each calendar year. The Hanford Site Environmental Report for Calendar Year 1990 is a summary of offsite and onsite environmental monitoring data collected during 1990 by PNL`s Environmental Monitoring Program. The data summaries included in the annual report were created from individual surface and river monitoring results. This volume contains the individual results used to create those summaries. This volume also includes additional data summaries which do not appear in the annual report.

  10. Adsorption on heterogeneous surfaces: site energy distribution functions from Fritz-Schlüender isotherms.

    PubMed

    Kumar, Kannuchamy Vasanth; Monteiro de Castro, Mateus Carvalho; Martinez-Escandell, Manuel; Molina-Sabio, Miguel; Rodriguez-Reinoso, Francisco

    2010-08-23

    Different site energy distribution functions based on the condensation approximation method are proposed for the liquid-phase or gas-phase adsorption equilibrium data following the Fritz-Schlüender isotherm. Energy distribution functions for the four limiting cases of the Fritz-Schlüender isotherm are also discussed. The proposed models are successfully applied to the experimental equilibrium data of nitrogen molecules at 77 K on a pitch-based activated carbon (PA) and a pitch-based activated carbon containing boron (PBA). An energy distribution function based on FS isotherm containing five parameters suggest a unimodal distribution of binding sites for carbon PA, the binding site energies being distributed as exponential or unimodal, depending on the pressure, in the case of carbon PBA. The advantages of the proposed models are discussed.

  11. Surface-based test plan, Deaf Smith County, Texas Site: Draft

    SciTech Connect

    Not Available

    1985-05-08

    The Surface-Based Test Plan (SBTP) is the plan which accounts for all surface-based site field work to be conducted at the Permian salt site selected for characterization. The SBTP relates data needs from program requirement documents and presents plans to satisfy the data needs. The SBTP excludes plans for construction of the Exploratory Shaft Facility (ESF) and plans for the in situ testing. The SBTP is a hierarchical plan stemming from the Technical Program Plan. The SBTP describes in detail the process by which surface-based study plans are defined, developed, and controlled. The plans hierarchy extends downward thru subordinate Site Study Plans (SSPs), which describe in detail elements of field work to be done, to detailed Procedures which document the exact methodologies to be employed in the conduct of field work. The plan is a QA level S document, although some of its elements are at lower QA levels. The plan is a controlled document, and any proposed amendments to the plan or subordinate documents can only be implemented through the specified change control procedure.

  12. Activities affecting surface water resources: A general overview

    SciTech Connect

    Not Available

    1990-01-01

    In November 1987, P.E.I. signed a federal/provincial work-sharing arrangement on water resource management focusing on groundwater pollution, surface water degradation and estuarine eutrophication. The surface water program was designed to identify current surface water uses and users within 12 major watersheds across the Island containing 26 individual rivers, as well as problems arising due to practices that degrade the quality of surface water and restricts its value to other user groups. This report presents a general overview of the program, covering the general characteristics of the Island; operations in agriculture, fish and wildlife, forestry, recreation, fisheries, and industry; alterations of natural features of waterways; wetlands; additional watershed activities such as hydrometric stations and subdivision development; and activities affecting surface water resources such as sedimentation sources, pollution point sources and instream obstructions.

  13. Contaminants in surface water and sediments near the Tynagh silver mine site, County Galway, Ireland.

    PubMed

    O'Neill, A; Phillips, D H; Bowen, J; Sen Gupta, B

    2015-04-15

    A former silver mine in Tynagh, Co. Galway, Ireland is one of the most contaminated mine sites in Europe with maximum concentrations of Zn, As, Pb, Mn, Ni, Cu, and Cd far exceeding guideline values for water and sediment. The aims of this research were to 1) further assess the contamination, particularly metals, in surface water and sediment around the site, and 2) determine if the contamination has increased 10 years after the Environmental Protection Agency Ireland (EPAI) identified off-site contamination. Site pH is alkaline to neutral because CaCO3-rich sediment and rock material buffer the exposed acid generating sulphide-rich ore. When this study was compared to the previous EPAI study conducted 10 years earlier, it appeared that further weathering of exposed surface sediment had increased concentrations of As and other potentially toxic elements. Water samples from the tailings ponds and adjacent Barnacullia Stream had concentrations of Al, Cd, Mn, Zn and Pb above guideline values. Lead and Zn concentrations from the tailings pond sediment were 16 and 5 times higher, respectively, than concentrations reported 10 years earlier. Pb and Zn levels in most sediment samples exceeded the Expert Group (EGS) guidelines of 1000 and 5000 mg/kg, respectively. Arsenic concentrations were as high as 6238 mg/kg in the tailings ponds sediment, which is 62 and 862 times greater than the EGS and Canadian Soil Quality Guidelines (CSQG), respectively. Cadmium, Cu, Fe, Mn, Pb and Zn concentrations in water and sediment were above guideline values downstream of the site. Additionally, Fe, Mn and organic matter (OM) were strongly correlated and correlated to Zn, Pb, As, Cd, Cu and Ni in stream sediment. Therefore, the nearby Barnacullia Stream is also a significant pathway for contaminant transport to downstream areas. Further rehabilitation of the site may decrease the contamination around the area. PMID:25634731

  14. Identification of the prooxidant site of human ceruloplasmin: a model for oxidative damage by copper bound to protein surfaces

    NASA Technical Reports Server (NTRS)

    Mukhopadhyay, C. K.; Mazumder, B.; Lindley, P. F.; Fox, P. L.

    1997-01-01

    Free transition metal ions oxidize lipids and lipoproteins in vitro; however, recent evidence suggests that free metal ion-independent mechanisms are more likely in vivo. We have shown previously that human ceruloplasmin (Cp), a serum protein containing seven Cu atoms, induces low density lipoprotein oxidation in vitro and that the activity depends on the presence of a single, chelatable Cu atom. We here use biochemical and molecular approaches to determine the site responsible for Cp prooxidant activity. Experiments with the His-specific reagent diethylpyrocarbonate (DEPC) showed that one or more His residues was specifically required. Quantitative [14C]DEPC binding studies indicated the importance of a single His residue because only one was exposed upon removal of the prooxidant Cu. Plasmin digestion of [14C]DEPC-treated Cp (and N-terminal sequence analysis of the fragments) showed that the critical His was in a 17-kDa region containing four His residues in the second major sequence homology domain of Cp. A full length human Cp cDNA was modified by site-directed mutagenesis to give His-to-Ala substitutions at each of the four positions and was transfected into COS-7 cells, and low density lipoprotein oxidation was measured. The prooxidant site was localized to a region containing His426 because CpH426A almost completely lacked prooxidant activity whereas the other mutants expressed normal activity. These observations support the hypothesis that Cu bound at specific sites on protein surfaces can cause oxidative damage to macromolecules in their environment. Cp may serve as a model protein for understanding mechanisms of oxidant damage by copper-containing (or -binding) proteins such as Cu, Zn superoxide dismutase, and amyloid precursor protein.

  15. Surface elevation change artifact at the NEEM ice core drilling site, North Greenland.

    NASA Astrophysics Data System (ADS)

    Berg Larsen, Lars; Schøtt Hvidberg, Christine; Dahl-Jensen, Dorthe; Lilja Buchardt, Susanne

    2014-05-01

    The NEEM deep drilling site (77.45°N 51.06°W) is located at the main ice divide in North Greenland. For the ice core drilling project, a number of buildings was erected and left on the snow surface during the five-year project period. The structures created snowdrifts that formed accordingly to the predominant wind direction on the lee side on the buildings and the overwintering cargo. To get access to the buildings, the snowdrifts and the accumulated snow were removed and the surface in the camp was leveled with heavy machinery each summer. In the camp a GPS reference pole was placed as a part of the NEEM strain net, 12 poles placed in three diamonds at distances of 2,5 km, 7,5 km and 25 km they were all measured with high precision GPS every year. Around the reference pole, a 1 km x 1 km grid with a spacing of 100 m was measured with differential GPS each year. In this work, we present results from the GPS surface topography measurements in and around the campsite. The mapping of the topography in and around the campsite shows how the snowdrifts evolve and are the reason for the lift of the camp site area. The accumulated snowdrifts are compared to the dominant wind directions from year to year. The annual snow accumulation at the NEEM site is 0.60 m. The reference pole in the camp indicates an additional snow accumulation of 0.50 m per year caused by collected drifting snow. The surface topography mapping shows that this artificially elevated surface extends up to several kilometers out in the terrain. This could have possible implications on other glaciological and geophysical measurements in the area i.e. pit and snow accumulation studies.

  16. Surface properties of the Mars Science Laboratory candidate landing sites: characterization from orbit and predictions

    USGS Publications Warehouse

    Fergason, R.L.; Christensen, P.R.; Golombek, M.P.; Parker, T.J.

    2012-01-01

    This work describes the interpretation of THEMIS-derived thermal inertia data at the Eberswalde, Gale, Holden, and Mawrth Vallis Mars Science Laboratory (MSL) candidate landing sites and determines how thermophysical variations correspond to morphology and, when apparent, mineralogical diversity. At Eberswalde, the proportion of likely unconsolidated material relative to exposed bedrock or highly indurated surfaces controls the thermal inertia of a given region. At Gale, the majority of the landing site region has a moderate thermal inertia (250 to 410 J m-2 K-1 s-1/2), which is likely an indurated surface mixed with unconsolidated materials. The primary difference between higher and moderate thermal inertia surfaces may be due to the amount of mantling material present. Within the mound of stratified material in Gale, layers are distinguished in the thermal inertia data; the MSL rover could be traversing through materials that are both thermophysically and compositionally diverse. The majority of the Holden ellipse has a thermal inertia of 340 to 475 J m-2 K-1 s-1/2 and consists of bed forms with some consolidated material intermixed. Mawrth Vallis has a mean thermal inertia of 310 J m-2 K-1 s-1/2 and a wide variety of materials is present contributing to the moderate thermal inertia surfaces, including a mixture of bedrock, indurated surfaces, bed forms, and unconsolidated fines. Phyllosilicates have been identified at all four candidate landing sites, and these clay-bearing units typically have a similar thermal inertia value (400 to 500 J m-2 K-1 s-1/2), suggesting physical properties that are also similar.

  17. Surface Properties of the Mars Science Laboratory Candidate Landing Sites: Characterization from Orbit and Predictions

    NASA Astrophysics Data System (ADS)

    Fergason, R. L.; Christensen, P. R.; Golombek, M. P.; Parker, T. J.

    2012-09-01

    This work describes the interpretation of THEMIS-derived thermal inertia data at the Eberswalde, Gale, Holden, and Mawrth Vallis Mars Science Laboratory (MSL) candidate landing sites and determines how thermophysical variations correspond to morphology and, when apparent, mineralogical diversity. At Eberswalde, the proportion of likely unconsolidated material relative to exposed bedrock or highly indurated surfaces controls the thermal inertia of a given region. At Gale, the majority of the landing site region has a moderate thermal inertia (250 to 410 J m-2 K-1 s-1/2), which is likely an indurated surface mixed with unconsolidated materials. The primary difference between higher and moderate thermal inertia surfaces may be due to the amount of mantling material present. Within the mound of stratified material in Gale, layers are distinguished in the thermal inertia data; the MSL rover could be traversing through materials that are both thermophysically and compositionally diverse. The majority of the Holden ellipse has a thermal inertia of 340 to 475 J m-2 K-1 s-1/2 and consists of bed forms with some consolidated material intermixed. Mawrth Vallis has a mean thermal inertia of 310 J m-2 K-1 s-1/2 and a wide variety of materials is present contributing to the moderate thermal inertia surfaces, including a mixture of bedrock, indurated surfaces, bed forms, and unconsolidated fines. Phyllosilicates have been identified at all four candidate landing sites, and these clay-bearing units typically have a similar thermal inertia value (400 to 500 J m-2 K-1 s-1/2), suggesting physical properties that are also similar.

  18. Multiple, Ligand-Dependent Routes from the Active Site of Cytochrome P450 2C9

    SciTech Connect

    Cojocaru, Vlad; Winn, Peter J.; Wade, Rebecca C.

    2012-02-13

    The active site of liver-specific, drug-metabolizing cytochrome P450 (CYP) monooxygenases is deeply buried in the protein and is connected to the protein surface through multiple tunnels, many of which were found open in different CYP crystal structures. It has been shown that different tunnels could serve as ligand passage routes in different CYPs. However, it is not understood whether one CYP uses multiple routes for substrate access and product release and whether these routes depend on ligand properties. From 300 ns of molecular dynamics simulations of CYP2C9, the second most abundant CYP in the human liver we found four main ligand exit routes, the occurrence of each depending on the ligand type and the conformation of the F-G loop, which is likely to be affected by the CYP-membrane interaction. A non-helical F-G loop favored exit towards the putative membrane-embedded region. Important protein features that direct ligand exit include aromatic residues that divide the active site and whose motions control access to two pathways. The ligands interacted with positively charged residues on the protein surface through hydrogen bonds that appear to select for acidic substrates. The observation of multiple, ligand-dependent routes in a CYP aids understanding of how CYP mutations affect drug metabolism and provides new possibilities for CYP inhibition.

  19. Surface-Water Hydrology and Quality at the Pike Hill Superfund Site, Corinth, Vermont, October 2004 to December 2005

    USGS Publications Warehouse

    Kiah, Richard G.; Deacon, Jeffrey R.; Piatak, Nadine M.; Seal, Robert R., II; Coles, James F.; Hammarstrom, Jane M.

    2007-01-01

    The hydrology and quality of surface water in and around the Pike Hill Brook watershed, in Corinth, Vermont, was studied from October 2004 to December 2005 by the U.S. Geological Survey in cooperation with the U.S. Environmental Protection Agency (USEPA). Pike Hill was mined intermittently for copper from 1847 to 1919 and the site is known to be contributing trace elements and acidity to Pike Hill Brook and an unnamed tributary to Cookville Brook. The site has been listed as a Superfund site since 2004. Streamflow, specific conductance, pH, and water temperature were measured continuously and monthly at three sites on Pike Hill Brook to determine the variation in these parameters over an annual cycle. Synoptic water-quality sampling was done at 10 stream sites in October 2004, April 2005, and June 2005 and at 13 stream sites in August 2005 to characterize the quality of surface water in the watershed on a seasonal and spatial basis, as well as to assess the effects of wetlands on water quality. Samples for analysis of benthic macroinvertebrate populations were collected at 11 stream sites in August 2005. Water samples were analyzed for 5 major ions and 32 trace elements. Concentrations of trace elements at sites in the Pike Hill Brook watershed exceeded USEPA National Recommended Water Quality Criteria acute and chronic toxicity standards for aluminum, iron, cadmium, copper, and zinc. Concentrations of copper exceeded the chronic criteria in an unnamed tributary to Cookville Brook in one sample. Concentrations of sulfate, calcium, aluminum, iron, cadmium, copper, and zinc decreased with distance from a site directly downstream from the mine (site 1), as a result of dilution and through sorption and precipitation of the trace elements. Maximum concentrations of aluminum, iron, cadmium, copper, and zinc were observed during spring snowmelt. Concentrations of sulfate, calcium, cadmium, copper, and zinc, and instantaneous loads of calcium and aluminum were

  20. Elucidating the mechanism and active site of the cyclohexanol dehydrogenation on copper-based catalysts: A density functional theory study

    NASA Astrophysics Data System (ADS)

    Wang, Ziyun; Liu, Xinyi; Rooney, D. W.; Hu, P.

    2015-10-01

    The dehydrogenation of cyclohexanol to cyclohexanone is very important in the manufacture of nylon. Copper-based catalysts are the most popular catalysts for this reaction, and on these catalysts the reaction mechanism and active site are in debate. In order to elucidate the mechanism and active site of the cyclohexanol dehydrogenation on copper-based catalysts, density functional theory with dispersion corrections were performed on up to six facets of copper in two different oxidation states: monovalent copper and metallic copper. By calculating the surface energies of these facets, Cu(111) and Cu2O(111) were found to be the most stable facets for metallic copper and for monovalent copper, respectively. On these two facets, all the possible elementary steps in the dehydrogenation pathway of cyclohexanol were calculated, including the adsorption, dehydrogenation, hydrogen coupling and desorption. Two different reaction pathways for dehydrogenation were considered on both surfaces. It was revealed that the dehydrogenation mechanisms are different on these two surfaces: on Cu(111) the hydrogen belonging to the hydroxyl is removed first, then the hydrogen belonging to the carbon is subtracted, while on Cu2O(111) the hydrogen belonging to the carbon is removed followed by the subtraction of the hydrogen in the hydroxyl group. Furthermore, by comparing the energy profiles of these two surfaces, Cu2O(111) was found to be more active for cyclohexanol dehydrogenation than Cu(111). In addition, we found that the coordinatively unsaturated copper sites on Cu2O(111) are the reaction sites for all the steps. Therefore, the coordinatively unsaturated copper site on Cu2O(111) is likely to be the active site for cyclohexanol dehydrogenation on the copper-based catalysts.

  1. The Activity of Antimicrobial Surfaces Varies by Testing Protocol Utilized

    PubMed Central

    Campos, Matias D.; Zucchi, Paola C.; Phung, Ann; Leonard, Steven N.; Hirsch, Elizabeth B.

    2016-01-01

    Background Contaminated hospital surfaces are an important source of nosocomial infections. A major obstacle in marketing antimicrobial surfaces is a lack of efficacy data based on standardized testing protocols. Aim We compared the efficacy of multiple testing protocols against several “antimicrobial” film surfaces. Methods Four clinical isolates were used: one Escherichia coli, one Klebsiella pneumoniae, and two Staphylococcus aureus strains. Two industry methods (modified ISO 22196 and ASTM E2149), a “dried droplet”, and a “transfer” method were tested against two commercially available antimicrobial films, one film in development, an untreated control, and a positive (silver) control film. At 2 (only ISO) and 24 hours following inoculation, bacteria were collected from film surfaces and enumerated. Results Compared to untreated films in all protocols, there were no significant differences in recovery on either commercial brand at 2 or 24 hours after inoculation. The silver surface demonstrated significant microbicidal activity (mean loss 4.9 Log10 CFU/ml) in all methods and time points with the exception of 2 hours in the ISO protocol and the transfer method. Using our novel droplet method, no differences between placebo and active surfaces were detected. The surface in development demonstrated variable activity depending on method, organism, and time point. The ISO demonstrated minimal activity at 2 hours but significant activity at 24 hours (mean 4.5 Log10 CFU/ml difference versus placebo). The ASTEM protocol exhibited significant differences in recovery of staphylococci (mean 5 Log10 CFU/ml) but not Gram-negative isolates (10 fold decrease). Minimal activity was observed with this film in the transfer method. Conclusions Varying results between protocols suggested that efficacy of antimicrobial surfaces cannot be easily and reproducibly compared. Clinical use should be considered and further development of representative methods is needed. PMID

  2. Direct Epoxidation of Propylene over Stabilized Cu+ Surface Sites on Ti Modified Cu2O

    SciTech Connect

    Yang, X.; Kattel, S.; Xiong, K.; Mudiyanselage, K.; Rykov, S.; Senanayake, S. D.; Rodriguez, J. A.; Liu, P.; Stacchiola, D. J.; Chen, J. G.

    2015-07-17

    Direct propylene epoxidation by O2 is a challenging reaction because of the strong tendency for complete combustion. Results from the current study demonstrate the feasibility to tune the epoxidation selectivity by generating highly dispersed and stabilized Cu+ active sites in a TiCuOx mixed oxide. The TiCuOx surface anchors the key surface intermediate, oxametallacycle, leading to higher selectivity for epoxidation of propylene.

  3. 10 CFR 63.16 - Review of site characterization activities. 2

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of... conduct of site characterization activities at the Yucca Mountain site, DOE shall report the nature and... activities at the Yucca Mountain site, NRC staff shall be permitted to visit and inspect the locations...

  4. 10 CFR 63.16 - Review of site characterization activities. 2

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of... conduct of site characterization activities at the Yucca Mountain site, DOE shall report the nature and... activities at the Yucca Mountain site, NRC staff shall be permitted to visit and inspect the locations...

  5. 10 CFR 63.16 - Review of site characterization activities. 2

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of... conduct of site characterization activities at the Yucca Mountain site, DOE shall report the nature and... activities at the Yucca Mountain site, NRC staff shall be permitted to visit and inspect the locations...

  6. 10 CFR 63.16 - Review of site characterization activities. 2

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of... conduct of site characterization activities at the Yucca Mountain site, DOE shall report the nature and... activities at the Yucca Mountain site, NRC staff shall be permitted to visit and inspect the locations...

  7. 10 CFR 63.16 - Review of site characterization activities. 2

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of... conduct of site characterization activities at the Yucca Mountain site, DOE shall report the nature and... activities at the Yucca Mountain site, NRC staff shall be permitted to visit and inspect the locations...

  8. ChemCam passive reflectance spectroscopy of surface materials at the Curiosity landing site, Mars

    NASA Astrophysics Data System (ADS)

    Johnson, Jeffrey R.; Bell, J. F.; Bender, S.; Blaney, D.; Cloutis, E.; DeFlores, L.; Ehlmann, B.; Gasnault, O.; Gondet, B.; Kinch, K.; Lemmon, M.; Le Mouélic, S.; Maurice, S.; Rice, M.; Wiens, R. C.

    2015-03-01

    The spectrometers on the Mars Science Laboratory (MSL) ChemCam instrument were used in passive mode to record visible/near-infrared (400-840 nm) radiance from the martian surface. Using the onboard ChemCam calibration targets' housing as a reflectance standard, we developed methods to collect, calibrate, and reduce radiance observations to relative reflectance. Such measurements accurately reproduce the known reflectance spectra of other calibration targets on the rover, and represent the highest spatial resolution (0.65 mrad) and spectral sampling (<1 nm) visible/near-infrared reflectance spectra from a landed platform on Mars. Relative reflectance spectra of surface rocks and soils match those from orbital observations and multispectral data from the MSL Mastcam camera. Preliminary analyses of the band depths, spectral slopes, and reflectance ratios of the more than 2000 spectra taken during the first year of MSL operations demonstrate at least six spectral classes of materials distinguished by variations in ferrous and ferric components. Initial comparisons of ChemCam spectra to laboratory spectra of minerals and Mars analog materials demonstrate similarities with palagonitic soils and indications of orthopyroxene in some dark rocks. Magnesium-rich "raised ridges" tend to exhibit distinct near-infrared slopes. The ferric absorption downturn typically found for martian materials at <600 nm is greatly subdued in brushed rocks and drill tailings, consistent with their more ferrous nature. Calcium-sulfate veins exhibit the highest relative reflectances observed, but are still relatively red owing to the effects of residual dust. Such dust is overall less prominent on rocks sampled within the "blast zone" immediately surrounding the landing site. These samples were likely affected by the landing thrusters, which partially removed the ubiquitous dust coatings. Increased dust coatings on the calibration targets during the first year of the mission were documented by

  9. Establishment of Epithelial Attachment on Titanium Surface Coated with Platelet Activating Peptide

    PubMed Central

    Sugawara, Shiho; Maeno, Masahiko; Lee, Cliff; Nagai, Shigemi; Kim, David M.; Da Silva, John; Kondo, Hisatomo

    2016-01-01

    The aim of this study was to produce epithelial attachment on a typical implant abutment surface of smooth titanium. A challenging complication that hinders the success of dental implants is peri-implantitis. A common cause of peri-implantitis may results from the lack of epithelial sealing at the peri-implant collar. Histologically, epithelial sealing is recognized as the attachment of the basement membrane (BM). BM-attachment is promoted by activated platelet aggregates at surgical wound sites. On the other hand, platelets did not aggregate on smooth titanium, the surface typical of the implant abutment. We then hypothesized that epithelial BM-attachment was produced when titanium surface was modified to allow platelet aggregation. Titanium surfaces were coated with a protease activated receptor 4-activating peptide (PAR4-AP). PAR4-AP coating yielded rapid aggregation of platelets on the titanium surface. Platelet aggregates released robust amount of epithelial chemoattractants (IGF-I, TGF-β) and growth factors (EGF, VEGF) on the titanium surface. Human gingival epithelial cells, when they were co-cultured on the platelet aggregates, successfully attached to the PAR4-AP coated titanium surface with spread laminin5 positive BM and consecutive staining of the epithelial tight junction component ZO1, indicating the formation of complete epithelial sheet. These in-vitro results indicate the establishment of epithelial BM-attachment to the titanium surface. PMID:27741287

  10. Sand dune ridge alignment effects on surface BRF over the Libya-4 CEOS calibration site.

    PubMed

    Govaerts, Yves M

    2015-01-01

    The Libya-4 desert area, located in the Great Sand Sea, is one of the most important bright desert CEOS pseudo-invariant calibration sites by its size and radiometric stability. This site is intensively used for radiometer drift monitoring, sensor intercalibration and as an absolute calibration reference based on simulated radiances traceable to the SI standard. The Libya-4 morphology is composed of oriented sand dunes shaped by dominant winds. The effects of sand dune spatial organization on the surface bidirectional reflectance factor is analyzed in this paper using Raytran, a 3D radiative transfer model. The topography is characterized with the 30 m resolution ASTER digital elevation model. Four different regions-of-interest sizes, ranging from 10 km up to 100 km, are analyzed. Results show that sand dunes generate more backscattering than forward scattering at the surface. The mean surface reflectance averaged over different viewing and illumination angles is pretty much independent of the size of the selected area, though the standard deviation differs. Sun azimuth position has an effect on the surface reflectance field, which is more pronounced for high Sun zenith angles. Such 3D azimuthal effects should be taken into account to decrease the simulated radiance uncertainty over Libya-4 below 3% for wavelengths larger than 600 nm. PMID:25654721

  11. Sand dune ridge alignment effects on surface BRF over the Libya-4 CEOS calibration site.

    PubMed

    Govaerts, Yves M

    2015-02-03

    The Libya-4 desert area, located in the Great Sand Sea, is one of the most important bright desert CEOS pseudo-invariant calibration sites by its size and radiometric stability. This site is intensively used for radiometer drift monitoring, sensor intercalibration and as an absolute calibration reference based on simulated radiances traceable to the SI standard. The Libya-4 morphology is composed of oriented sand dunes shaped by dominant winds. The effects of sand dune spatial organization on the surface bidirectional reflectance factor is analyzed in this paper using Raytran, a 3D radiative transfer model. The topography is characterized with the 30 m resolution ASTER digital elevation model. Four different regions-of-interest sizes, ranging from 10 km up to 100 km, are analyzed. Results show that sand dunes generate more backscattering than forward scattering at the surface. The mean surface reflectance averaged over different viewing and illumination angles is pretty much independent of the size of the selected area, though the standard deviation differs. Sun azimuth position has an effect on the surface reflectance field, which is more pronounced for high Sun zenith angles. Such 3D azimuthal effects should be taken into account to decrease the simulated radiance uncertainty over Libya-4 below 3% for wavelengths larger than 600 nm.

  12. Sand Dune Ridge Alignment Effects on Surface BRF over the Libya-4 CEOS Calibration Site

    PubMed Central

    Govaerts, Yves M.

    2015-01-01

    The Libya-4 desert area, located in the Great Sand Sea, is one of the most important bright desert CEOS pseudo-invariant calibration sites by its size and radiometric stability. This site is intensively used for radiometer drift monitoring, sensor intercalibration and as an absolute calibration reference based on simulated radiances traceable to the SI standard. The Libya-4 morphology is composed of oriented sand dunes shaped by dominant winds. The effects of sand dune spatial organization on the surface bidirectional reflectance factor is analyzed in this paper using Raytran, a 3D radiative transfer model. The topography is characterized with the 30 m resolution ASTER digital elevation model. Four different regions-of-interest sizes, ranging from 10 km up to 100 km, are analyzed. Results show that sand dunes generate more backscattering than forward scattering at the surface. The mean surface reflectance averaged over different viewing and illumination angles is pretty much independent of the size of the selected area, though the standard deviation differs. Sun azimuth position has an effect on the surface reflectance field, which is more pronounced for high Sun zenith angles. Such 3D azimuthal effects should be taken into account to decrease the simulated radiance uncertainty over Libya-4 below 3% for wavelengths larger than 600 nm. PMID:25654721

  13. Sand Dune Ridge Alignment Effects on Surface BRF over Libya-4 Calibration Site

    NASA Astrophysics Data System (ADS)

    Govaerts, Yves

    2015-12-01

    The Libya-4 desert area, located in the Great Sand Sea, is one of the most important bright desert CEOS pseudo-invariant calibration sites by its size and radiometric stability. This site is intensively used for radiometer drift monitoring, sensor intercalibration and as an absolute calibration reference based on simulated radiances traceable to the SI standard. The Libya-4 morphology is composed of oriented sand dunes shaped by dominant winds. The effects of sand dune spatial organization on the surface bidirectional reflectance factor is analyzed in this paper using Raytran, a 3D radiative transfer model. The topography is characterized with the 30 m resolution ASTER digital elevation model. Four different regions-of-interest sizes, ranging from 10 km up to 100 km, are analyzed. Results show that sand dunes generate more backscattering than forward scattering at the surface. The mean surface reflectance averaged over different viewing and illumination angles is pretty much independent of the size of the selected area, though the standard deviation differs. Sun azimuth position has an effect on the surface reflectance field, which is more pronounced for high Sun zenith angles. Such 3D azimuthal effects should be taken into account to decrease the simulated radiance uncertainty over Libya-4 below 3% for wavelengths larger than 600 nm..

  14. Active Acetylcholinesterase Immobilization on a Functionalized Silicon Surface.

    PubMed

    Khaldi, K; Sam, S; Gouget-Laemmel, A C; Henry de Villeneuve, C; Moraillon, A; Ozanam, F; Yang, J; Kermad, A; Ghellai, N; Gabouze, N

    2015-08-01

    In this work, we studied the attachment of active acetylcholinesterase (AChE) enzyme on a silicon substrate as a potential biomarker for the detection of organophosphorous (OP) pesticides. A multistep functionalization strategy was developed on a crystalline silicon surface: a carboxylic acid-terminated monolayer was grafted onto a hydrogen-terminated silicon surface by photochemical hydrosilylation, and then AChE was covalently attached through amide bonds using an activation EDC/NHS process. Each step of the modification was quantitatively characterized by ex-situ Fourier transform infrared spectroscopy in attenuated-total-reflection geometry (ATR-FTIR) and atomic force microscopy (AFM). The kinetics of enzyme immobilization was investigated using in situ real-time infrared spectroscopy. The enzymatic activity of immobilized acetylcholinesterase enzymes was determined with a colorimetric test. The surface concentration of active AChE was estimated to be Γ = 1.72 × 10(10) cm(-2).

  15. Potential Biosignificant Interest and Surface Activity of Efficient Heterocyclic Derivatives.

    PubMed

    El-Sayed, Refat; Althagafi, Ismail

    2016-01-01

    Some functionalized pyridine and fused system derivatives were synthesized using enaminonitrile derivative 5 as a starting material for the reaction, with various reagents under different conditions. Propoxylation of these compounds using different moles of propylene oxide (3, 5 and 7 moles) leads to a novel group of surface active agents. The antimicrobial and surface activities of the synthesized compounds were investigated. Most of the evaluated compounds proved to be active as antibacterial and antifungal agents and showed good surface activity, which makes them suitable for diverse applications such as the manufacturing of emulsifiers, cosmetics, drugs, pesticides, etc. Additionally, biodegradation testing exhibits significant breakdown within six to seven days, and hence, lowers the toxicity to human beings and becomes environmentally friendly.

  16. Improving surface-subsurface water budgeting for Brownfield study sites using high resolution satellite imagery

    NASA Astrophysics Data System (ADS)

    Dujardin, J.; Boel, S.; Anibas, C.; Batelaan, O.; Canters, F.

    2009-04-01

    Countries around the world have problems with contaminated brownfield sites as resulting from a relatively anarchic economical and industrial development during the 19th and 20th centuries. Since a few decades policy makers and stakeholders have become more aware of the risk posed by these sites because some of these sites present direct public hazards. Water is often the main vector of the mobility of contaminants. In order to propose remediation measures for the contaminated sites, it is required to describe and to quantify as accurately as possible the surface and subsurface water fluxes in the polluted site. In this research a modelling approach with integrated remote sensing analysis has been developed for accurately calculating water and contaminant fluxes on the polluted sites. Groundwater pollution in urban environments is linked to patterns of land use, so to identify the sources of contamination with great accuracy in urban environments it is essential to characterize the land cover in a detailed way. The use of high resolution spatial information is required because of the complexity of the urban land use. An object-oriented classification approach applied on high resolution satellite data has been adopted. Cluster separability analysis and visual interpretation of the image objects belonging to each cluster resulted in the selection of 8 land-cover categories (water, bare soil, meadow, mixed forest, grey urban surfaces, red roofs, bright roofs and shadow).To assign the image objects to one of the 8 selected classes a multiple layer perceptron (MLP) approach was adopted, using the NeuralWorks Predict software. After a post-classification shadow removal and a rule-based classification enhancement a kappa-value of 0.86 was obtained. Once the land cover was characterized, the groundwater recharge has been simulated using the spatially distributed WetSpass model and the subsurface water flow was simulated with GMS 6.0 in order to identify and budget the

  17. Establishment of bryophytes on a reclaimed surface mine site at Goose Lake Prairie State Park, Illinois

    SciTech Connect

    Rastorfer, J.R.

    1980-01-01

    The location of the site at Goose Lake Prairie State Park provided an impetus to revegetate the reclaimed acid minesoil as a demonstration site with prairie floristic species. Because many bryophytes are pioneer plants and because baseline data were needed, surveys were made (1976-1978) to ascertain the natural establishment of mosses and liverworts on the site. Different habitats were surveyed with respect to types of fine-textured mineral soils; namely, abandoned (cultivated) field soil, old minesoil (spoil), and two reclaimed minesoils distinguished by reclamation efforts initiated in 1972 to 1973 and 1975 to 1976. Thirty moss species and one liverwort species were identified from the entire site, and two additional moss species were found in areas adjacent to the site. The role of bryophytes in the development of prairie plant communities on reclaimed minesoil is still uncertain. However, existing research data provide support for the following hypotheses: (1) bryophytes should help reduce soil erosion by binding soil particles via their rhizoidal systems, and by the relatively high water-holding capacity of their gametophytic shoots; (2) bryophytes might reduce heavy-metal toxicity to certain vascular plants at soil surfaces, because they have an ability to accumulate these elements; and (3) bryophytes may enhance nitrogen fixation through their associations with blue-green algae and possibly with nitrogen-fixing bacteria.

  18. Geomorphic Surface Maps of Northern Frenchman Flat, Nevada Test Site, Southern Nevada

    SciTech Connect

    Bechtel Nevada

    2005-08-01

    Large-scale (1:6000) surficial geology maps of northern Frenchman Flat were developed in 1995 as part of comprehensive site characterization required to operate a low-level radioactive waste disposal facility in that area. Seven surficial geology maps provide fundamental data on natural processes and are the platform needed to reconstruct the Quaternary history of northern Frenchman Flat. Reconstruction of the Quaternary history provides an understanding of the natural processes that act to develop the landscape, and the time-frames involved in landscape development. The mapping was conducted using color and color-infrared aerial photographs and field verification of map unit composition and boundaries. Criteria for defining the map unit composition of geomorphic surface units are based on relative geomorphic position, landform morphology, and degree of preservation of surface morphology. Seven geomorphic surfaces (Units 1 through 7) are recognized, spanning from the early Quaternary to present time.

  19. Remarkable enhancement of O₂ activation on yttrium-stabilized zirconia surface in a dual catalyst bed.

    PubMed

    Richard, Mélissandre; Can, Fabien; Duprez, Daniel; Gil, Sonia; Giroir-Fendler, Anne; Bion, Nicolas

    2014-10-13

    Yttrium-stabilized zirconia (YSZ) has been extensively studied as an electrolyte material for solid oxide fuel cells (SOFC) but its performance in heterogeneous catalysis is also the object of a growing number of publications. In both applications, oxygen activation on the YSZ surface remains the step that hinders utilization at moderate temperature. It was demonstrated by oxygen isotope exchange that a dual catalyst bed system consisting of two successive LaMnO3 and YSZ beds without intimate contact drastically enhances oxygen activation on the YSZ surface at 698 K. It can be concluded that LaMnO3 activates the triplet ground-state of molecular oxygen into a low-lying singlet state, thereby facilitating the activation of the O2 molecule on the YSZ oxygen vacancy sites. This phenomenon is shown to improve the catalytic activity of the LaMnO3-Pd/YSZ system for the partial oxidation of methane.

  20. GAS HYDRATES AT TWO SITES OF AN ACTIVE CONTINENTAL MARGIN.

    USGS Publications Warehouse

    Kvenvolden, K.A.

    1985-01-01

    Sediment containing gas hydrates from two distant Deep Sea Drilling Project sites (565 and 568), located about 670 km apart on the landward flank of the Middle America Trench, was studied to determine the geochemical conditions that characterize the occurrence of gas hydrates. Site 565 was located in the Pacific Ocean offshore the Nicoya Peninsula of Costa Rica in 3,111 m of water. The depth of the hole at this site was 328 m, and gas hydrates were recovered from 285 and 319 m. Site 568 was located about 670 km to the northwest offshore Guatemala in 2,031 m of water. At this site the hole penetrated to 418 m, and gas hydrates were encountered at 404 m.

  1. Control of active sites in selective flocculation: III -- Mechanism of site blocking

    SciTech Connect

    Behl, S.; Moudgil, B.M. . Dept. of Materials Science and Engineering)

    1993-12-01

    It has been shown in Parts I and II of this paper that heteroflocculation can be controlled by poisoning the sites for flocculant adsorption using a site blocking agent (SBA). An efficient SBA was determined to be the lower molecular weight fraction of the flocculant. In this paper, the underlying mechanism of SBA action is described. Also, the mathematical model detailed in Part I is used to determine the effect of different SBAs on apatite-dolomite separation efficiency. It has been demonstrated that the depression in flocculation is directly related to the site blocking parameter ([bar [Phi

  2. Dynamically achieved active site precision in enzyme catalysis.

    PubMed

    Klinman, Judith P

    2015-02-17

    CONSPECTUS: The grand challenge in enzymology is to define and understand all of the parameters that contribute to enzymes' enormous rate accelerations. The property of hydrogen tunneling in enzyme reactions has moved the focus of research away from an exclusive focus on transition state stabilization toward the importance of the motions of the heavy atoms of the protein, a role for reduced barrier width in catalysis, and the sampling of a protein conformational landscape to achieve a family of protein substates that optimize enzyme-substrate interactions and beyond. This Account focuses on a thermophilic alcohol dehydrogenase for which the chemical step of hydride transfer is rate determining across a wide range of experimental conditions. The properties of the chemical coordinate have been probed using kinetic isotope effects, indicating a transition in behavior below 30 °C that distinguishes nonoptimal from optimal C-H activation. Further, the introduction of single site mutants has the impact of either enhancing or eliminating the temperature dependent transition in catalysis. Biophysical probes, which include time dependent hydrogen/deuterium exchange and fluorescent lifetimes and Stokes shifts, have also been pursued. These studies allow the correlation of spatially resolved transitions in protein motions with catalysis. It is now possible to define a long-range network of protein motions in ht-ADH that extends from a dimer interface to the substrate binding domain across to the cofactor binding domain, over a distance of ca. 30 Å. The ongoing challenge to obtaining spatial and temporal resolution of catalysis-linked protein motions is discussed.

  3. Uncertainty analysis of the Operational Simplified Surface Energy Balance (SSEBop) model at multiple flux tower sites

    NASA Astrophysics Data System (ADS)

    Chen, Mingshi; Senay, Gabriel B.; Singh, Ramesh K.; Verdin, James P.

    2016-05-01

    Evapotranspiration (ET) is an important component of the water cycle - ET from the land surface returns approximately 60% of the global precipitation back to the atmosphere. ET also plays an important role in energy transport among the biosphere, atmosphere, and hydrosphere. Current regional to global and daily to annual ET estimation relies mainly on surface energy balance (SEB) ET models or statistical and empirical methods driven by remote sensing data and various climatological databases. These models have uncertainties due to inevitable input errors, poorly defined parameters, and inadequate model structures. The eddy covariance measurements on water, energy, and carbon fluxes at the AmeriFlux tower sites provide an opportunity to assess the ET modeling uncertainties. In this study, we focused on uncertainty analysis of the Operational Simplified Surface Energy Balance (SSEBop) model for ET estimation at multiple AmeriFlux tower sites with diverse land cover characteristics and climatic conditions. The 8-day composite 1-km MODerate resolution Imaging Spectroradiometer (MODIS) land surface temperature (LST) was used as input land surface temperature for the SSEBop algorithms. The other input data were taken from the AmeriFlux database. Results of statistical analysis indicated that the SSEBop model performed well in estimating ET with an R2 of 0.86 between estimated ET and eddy covariance measurements at 42 AmeriFlux tower sites during 2001-2007. It was encouraging to see that the best performance was observed for croplands, where R2 was 0.92 with a root mean square error of 13 mm/month. The uncertainties or random errors from input variables and parameters of the SSEBop model led to monthly ET estimates with relative errors less than 20% across multiple flux tower sites distributed across different biomes. This uncertainty of the SSEBop model lies within the error range of other SEB models, suggesting systematic error or bias of the SSEBop model is within the

  4. Uncertainty analysis of the Operational Simplified Surface Energy Balance (SSEBop) model at multiple flux tower sites

    USGS Publications Warehouse

    Chen, Mingshi; Senay, Gabriel B.; Singh, Ramesh K.; Verdin, James P.

    2016-01-01

    Evapotranspiration (ET) is an important component of the water cycle – ET from the land surface returns approximately 60% of the global precipitation back to the atmosphere. ET also plays an important role in energy transport among the biosphere, atmosphere, and hydrosphere. Current regional to global and daily to annual ET estimation relies mainly on surface energy balance (SEB) ET models or statistical and empirical methods driven by remote sensing data and various climatological databases. These models have uncertainties due to inevitable input errors, poorly defined parameters, and inadequate model structures. The eddy covariance measurements on water, energy, and carbon fluxes at the AmeriFlux tower sites provide an opportunity to assess the ET modeling uncertainties. In this study, we focused on uncertainty analysis of the Operational Simplified Surface Energy Balance (SSEBop) model for ET estimation at multiple AmeriFlux tower sites with diverse land cover characteristics and climatic conditions. The 8-day composite 1-km MODerate resolution Imaging Spectroradiometer (MODIS) land surface temperature (LST) was used as input land surface temperature for the SSEBop algorithms. The other input data were taken from the AmeriFlux database. Results of statistical analysis indicated that the SSEBop model performed well in estimating ET with an R2 of 0.86 between estimated ET and eddy covariance measurements at 42 AmeriFlux tower sites during 2001–2007. It was encouraging to see that the best performance was observed for croplands, where R2 was 0.92 with a root mean square error of 13 mm/month. The uncertainties or random errors from input variables and parameters of the SSEBop model led to monthly ET estimates with relative errors less than 20% across multiple flux tower sites distributed across different biomes. This uncertainty of the SSEBop model lies within the error range of other SEB models, suggesting systematic error or bias of the SSEBop model is within

  5. Lethal Factor Active-Site Mutations Affect Catalytic Activity In Vitro

    PubMed Central

    Hammond, S. E.; Hanna, P. C.

    1998-01-01

    The lethal factor (LF) protein of Bacillus anthracis lethal toxin contains the thermolysin-like active-site and zinc-binding consensus motif HEXXH (K. R. Klimpel, N. Arora, and S. H. Leppla, Mol. Microbiol. 13:1093–1100, 1994). LF is hypothesized to act as a Zn2+ metalloprotease in the cytoplasm of macrophages, but no proteolytic activities have been previously shown on any target substrate. Here, synthetic peptides are hydrolyzed by LF in vitro. Mass spectroscopy and peptide sequencing of isolated cleavage products separated by reverse-phase high-pressure liquid chromatography indicate that LF seems to prefer proline-containing substrates. Substitution mutations within the consensus active-site residues completely abolish all in vitro catalytic functions, as does addition of 1,10-phenanthroline, EDTA, and certain amino acid hydroxamates, including the novel zinc metalloprotease inhibitor ZINCOV. In contrast, the protease inhibitors bestatin and lysine CMK, previously shown to block LF activity on macrophages, did not block LF activity in vitro. These data provide the first direct evidence that LF may act as an endopeptidase. PMID:9573135

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

    PubMed

    Hiyamuta, S; Ito, K

    1994-04-01

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

  7. Enhanced Surfactant Adsorption on Activated Carbon through Manipulation of Surface Oxygen Groups

    NASA Astrophysics Data System (ADS)

    Collins, John; Qu, Deyang; Foster, Michelle

    2012-02-01

    Passive energy storage is a necessary component for balancing the lifecycle budget with new forms of green energy. The work presented describes how surface oxygen groups (SOG) on granulated activated carbon have been manipulated using Nitric Acid in a controlled, stepwise fashion. The structure and surface functionality of the activated carbon samples were characterized using DRIFTS, Raman Spectroscopy and Porosimetry. Total surface area was found to increase proportionally with the removal of heteroatom material, exposing previously insulated active sites responsible for SOG attachment. Broad oxide peaks were deconvoluted and analyzed, allowing for absolute identification of evolving functionality at each oxidation stage. SOGs were maximized on the third oxidation cycle with the presence of conjugated aromatic, phenol, lactone, and carboxylic acid groups. FSN Zonyl nonionic was applied to all oxidized samples at various concentrations. Total adsorbed surfactant was quantified for each concentration / oxidation scheme using attenuated total reflection. The relative quantity and polarity of chemisorbed surfactant were qualitatively assessed for each equilibrium concentration.

  8. Characterization of heparin-binding site of tissue transglutaminase: its importance in cell surface targeting, matrix deposition, and cell signaling.

    PubMed

    Wang, Zhuo; Collighan, Russell J; Pytel, Kamila; Rathbone, Daniel L; Li, Xiaoling; Griffin, Martin

    2012-04-13

    Tissue transglutaminase (TG2) is a multifunctional Ca(2+)-activated protein cross-linking enzyme secreted into the extracellular matrix (ECM), where it is involved in wound healing and scarring, tissue fibrosis, celiac disease, and metastatic cancer. Extracellular TG2 can also facilitate cell adhesion important in wound healing through a nontransamidating mechanism via its association with fibronectin, heparan sulfates (HS), and integrins. Regulating the mechanism how TG2 is translocated into the ECM therefore provides a strategy for modulating these physiological and pathological functions of the enzyme. Here, through molecular modeling and mutagenesis, we have identified the HS-binding site of TG2 (202)KFLKNAGRDCSRRSSPVYVGR(222). We demonstrate the requirement of this binding site for translocation of TG2 into the ECM through a mechanism involving cell surface shedding of HS. By synthesizing a peptide NPKFLKNAGRDCSRRSS corresponding to the HS-binding site within TG2, we also demonstrate how this mimicking peptide can in isolation compensate for the RGD-induced loss of cell adhesion on fibronectin via binding to syndecan-4, leading to activation of PKCα, pFAK-397, and ERK1/2 and the subsequent formation of focal adhesions and actin cytoskeleton organization. A novel regulatory mechanism for TG2 translocation into the extracellular compartment that depends upon TG2 conformation and the binding of HS is proposed.

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

    SciTech Connect

    Teese, G.D.

    1995-09-28

    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.

  10. Control of active sites in selective flocculation: II -- Role of site blocking agents

    SciTech Connect

    Behl, S.; Moudgil, B.M. . Dept. of Materials Science and Engineering)

    1993-12-01

    Control of heteroflocculation using a lower molecular weight fraction of the flocculant as a site blocking agent is demonstrated in the apatite-dolomite-polyethylene oxide system. The most effective SBA (site blocking agent) was determined to be the highest molecular weight fraction of the flocculant itself which was not capable of flocculating any of the components of the mixture. In the presence of the SBA, flocculant adsorption decreased significantly on apatite particles, thereby inhibiting coflocculation.

  11. Integrated Cropland and Grassland Flux Tower Observation Sites over Grazinglands for Quantifying Surface-Atmosphere Exchange

    NASA Astrophysics Data System (ADS)

    Mahan, H. R.; Wagle, P.; Bajgain, R.; Zhou, Y.; Basara, J. B.; Xiao, X.; Duckles, J. M.; Steiner, J. L.; Starks, P. J.; Northup, B. K.

    2014-12-01

    Quantifying methane (CH4), carbon dioxide (CO2), and water vapor fluxes between land surface and boundary layer using the eddy covariance method have many applicable uses across several disciplines. Three eddy flux towers have been established over no-till winter wheat (Triticum aestivum L.), and native and improved pastures at the USDA ARS Grazinglands Research Laboratory, El Reno, OK. An additional tower will be established in fall 2014 over till winter wheat. Each flux site is equipped with an eddy covariance system, PhenoCam, COSMOS, and in-situ observations of soil and atmospheric state variables. The objective of this research is to measure, compare, and model the land-atmosphere exchange of CO2, water vapor, and CH4 in different land cover types and management practices (till vs no-till, grazing vs no-grazing, native vs improved pasture). Models that focus on net ecosystem CO2 exchange (NEE), gross primary production (GPP), evapotranspiration (ET), and CH4 fluxes can be improved by the cross verification of these measurements. Another application will be to link the in-situ measurements with satellite remote sensing in order to scale-up flux measurements from small spatial scales to local and regional scales. Preliminary data analysis from the native grassland site revealed that CH4 concentration was negligible (~ 0), and it increased significantly when cattle were introduced into the site. In summer 2014, daily ET magnitude was about 4-5 mm day-1 and the NEE magnitude was 4-5 g C day-1 at the native grassland site. Further analysis of data for all the sites for longer temporal periods will enhance understanding of biotic and abiotic factors that govern carbon, water, and energy exchanges between the land surface and atmosphere under different land cover and management systems. The research findings will help predict the responses of these ecosystems to management practices and global environmental change in the future.

  12. Competitive sorption of copper and lead at the oxide-water interface: Implications for surface site density

    NASA Astrophysics Data System (ADS)

    Christl, Iso; Kretzschmar, Ruben

    1999-10-01

    The competitive sorption of Cu(II) and Pb(II) to colloidal hematite was investigated as a function of pH and total metal concentration. Acid-base titrations of the hematite and single-metal sorption experiments for Cu and Pb at low to medium surface coverages were used to calibrate two surface complexation models, the triple layer model, and a 2-pK basic Stern model with ion-pair formation. The surface site density was systematically varied from 2 to 20 sites/nm2. Three different metal surface complexes were considered: (1) an inner-sphere metal complex; (2) an outer-sphere metal complex; and (3) an outer-sphere complex of singly hydrolyzed metal cations. Both models provided excellent fits to acid-base titration and single-metal sorption data, regardless of the surface site density used. With increasing site density, ΔpK of the stability constants for protonation reactions increased and metal surface complexes decreased steadily. The calibrated models based on different site densities were used to predict competitive sorption effects between Cu and Pb and single-metal sorption at higher total metal concentrations. Precipitation of oversaturated solid phases was included in the calculations. Best predictions of competitive sorption effects were obtained with surface site densities between 5 and 10 sites/nm2. The results demonstrate that surface site density is a key parameter if surface complexation models are exposed to more complex, multicomponent environments. We conclude that competitive metal sorption experiments can be used to obtain additional information about the relevant surface site density of oxide mineral surfaces.

  13. Catalytic surface radical in dye-decolorizing peroxidase: a computational, spectroscopic and site-directed mutagenesis study

    PubMed Central

    Linde, Dolores; Pogni, Rebecca; Cañellas, Marina; Lucas, Fátima; Guallar, Victor; Baratto, Maria Camilla; Sinicropi, Adalgisa; Sáez-Jiménez, Verónica; Coscolín, Cristina; Romero, Antonio; Medrano, Francisco Javier; Ruiz-Dueñas, Francisco J.; Martínez, Angel T.

    2014-01-01

    Dye-decolorizing peroxidase (DyP) of Auricularia auricula-judae has been expressed in Escherichia coli as a representative of a new DyP family, and subjected to mutagenic, spectroscopic, crystallographic and computational studies. The crystal structure of DyP shows a buried haem cofactor, and surface tryptophan and tyrosine residues potentially involved in long-range electron transfer from bulky dyes. Simulations using PELE (Protein Energy Landscape Exploration) software provided several binding-energy optima for the anthraquinone-type RB19 (Reactive Blue 19) near the above aromatic residues and the haem access-channel. Subsequent QM/MM (quantum mechanics/molecular mechanics) calculations showed a higher tendency of Trp-377 than other exposed haem-neighbouring residues to harbour a catalytic protein radical, and identified the electron-transfer pathway. The existence of such a radical in H2O2-activated DyP was shown by low-temperature EPR, being identified as a mixed tryptophanyl/tyrosyl radical in multifrequency experiments. The signal was dominated by the Trp-377 neutral radical contribution, which disappeared in the W377S variant, and included a tyrosyl contribution assigned to Tyr-337 after analysing the W377S spectra. Kinetics of substrate oxidation by DyP suggests the existence of high- and low-turnover sites. The high-turnover site for oxidation of RB19 (kcat> 200 s−1) and other DyP substrates was assigned to Trp-377 since it was absent from the W377S variant. The low-turnover site/s (RB19 kcat ~20 s−1) could correspond to the haem access-channel, since activity was decreased when the haem channel was occluded by the G169L mutation. If a tyrosine residue is also involved, it will be different from Tyr-337 since all activities are largely unaffected in the Y337S variant. PMID:25495127

  14. Ammonia removal using activated carbons: effect of the surface chemistry in dry and moist conditions.

    PubMed

    Gonçalves, Maraisa; Sánchez-García, Laura; Oliveira Jardim, Erika de; Silvestre-Albero, Joaquín; Rodríguez-Reinoso, Francisco

    2011-12-15

    The effect of surface chemistry (nature and amount of oxygen groups) in the removal of ammonia was studied using a modified resin-based activated carbon. NH(3) breakthrough column experiments show that the modification of the original activated carbon with nitric acid, that is, the incorporation of oxygen surface groups, highly improves the adsorption behavior at room temperature. Apparently, there is a linear relationship between the total adsorption capacity and the amount of the more acidic and less stable oxygen surface groups. Similar experiments using moist air clearly show that the effect of humidity highly depends on the surface chemistry of the carbon used. Moisture highly improves the adsorption behavior for samples with a low concentration of oxygen functionalities, probably due to the preferential adsorption of ammonia via dissolution into water. On the contrary, moisture exhibits a small effect on samples with a rich surface chemistry due to the preferential adsorption pathway via Brønsted and Lewis acid centers from the carbon surface. FTIR analyses of the exhausted oxidized samples confirm both the formation of NH(4)(+) species interacting with the Brønsted acid sites, together with the presence of NH(3) species coordinated, through the lone pair electron, to Lewis acid sites on the graphene layers.

  15. Indium phosphide negative electron affinity photocathodes: Surface cleaning and activation

    NASA Astrophysics Data System (ADS)

    Sun, Yun

    InP(100) is a very important semi-conductor for many applications. When activated by Cs and oxygen, the InP surface achieves the state of Negative Electron Affinity (NEA) making the Cs+O/InP system a very efficient electron source. Despite many years of study, the chemical cleaning and activation of InP are still not well understood. In our work, we have established an understanding of the basic physics and chemistry for the chemical cleaning and activation of the InP(100) surface. Synchrotron Radiation Photoelectron Spectroscopy is the main technique used in this study because of its high surface sensitivity and ability to identify chemical species present on the surface at each stage of our process. A clean, stoichiometric InP(100) surface is crucial for obtaining high performance of NEA photocathodes. Therefore, the first part of our study focused on the chemical cleaning of InP(100). We found that hydrogen peroxide based solutions alone, originally developed to clean GaAs(100) surfaces and widely used for InP(100), do not result in clean InP(I00) surfaces because oxide is left on the surface. A second cleaning step, which uses acid solutions like HCl or H2SO4, can remove all the oxide and leave a 0.4 ML protective layer of elemental phosphorous on the surface. The elemental phosphorous can be removed by annealing at 330°C and a clean InP(100) surface can be obtained. Cs deposition on InP(100) surface shows clear charge transfer from the Cs ad-atoms to the substrate. When the Cs/InP(100) surface is dosed with oxygen, the charge transfer from the Cs to substrate is reduced and substrate is oxidized. The activation of InP as a NEA photocathode is carried out by an alternating series of steps consisting of Cs deposition and Cs+O co-deposition. Two types of oxygen are found after activation. The first is dissociated oxygen and the other is a di-oxygen species (peroxide or superoxide). The decay of quantum-yield with time and with annealing is studied and changes in

  16. Screening Mixtures of Small Molecules for Binding to Multiple Sites on the Surface Tetanus Toxin C Fragment by Bioaffinity NMR

    SciTech Connect

    Cosman, M; Zeller, L; Lightstone, F C; Krishnan, V V; Balhorn, R

    2002-01-01

    The clostridial neurotoxins include the closely related tetanus (TeNT) and botulinum (BoNT) toxins. Botulinum toxin is used to treat severe muscle disorders and as a cosmetic wrinkle reducer. Large quantities of botulinum toxin have also been produced by terrorists for use as a biological weapon. Because there are no known antidotes for these toxins, they thus pose a potential threat to human health whether by an accidental overdose or by a hostile deployment. Thus, the discovery of high specificity and affinity compounds that can inhibit their binding to neural cells can be used as antidotes or in the design of chemical detectors. Using the crystal structure of the C fragment of the tetanus toxin (TetC), which is the cell recognition and cell surface binding domain, and the computational program DOCK, sets of small molecules have been predicted to bind to two different sites located on the surface of this protein. While Site-1 is common to the TeNT and BoNTs, Site-2 is unique to TeNT. Pairs of these molecules from each site can then be linked together synthetically to thereby increase the specificity and affinity for this toxin. Electrospray ionization mass spectroscopy was used to experimentally screen each compound for binding. Mixtures containing binders were further screened for activity under biologically relevant conditions using nuclear magnetic resonance (NMR) methods. The screening of mixtures of compounds offers increased efficiency and throughput as compared to testing single compounds and can also evaluate how possible structural changes induced by the binding of one ligand can influence the binding of the second ligand. In addition, competitive binding experiments with mixtures containing ligands predicted to bind the same site could identify the best binder for that site. NMR transfer nuclear Overhauser effect (trNOE) confirm that TetC binds doxorubicin but that this molecule is displaced by N-acetylneuraminic acid (sialic acid) in a mixture that

  17. Fluoride adsorption on goethite in relation to different types of surface sites

    SciTech Connect

    Hiemstra, T.; Van Riemsdijk, W.H.

    2000-05-01

    Metal (hydr)oxides have different types of surface groups. Fluoride ions have been used as a probe to assess the number of surface sites. The authors have studied the F{sup {minus}} adsorption on goethite by measuring the F{sup {minus}} and H{sup +} interaction and F{sup {minus}} adsorption isotherms. Fluoride ions exchange against singly coordinated surface hydroxyls at low F{sup {minus}} concentrations. At higher concentrations also the doubly coordinated OH groups are involved. The replacement of a surface OH{sup {minus}} by F{sup {minus}} suggests that all F charge ({minus}1) is located at the surface in contrast to oxyanions which have a charge distribution in the interface due to the binding structure in which the anion only partially coordinates with the surface. Analysis of their F{sup {minus}} data with the CD-MUSIC approach shows that the formation of the fluoride surface complex is accompanied by a redistribution of charge. This is supposed to be due to a net switch in the H bonding as a result of the change of the type of surface complex from donating (FeOH, FeOH{sub 2}) to proton accepting (FeF). The modeled redistribution of charge is approximately equivalent with the change of a donating H bond into an accepting H bond. At high F{sup {minus}} concentrations precipitation of F{sup {minus}}, as for instance FeF{sub 3}(s), may occur. The rate of formation is catalyzed by the presence of high electrolyte concentrations.

  18. Investigation of the active sites of rhodium sulfide for hydrogen evolution/oxidation using carbon monoxide as a probe.

    PubMed

    Singh, Nirala; Upham, David C; Liu, Ru-Fen; Burk, Jonathan; Economou, Nick; Buratto, Steven; Metiu, Horia; McFarland, Eric W

    2014-05-20

    Carbon monoxide (CO) was observed to decrease the activity for hydrogen evolution, hydrogen oxidation, and H2-D2 exchange on rhodium sulfide, platinum, and rhodium metal. The temperature at which the CO was desorbed from the catalyst surface (detected by recovery in the H2-D2 exchange activity of the catalyst) was used as a descriptor for the CO binding energy to the active site. The differences in the CO desorption temperature between the different catalysts showed that the rhodium sulfide active site is not metallic rhodium. Using density functional theory, the binding energy of CO to the Rh sites in rhodium sulfide is found comparable to the binding energy on Pt. Coupled with experiment this supports the proposition that rhodium rather than sulfur atoms in the rhodium sulfide are the active site for the hydrogen reaction. This would indicate the active sites for hydrogen evolution/oxidation as well as oxygen reduction (determined by other groups using X-ray absorption spectroscopy) may be the same.

  19. Structural Characterization of Human 8-Oxoguanine DNA Glycosylase Variants Bearing Active Site Mutations

    SciTech Connect

    Radom,C.; Banerjee, A.; Verdine, G.

    2007-01-01

    The human 8-oxoguanine DNA glycosylase (hOGG1) protein is responsible for initiating base excision DNA repair of the endogenous mutagen 8-oxoguanine. Like nearly all DNA glycosylases, hOGG1 extrudes its substrate from the DNA helix and inserts it into an extrahelical enzyme active site pocket lined with residues that participate in lesion recognition and catalysis. Structural analysis has been performed on mutant versions of hOGG1 having changes in catalytic residues but not on variants having altered 7,8-dihydro-8-oxoguanine (oxoG) contact residues. Here we report high resolution structural analysis of such recognition variants. We found that Ala substitution at residues that contact the phosphate 5 to the lesion (H270A mutation) and its Watson-Crick face (Q315A mutation) simply removed key functionality from the contact interface but otherwise had no effect on structure. Ala substitution at the only residue making an oxoG-specific contact (G42A mutation) introduced torsional stress into the DNA contact surface of hOGG1, but this was overcome by local interactions within the folded protein, indicating that this oxoG recognition motif is 'hardwired'. Introduction of a side chain intended to sterically obstruct the active site pocket (Q315F mutation) led to two different structures, one of which (Q315F{sup *149}) has the oxoG lesion in an exosite flanking the active site and the other of which (Q315F{sup *292}) has the oxoG inserted nearly completely into the lesion recognition pocket. The latter structure offers a view of the latest stage in the base extrusion pathway yet observed, and its lack of catalytic activity demonstrates that the transition state for displacement of the lesion base is geometrically demanding.

  20. Remaining Sites Verification Package for the 100-B-1 Surface Chemical and Solid Waste Dumping Area, Waste Site Reclassification Form 2006-003

    SciTech Connect

    R. A. Carlson

    2006-04-24

    The 100-B-1 waste site was a dumping site that was divided into two areas. One area was used as a laydown area for construction materials, and the other area was used as a chemical dumping area. The 100-B-1 Surface Chemical and Solid Waste Dumping Area site meets the remedial action objectives specified in the Remaining Sites ROD. The results demonstrate that residual contaminant concentrations support future unrestricted land uses that can be represented by a rural-residential scenario. The results also demonstrate that residual contaminant concentrations are protective of groundwater and the Columbia River.

  1. TRITIUM UNCERTAINTY ANALYSIS FOR SURFACE WATER SAMPLES AT THE SAVANNAH RIVER SITE

    SciTech Connect

    Atkinson, R.

    2012-07-31

    Radiochemical analyses of surface water samples, in the framework of Environmental Monitoring, have associated uncertainties for the radioisotopic results reported. These uncertainty analyses pertain to the tritium results from surface water samples collected at five locations on the Savannah River near the U.S. Department of Energy's Savannah River Site (SRS). Uncertainties can result from the field-sampling routine, can be incurred during transport due to the physical properties of the sample, from equipment limitations, and from the measurement instrumentation used. The uncertainty reported by the SRS in their Annual Site Environmental Report currently considers only the counting uncertainty in the measurements, which is the standard reporting protocol for radioanalytical chemistry results. The focus of this work is to provide an overview of all uncertainty components associated with SRS tritium measurements, estimate the total uncertainty according to ISO 17025, and to propose additional experiments to verify some of the estimated uncertainties. The main uncertainty components discovered and investigated in this paper are tritium absorption or desorption in the sample container, HTO/H{sub 2}O isotopic effect during distillation, pipette volume, and tritium standard uncertainty. The goal is to quantify these uncertainties and to establish a combined uncertainty in order to increase the scientific depth of the SRS Annual Site Environmental Report.

  2. Final Clean Closure Report Site 300 Surface Impoundments Closure Lawrence Livermore National Laboratory Livermore, California

    SciTech Connect

    Haskell, K

    2006-02-14

    Lawrence Livermore National Laboratory operated two Class II surface impoundments that stored wastewater that was discharged from a number of buildings located on the Site 300 Facility (Site 300). The wastewater was the by-product of explosives processing. Reduction in the volume of water discharged from these buildings over the past several years significantly reduced the wastewater storage needs. In addition, the impoundments were constructed in 1984, and the high-density polyethylene (HDPE) geomembrane liners were nearing the end of their service life. The purpose of this project was to clean close the surface impoundments and provide new wastewater storage using above ground storage tanks at six locations. The tanks were installed and put into service prior to closure of the impoundments. This Clean Closure Report (Closure Report) complies with State Water Resources Control Board (SWRCB) Section 21400 of the California Code of Regulations Title 27 (27 CCR section 21400). As required by these regulations and guidance, this Closure Report provides the following information: (1) a brief site description; (2) the regulatory requirements relevant to clean closure of the impoundments; (3) the closure procedures; and (4) the findings and documentation of clean closure.

  3. Predicting Ligand Binding Sites on Protein Surfaces by 3-Dimensional Probability Density Distributions of Interacting Atoms

    PubMed Central

    Jian, Jhih-Wei; Elumalai, Pavadai; Pitti, Thejkiran; Wu, Chih Yuan; Tsai, Keng-Chang; Chang, Jeng-Yih; Peng, Hung-Pin; Yang, An-Suei

    2016-01-01

    Predicting ligand binding sites (LBSs) on protein structures, which are obtained either from experimental or computational methods, is a useful first step in functional annotation or structure-based drug design for the protein structures. In this work, the structure-based machine learning algorithm ISMBLab-LIG was developed to predict LBSs on protein surfaces with input attributes derived from the three-dimensional probability density maps of interacting atoms, which were reconstructed on the query protein surfaces and were relatively insensitive to local conformational variations of the tentative ligand binding sites. The prediction accuracy of the ISMBLab-LIG predictors is comparable to that of the best LBS predictors benchmarked on several well-established testing datasets. More importantly, the ISMBLab-LIG algorithm has substantial tolerance to the prediction uncertainties of computationally derived protein structure models. As such, the method is particularly useful for predicting LBSs not only on experimental protein structures without known LBS templates in the database but also on computationally predicted model protein structures with structural uncertainties in the tentative ligand binding sites. PMID:27513851

  4. Titan's surface spectra at the Huygens landing site and Shangri-La

    NASA Astrophysics Data System (ADS)

    Rannou, P.; Toledo, D.; Lavvas, P.; D'Aversa, E.; Moriconi, M. L.; Adriani, A.; Le Mouélic, S.; Sotin, C.; Brown, R.

    2016-05-01

    Titan is an icy satellite of Saturn with a dense atmosphere and covered by a global photochemical organic haze. Ground based observations and the Huygens descent probe allowed to retrieve the main spectral signature of the water ice (Griffith, C.A. et al. [2003]. Science 300(5619), 628-630; Coustenis, A. et al. [2005]. Icarus 177, 89-105) at the surface, possibly covered by a layer of sedimented organic material (Tomasko, M.G. et al. [2005]. Nature 438(7069), 765-778). However, the spectrum of the surface is not yet understood. In this study, we find that the surface reflectivity at the Huygens Landing Site (HLS) is well modeled by a layer of water ice grains overlaid by a moist layer of weakly compacted photochemical aggregated aerosols. Moist soils have spectra shifted toward short wavelengths relatively to spectra of dry soils. Cassini observations of Shangri-La region from orbit also show a very dark surface with a reflectivity peak shifted toward short wavelengths in respect to the reflectivity peak of bright surfaces, revealing a dichotomy between terrains based to their spectra in visible.

  5. Polymeric surfaces exhibiting photocatalytic activity and controlled anisotropic wettability

    NASA Astrophysics Data System (ADS)

    Anastasiadis, Spiros H.; Frysali, Melani A.; Papoutsakis, Lampros; Kenanakis, George; Stratakis, Emmanuel; Vamvakaki, Maria; Mountrichas, Grigoris; Pispas, Stergios

    2015-03-01

    In this work we focus on surfaces, which exhibit controlled, switchable wettability in response to one or more external stimuli as well as photocatalytic activity. For this we are inspired from nature to produce surfaces with a dual-scale hierarchical roughness and combine them with the appropriate inorganic and/or polymer coating. The combination of the hierarchical surface with a ZnO coating and a pH- or temperature-responsive polymer results in efficient photo-active properties as well as reversible superhydrophobic / superhydrophilic surfaces. Furthermore, we fabricate surfaces with unidirectional wettability variation. Overall, such complex surfaces require advanced design, combining hierarchically structured surfaces with suitable polymeric materials. Acknowledgment: This research was partially supported by the European Union (European Social Fund, ESF) and Greek national funds through the ``ARISTEIA II'' Action (SMART-SURF) of the Operational Programme ``Education and Lifelong Learning,'' NSRF 2007-2013, via the General Secretariat for Research & Technology, Ministry of Education and Religious Affairs, Greece.

  6. Screening breeding sites of the common toad (Bufo bufo) in England and Wales for evidence of endocrine disrupting activity.

    PubMed

    Pickford, Daniel B; Jones, Alexandra; Velez-Pelez, Alejandra; Orton, Frances; Iguchi, Taisen; Mitsui, Naoko; Tooi, Osamu

    2015-07-01

    Anuran amphibians are often present in agricultural landscapes and may therefore be exposed to chemicals in surface waters used for breeding. We used passive accumulation devices (SPMD and POCIS) to sample contaminants from nine breeding sites of the Common toad (Bufo bufo) across England and Wales, measuring endocrine activity of the extracts in a recombinant yeast androgen screen (YAS) and yeast estrogen screen (YES) and an in vitro vitellogenin induction screen in primary culture of Xenopus laevis hepatocytes. We also assessed hatching, growth, survival, and development in caged larvae in situ, and sampled metamorphs for gonadal histopathology. None of the SPMD extracts exhibited estrogen receptor or androgen receptor agonist activity, while POCIS extracts from two sites in west-central England exhibited concentration-dependent androgenic activity in the YAS. Three sites exhibited significant estrogenic activity in both the YES and the Xenopus hepatocyte. Hatching rates varied widely among sites, but there was no consistent correlation between hatching rate and intensity of agricultural activity, predicted concentrations of agrochemicals, or endocrine activity measured in YES/YAS assays. While a small number of intersex individuals were observed, their incidence could not be associated with predicted pesticide exposure or endocrine activitity measured in the in vitro screens. There were no significant differences in sex ratio, as determined by gonadal histomorphology among the study sites, and no significant correlation was observed between proportion of males and predicted exposure to agrochemicals. However, a negative correlation did become apparent in later sampling periods between proportion of males and estrogenic activity of the POCIS sample, as measured in the YES. Our results suggest that larval and adult amphibians may be exposed to endocrine disrupting chemicals in breeding ponds, albeit at low concentrations, and that chemical contaminants other than

  7. Influence of secondary treatment with CO2 laser irradiation for mitigation site on fused silica surface

    NASA Astrophysics Data System (ADS)

    Jiang, Yong; Zhou, Qiang; Qiu, Rong; Gao, Xiang; Wang, Hui-Li; Yao, Cai-Zhen; Wang, Jun-Bo; Zhao, Xin; Liu, Chun-Ming; Xiang, Xia; Zu, Xiao-Tao; Yuan, Xiao-Dong; Miao, Xin-Xiang

    2016-10-01

    The ablation debris and raised rim, as well as residual stress and deep crater will be formed during the mitigation of damage site with a CO2 laser irradiation on fused silica surface, which greatly affects the laser damage resistance of optics. In this study, the experimental study combined with numerical simulation is utilized to investigate the effect of the secondary treatment on a mitigated site by CO2 laser irradiation. The results indicate that the ablation debris and the raised rim can be completely eliminated and the depth of crater can be reduced. Notable results show that the residual stress of the mitigation site after treatment will reduce two-thirds of the original stress. Finally, the elimination and the controlling mechanism of secondary treatment on the debris and raised rim, as well as the reasons for changing the profile and stress are analyzed. The results can provide a reference for the optimization treatment of mitigation sites by CO2 laser secondary treatment. Project supported by the National Natural Science Foundation of China (Grant Nos. 61505170, 61505171, and 51535003), the Joint Fund of the National Natural Science Foundation of China, the Chinese Academy of Engineering Physics (Grant No. U1530109), and the China Postdoctoral Science Foundation (Grant No. 2016M592709).

  8. Surface site density, silicic acid retention and transport properties of compacted magnetite powder

    NASA Astrophysics Data System (ADS)

    Mayant, C.; Grambow, B.; Abdelouas, A.; Ribet, S.; Leclercq, S.

    In France, within the framework of investigations of the feasibility of deep geological disposal of high-level radioactive waste, studies on corrosion products of steel over packs are ongoing. Such studies concern silica and radionuclide retention. The objective of the present work is to study sorption of silicic acid on compacted magnetite in percolation cells to attempt to simulate confined site conditions. Potentiometric titration of commercial magnetite was carried out with both dispersed and compacted magnetite. The titration of the magnetite suspension has been made with two different methods: a batch method (several suspensions) and a direct fast method (one suspension). The Gran’s function gave 1.7 (±0.4) and 2.4 (±0.5) sorption sites nm -2 with these respective methods but site densities as high as 20/nm 2 could be obtained by modelling. The titration of magnetite compacted at 120 bars showed that the evolution of charge density on magnetite surfaces is similar for compacted and dispersed magnetite. Silicic acid sorption onto dispersed and compacted magnetite was similar with sorption site densities ranging between 2.2 and 4.4/nm 2.

  9. Evaluation of Cavity Collapse and Surface Crater Formation at the Salut Underground Nuclear Test in U20ak, Nevada National Security Site, and the Impact of Stability of the Ground Surface

    SciTech Connect

    Pawloski, G A

    2012-04-25

    At the request of Jerry Sweeney, the LLNL Containment Program performed a review of nuclear test-related data for the Salut underground nuclear test in U20ak to assist in evaluating this legacy site as a test bed for application technologies for use in On-Site Inspections (OSI) under the Comprehensive Nuclear Test Ban Treaty. Review of the Salut site is complicated because the test experienced a subsurface, rather than surface, collapse. Of particular interest is the stability of the ground surface above the Salut detonation point. Proposed methods for on-site verification include radiological signatures, artifacts from nuclear testing activities, and imaging to identify alteration to the subsurface hydrogeologogy due to the nuclear detonation. Sweeney's proposal requires physical access at or near the ground surface of specific underground nuclear test locations at the Nevada Nuclear Test Site (NNSS, formerly the Nevada Test Site), and focuses on possible activities such as visual observation, multispectral measurements, and shallow, and deep geophysical surveys.

  10. Lattice site dependent cathodoluminescence behavior and surface chemical changes in a Sr5(PO4)3F host

    NASA Astrophysics Data System (ADS)

    Nagpure, I. M.; Pitale, Shreyas S.; Coetsee, E.; Ntwaeaborwa, O. M.; Terblans, J. J.; Swart, H. C.

    2012-05-01

    Eu activated Sr5(PO4)3F phosphor powders have been subjected to the electron bombardment at 2 keV (10 μA) at an oxygen pressure of 1×10-6 Torr. The synthesized Sr5(PO4)3F phosphor was identical to the hexagonal apatite structure, with the Sr present at two different sites Cs (S1) and C3 (S2) in the Sr5(PO4)3F host, as inferred from the crystallographic study. Cathodoluminescence (CL) and Auger electron spectroscopy of the phosphor excited by the same electron beam were used to monitor changes in the surface state during prolonged electron bombardment. A direct correlation between the surface reactions and the degradation of the CL brightness was observed. Both C and F were depleted from the surface during electron bombardment. The postulated mechanism for the electron stimulated chemical reactions on the phosphor surface is electron beam dissociation of molecular species to atomic species, which subsequently react with C to form volatile compounds CO2, CH4, etc. and with Sr5(PO4)3F to form a non luminescence layer of metal oxides of Sr and P.

  11. (100) facets of γ-Al2O3: the active surfaces for alcohol dehydration reactions

    SciTech Connect

    Kwak, Ja Hun; Mei, Donghai; Peden, Charles HF; Rousseau, Roger J.; Szanyi, Janos

    2011-05-01

    Temperature programmed desorption (TPD) of ethanol, and methanol dehydration reaction were studied on γ-Al2O3 in order to identify the catalytic active sites for alcohol dehydration reactions. Two high temperature (> 473 K) desorption features were observed following ethanol adsorption. Samples calcined at T≤473 K displayed a desorption feature in the 523-533 K temperature range, while those calcined at T ≥ 673 K showed a single desorption feature at 498 K. The switch from the high to low temperature ethanol desorption correlated well with the dehydroxylation of the (100) facets of γ-Al2O3 that was predicted at 550 K DFT calculations. Theoretical DFT simulations of the mechanism of dehydration. on clean and hydroxylated γ-Al2O3(100) surfaces, find that a concerted elimination of ethylene from an ethanol molecule chemisorbed at an Al3+ pentacoordinated site is the rate limiting step for catalytic cycle on both surfaces. Furthermore, titration of the pentacoordinate Al3+ sites on the (100) facets of γ-Al2O3 by BaO completely turned off the methanol dehydration reaction activity. These results unambiguously demonstrate that only the (100) facets on γ-Al2O3 are the catalytic active surfaces for alcohol dehydration.

  12. Effects of sodium on cell surface and intracellular TH-naloxone binding sites

    SciTech Connect

    Pollack, A.E.; Wooten, G.F.

    1987-07-27

    The binding of the opiate antagonist TH-naloxone was examined in rat whole brain homogenates and in crude subcellular fractions of these homogenates (nuclear, synaptosomal, and mitochondrial fractions) using buffers that approximated intra- (low sodium concentration) and extracellular (high sodium concentration) fluids. Saturation studies showed a two-fold decrease in the dissociation constant (Kd) in all subcellular fractions examined in extracellular buffer compared to intracellular buffer. In contrast, there was no significant effect of the buffers on the Bmax. Thus, TH-naloxone did not distinguish between binding sites present on cell surface and intracellular tissues in these two buffers. These results show that the sodium effect of opiate antagonist binding is probably not a function of altered selection of intra- and extracellular binding sites. 17 references, 2 tables.

  13. Lunar Surface Closeup Stereoscopic Photography on the Ocean of Storms (Apollo 12 Landing Site)

    NASA Technical Reports Server (NTRS)

    Heiken, G.; Carrier, W. D., III

    1971-01-01

    To obtain information about in-place lunar rocks and soil, a closeup stereoscopic camera capable of photographing small scale surface features was used at the Apollo 12 landing site on the Ocean of Storms. Fifteen stereoscopic photograph pairs were obtained. The stereoscopic pairs were of excellent quality and showed the in-place lunar material in detail. The photographs were analyzed and the results compared with the results of the Apollo 12 core sample analysis and other investigations. Significant information about the physical composition and genesis of the lunar soil at the Apollo 12 landing site was obtained. The cohesive soil on the Ocean of Storms probably results from repetitive bombardment of basalt flows by meteorites over long periods of time.

  14. Mid-Piacenzian sea surface temperature record from ODP Site 1115 in the western equatorial Pacific

    USGS Publications Warehouse

    Stoll, Danielle

    2010-01-01

    Planktic foraminifer assemblages and alkenone unsaturation ratios have been analyzed for the mid-Piacen-zian (3.3 to 2.9 Ma) section of Ocean Drilling Program (ODP) Site 1115B, located in the western equatorial Pacific off the coast of New Guinea. Cold and warm season sea surface temperature (SST) estimates were determined using a modern analog technique. ODP Site 1115 is located just south of the transition between the planktic foraminifer tropical and subtropical faunal provinces and approximates the southern boundary of the western equatorial Pacific (WEP) warm pool. Comparison of the faunal and alkenone SST estimates (presented here) with an existing nannofossil climate proxy shows similar trends. Results of this analysis show increased seasonal variability during the middle of the sampled section (3.22 to 3.10 Ma), suggesting a possible northward migration of both the subtropical faunal province and the southern boundary of the WEP warm pool.

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

    PubMed

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

    2015-08-25

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

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

    SciTech Connect

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

    2015-08-25

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

  17. Activity of N-coordinated multi-metal-atom active site structures for Pt-free oxygen reduction reaction catalysis: Role of *OH ligands

    NASA Astrophysics Data System (ADS)

    Holby, Edward F.; Taylor, Christopher D.

    2015-03-01

    We report calculated oxygen reduction reaction energy pathways on multi-metal-atom structures that have previously been shown to be thermodynamically favorable. We predict that such sites have the ability to spontaneously cleave the O2 bond and then will proceed to over-bind reaction intermediates. In particular, the *OH bound state has lower energy than the final 2 H2O state at positive potentials. Contrary to traditional surface catalysts, this *OH binding does not poison the multi-metal-atom site but acts as a modifying ligand that will spontaneously form in aqueous environments leading to new active sites that have higher catalytic activities. These *OH bound structures have the highest calculated activity to date.

  18. Activity of N-coordinated multi-metal-atom active site structures for Pt-free oxygen reduction reaction catalysis: Role of *OH ligands

    DOE PAGES

    Holby, Edward F.; Taylor, Christopher D.

    2015-03-19

    We report calculated oxygen reduction reaction energy pathways on multi-metal-atom structures that have previously been shown to be thermodynamically favorable. We predict that such sites have the ability to spontaneously cleave the O₂ bond and then will proceed to over-bind reaction intermediates. In particular, the *OH bound state has lower energy than the final 2 H₂O state at positive potentials. Contrary to traditional surface catalysts, this *OH binding does not poison the multi-metal-atom site but acts as a modifying ligand that will spontaneously form in aqueous environments leading to new active sites that have higher catalytic activities. These *OH boundmore » structures have the highest calculated activity to date.« less

  19. Activity of N-coordinated multi-metal-atom active site structures for Pt-free oxygen reduction reaction catalysis: Role of *OH ligands

    SciTech Connect

    Holby, Edward F.; Taylor, Christopher D.

    2015-03-19

    We report calculated oxygen reduction reaction energy pathways on multi-metal-atom structures that have previously been shown to be thermodynamically favorable. We predict that such sites have the ability to spontaneously cleave the O₂ bond and then will proceed to over-bind reaction intermediates. In particular, the *OH bound state has lower energy than the final 2 H₂O state at positive potentials. Contrary to traditional surface catalysts, this *OH binding does not poison the multi-metal-atom site but acts as a modifying ligand that will spontaneously form in aqueous environments leading to new active sites that have higher catalytic activities. These *OH bound structures have the highest calculated activity to date.

  20. Activity of N-coordinated multi-metal-atom active site structures for Pt-free oxygen reduction reaction catalysis: Role of *OH ligands

    PubMed Central

    Holby, Edward F.; Taylor, Christopher D.

    2015-01-01

    We report calculated oxygen reduction reaction energy pathways on multi-metal-atom structures that have previously been shown to be thermodynamically favorable. We predict that such sites have the ability to spontaneously cleave the O2 bond and then will proceed to over-bind reaction intermediates. In particular, the *OH bound state has lower energy than the final 2 H2O state at positive potentials. Contrary to traditional surface catalysts, this *OH binding does not poison the multi-metal-atom site but acts as a modifying ligand that will spontaneously form in aqueous environments leading to new active sites that have higher catalytic activities. These *OH bound structures have the highest calculated activity to date. PMID:25788358

  1. Brachialis muscle activity can be assessed with surface electromyography.

    PubMed

    Staudenmann, Didier; Taube, Wolfgang

    2015-04-01

    The brachialis muscle (BR) represents an important elbow flexor and its activity has so far mainly been measured with intramuscular electromyography (EMG). The aim of this study was to examine whether the activity of the BR can be assessed with surface EMG without interference from the biceps brachii (BB). With eight subjects we measured surface EMG of the arm flexor synergists, BR, BB, and brachioradialis (BRR) during two isometric voluntary contraction types: (1) pure elbow flexion and (2) elbow flexion with a superimposed forearm supination. Since the BR and BB have a distinct biomechanical function, an individual activity of the BR can be expected for the second contraction type, if the BR can be assessed independently from the BB. The correlation coefficients between EMG amplitudes and flexion force (supination torque) were determined. During pure flexion the activities of all synergists were similarly correlated with the flexion force (r = 0.96 ± 0.02). During flexion+supination the activity of the BR was distinct from the activity of the BB, with a 14% higher correlation for the BR with the flexion force and a 40-64% lower correlation with the supination torque. The BB predicted supination torque substantially better than the BR and BRR (r = 0.93 ± 0.02). The current results demonstrate that the activity of the BR can be assessed with surface EMG as it was distinct from the BB during flexion+supination but predicted flexion force equally well as BB during the pure flexion contraction.

  2. The influence of small-mammal burrowing activity on water storage at the Hanford Site

    SciTech Connect

    Landeen, D.S.

    1994-12-31

    This paper summarizes the activities that were conducted in support of the long-term surface barrier development program by Westinghouse Hanford Company to determine the degree that small-mammal burrow systems affect the loss or retention of water in the soils at the Hanford Site in Washington state. An animal intrusion lysimeter facility was constructed, consisting of two outer boxes buried at grade, which served as receptacles for six animal intrusion lysimeters. Small burrowing animals common the Hanford Site were introduced over a 3- to 4-month period. Supplemental precipitation was added monthly to three of the lysimeters with a rainfall simulator (rainulator). Information collected from the five tests indicated that (1) during summer months, water was lost in all the lysimeters, including the supplemental precipitation added with the rainulator; and (2) during winter months, all lysimeters gained water. The data indicate little difference in the amount of water stored between control and animal lysimeters. The overall water loss was attributed to surface evaporation, a process that occurred equally in control and treatment lysimeters. Other causes of water loss are a result of (1) constant soil turnover and subsequent drying, and (2) burrow ventilation effects. This suggests that burrow systems will not contribute to any significant water storage at depth and, in fact, may enhance the removal of water from the soil.

  3. Meteorological data for four sites at surface-disruption features in Yucca Flat, Nevada Test Site, Nye County, Nevada, 1985--1986

    SciTech Connect

    Carman, R.L.

    1994-12-01

    Surface-disruption features, or craters, resulting from underground nuclear testing at the Nevada Test Site may increase the potential for ground-water recharge in an area that would normally produce little, if any, recharge. This report presents selected meteorological data resulting from a study of two surface-disruption features during May 1985 through June 1986. The data were collected at four adjacent sites in Yucca Flat, about 56 kilometers north of Mercury, Nevada. Three sites (one in each of two craters and one at an undisturbed site at the original land surface) were instrumented to collect meteorological data for calculating bare-soil evaporation. These data include (1) long-wave radiation, (2) short-wave radiation, (3) net radiation, (4) air temperature, and (5) soil surface temperature. Meteorological data also were collected at a weather station at an undisturbed site near the study craters. Data collected at this site include (1) air temperature, (2) relative humidity, (3) wind velocity, and (4) wind direction.

  4. Meteorological data for four sites at surface-disruption features in Yucca Flat, Nevada Test Site, Nye County, Nevada, 1985-86

    USGS Publications Warehouse

    Carman, Rita L.

    1994-01-01

    Surface-disruption features, or craters, resulting from underground nuclear testing at the Nevada Test Site may increase the potential for ground-water recharge in an area that would normally produce little, if any, recharge. This report presents selected meteorological data resulting from a study of two surface-disruption features during May 1985 through June 1986. The data were collected at four adjacent sites in Yucca Flat, about 56 kilometers north of Mercury, Nevada. Three sites (one in each of two craters and one at an undisturbed site at the original land surface) were instrumented to collect meteorological data for calculating bare-soil evaporation. These data include (1) long-wave radiation, (2) short-wave radiation, (3) net radiation, (4) air temperae, and (5) soil surface temperature. Meteorological data also were collected at a weather station at an undisturbed site near the study craters. Data collected at this site include (1) air temperature, (2) relative humidity, (3) wind velocity, and (4) wind direction.

  5. Dynamic Kinetics of Nitrogen Cycle in Groundwater-Surface Water Interaction Zone at Hanford Site

    NASA Astrophysics Data System (ADS)

    Liu, Y.; Liu, C.; Liu, Y.; Xu, F.; Yan, A.; Shi, L.; Zachara, J. M.; Gao, Y.; Qian, W.; Nelson, W.; Fredrickson, J.; Zhong, L.; Thompson, C.

    2015-12-01

    Nitrogen cycle carried out by microbes is an important geobiological process that has global implications for carbon and nitrogen cycling and climate change. This presentation describes a study of nitrogen cycle in groundwater-surface water interaction zone (GSIZ) at the US Department of Energy's Hanford Site. Groundwater at Hanford sites has long been documented with nitrate contamination. Nearby Columbia River stage changes of up to 3 m every day because of daily discharge fluctuation from upstream Priest Rapids Dam; resulting an exchange of groundwater and surface water in a short time period. Yet, nitrogen cycle in the GSIZ at Hanford Site remains unclear. Column studies have been used to identify nitrogen metabolism pathways and investigate kinetics of nitrogen cycle in groundwater saturated zone, surface water saturated zone, and GSIZ. Functional gene and protein abundances were determined by qPCR and PRISM-SRM (high-pressure, high-resolution separations coupled with intelligent selection and multiplexing for sensitive selected reaction monitoring) to identify key enzymatic reactions and metabolic pathways of nitrogen cycle. The results showed that dissimilatory nitrate reduction to ammonium (DNRA) competed with denitrification under anaerobic conditions, reducing 30% of NO3- to NH4+, a cation strongly retained on the sediments. As dissolved oxygen intruded the anaerobic zone with river water, NH4+ was oxidized to NO3-, increasing the mobility of NO3-. Multiplicative Monod models were established to describe nitrogen cycle in columns fed with O2 depleted synthetic groundwater and O2 saturated synthetic river water, respectively. The two models were then coupled to predict the dynamic kinetics of nitrogen cycle in GSIZ.

  6. Surface activation of dyed fabric for cellulase treatment.

    PubMed

    Schimper, Christian B; Ibanescu, Constanta; Bechtold, Thomas

    2011-10-01

    Surface activation of fabric made from cellulose fibres, such as viscose, lyocell, modal fibres and cotton, can be achieved by printing of a concentrated NaOH-containing paste. From the concentration of reducing sugars formed in solution, an increase in intensity of the cellulase hydrolysis by a factor of six to eight was observed, which was mainly concentrated at the activated parts of the fabric surface. This method of local activation is of particular interest for modification of materials that have been dyed with special processes to attain an uneven distribution of dyestuff within the yarn cross-section, e.g., indigo ring-dyed denim yarn for jeans production. Fabrics made from regenerated cellulose fibres were used as model substrate to express the effects of surface activation on indigo-dyed material. Wash-down experiments on indigo-dyed denim demonstrated significant colour removal from the activated surface at low overall weight loss of 4-5%. The method is of relevance for a more eco-friendly processing of jeans in the garment industry.

  7. Mutation at a Strictly Conserved, Active Site Tyrosine in the Copper Amine Oxidase Leads to Uncontrolled Oxygenase Activity

    SciTech Connect

    Chen, Zhi-wei; Datta, Saumen; DuBois, Jennifer L.; Klinman, Judith P.; Mathews, F. Scott

    2010-09-07

    The copper amine oxidases carry out two copper-dependent processes: production of their own redox-active cofactor (2,4,5-trihydroxyphenylalanine quinone, TPQ) and the subsequent oxidative deamination of substrate amines. Because the same active site pocket must facilitate both reactions, individual active site residues may serve multiple roles. We have examined the roles of a strictly conserved active site tyrosine Y305 in the copper amine oxidase from Hansenula polymorpha kinetically, spetroscopically (Dubois and Klinman (2006) Biochemistry 45, 3178), and, in the present work, structurally. While the Y305A enzyme is almost identical to the wild type, a novel, highly oxygenated species replaces TPQ in the Y305F active sites. This new structure not only provides the first direct detection of peroxy intermediates in cofactor biogenesis but also indicates the critical control of oxidation chemistry that can be conferred by a single active site residue.

  8. Viking landing sites, remote-sensing observations, and physical properties of Martian surface materials

    USGS Publications Warehouse

    Moore, H.J.; Jakosky, B.M.

    1989-01-01

    Important problems that confront future scientific exploration of Mars include the physical properties of Martian surface materials and the geologic processes that formed the materials. The design of landing spacecraft, roving vehicles, and sampling devices and the selection of landing sites, vehicle traverses, and sample sites will be, in part, guided by the physical properties of the materials. Four materials occur in the sample fields of the Viking landers: (1) drift, (2) crusty to cloddy, (3) blocky, and (4) rock. The first three are soillike. Drift materials is weak, loose, and porous. We estimate that it has a dielectric constant near 2.4 and a thermal inertia near 1 ?? 10-3 to 3 ?? 10-3 (cal cm-2 sec 1 2 K-1) because of its low bulk density, fine grain size, and small cohesion. Crusty to cloddy material is expected to have a dielectric constant near 2.8 and a thermal inertia near 4 ?? 10-3 to 7 ?? 10-3 because of its moderate bulk density and cementation of grains. Blocky material should have a dielectric constant near 3.3 and a thermal inertia near 7 ?? 10-3 to 9 ?? 10-3 because of its moderate bulk density and cementation. Common basaltic rocks have dielectric constans near 8 and thermal inertias near 30 ?? 10-3 to 60 ?? 10-3. Comparisons of estimated dielectric constants and thermal inertias of the materials at the landing sites with those obtained remotely by Earth-based radars and Viking Orbiter thermal sensors suggest that the materials at the landing sites are good analogs for materials elsewhere on Mars. Correlation of remotely estimated dielectric constant and thermal inertias indicates two modal values for paired values of dielectric constants and thermal inertias near (A) 2 and 2 ?? 10-3 and (B) 3 and 6 ?? 10-3, respectively. These two modes are comparable to the dielectric constants and thermal inertias for drift and crusty to cloddy material, respectively. Dielectric constants and thermal inertias for blocky material are larger but conistent

  9. Analyzing relationships between surface perturbations and local chemical reactivity of metal sites: Alkali promotion of O2 dissociation on Ag(111)

    NASA Astrophysics Data System (ADS)

    Xin, Hongliang; Linic, Suljo

    2016-06-01

    Many commercial heterogeneous catalysts are complex structures that contain metal active sites promoted by multiple additives. Developing fundamental understanding about the impact of these perturbations on the local surface reactivity is crucial for catalyst development and optimization. In this contribution, we develop a general framework for identifying underlying mechanisms that control the changes in the surface reactivity of a metal site (more specifically the adsorbate-surface interactions) upon a perturbation in the local environment. This framework allows us to interpret fairly complex interactions on metal surfaces in terms of specific, physically transparent contributions that can be evaluated independently of each other. We use Cs-promoted dissociation of O2 as an example to illustrate our approach. We concluded that the Cs adsorbate affects the outcome of the chemical reaction through a strong alkali-induced electric field interacting with the static dipole moment of the O2/Ag(111) system.

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

    PubMed Central

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

    2014-01-01

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

  11. Factor H-related proteins determine complement-activating surfaces.

    PubMed

    Józsi, Mihály; Tortajada, Agustin; Uzonyi, Barbara; Goicoechea de Jorge, Elena; Rodríguez de Córdoba, Santiago

    2015-06-01

    Complement factor H-related proteins (FHRs) are strongly associated with different diseases involving complement dysregulation, which suggests a major role for these proteins regulating complement activation. Because FHRs are evolutionarily and structurally related to complement inhibitor factor H (FH), the initial assumption was that the FHRs are also negative complement regulators. Whereas weak complement inhibiting activities were originally reported for these molecules, recent developments indicate that FHRs may enhance complement activation, with important implications for the role of these proteins in health and disease. We review these findings here, and propose that FHRs represent a complex set of surface recognition molecules that, by competing with FH, provide improved discrimination of self and non-self surfaces and play a central role in determining appropriate activation of the complement pathway.

  12. Effective removal of field-emitting sites from metallic surfaces by dry ice cleaning

    SciTech Connect

    Dangwal, Arti; Mueller, Guenter; Reschke, Detlef; Floettmann, Klaus; Singer, Xenia

    2007-08-15

    Systematic results of the field emission properties of polycrystalline copper and niobium and single-crystal Nb are reported. Dry ice cleaning (DIC) is found to suppress enhanced field emission from metallic surfaces. The cleaning effect on the emitting sites was investigated by means of field emission scanning microscopy up to fields of 250 MV/m and high-resolution scanning electron microscopy with energy dispersive x-ray analysis. The number density of emitters at given fields was drastically reduced by dry ice cleaning. Current-voltage measurements and derived Fowler-Nordheim parameters are partially discussed with respect to the morphology and impurity content of localized emitters. No emission from grain boundaries on large-grain Nb samples was observed. The microscopy results prove the effective removal of field-emitting particulates down to 400 nm as well as the partial smoothing of surface protrusions by DIC.

  13. Intramembrane Proton Binding Site Linked to Activation of Bacterial Pentameric Ion Channel*

    PubMed Central

    Wang, Hai-Long; Cheng, Xiaolin; Sine, Steven M.

    2012-01-01

    Prokaryotic orthologs of eukaryotic Cys-loop receptor channels recently emerged as structural and mechanistic surrogates to investigate this superfamily of intercellular signaling proteins. Here, we examine proton activation of the prokaryotic ortholog GLIC using patch clamp electrophysiology, mutagenesis, and molecular dynamics (MD) simulations. Whole-cell current recordings from human embryonic kidney (HEK) 293 cells expressing GLIC show half-maximal activation at pH 6, close to the pKa of histidine, implicating the three native His residues in proton sensing linked to activation. The mutation H235F abolishes proton activation, H277Y is without effect, and all nine mutations of His-127 prevent expression on the cell surface. In the GLIC crystal structure, His-235 on transmembrane (TM) α-helix 2, hydrogen bonds to the main chain carbonyl oxygen of Ile-259 on TM α-helix 3. MD simulations show that when His-235 is protonated, the hydrogen bond persists, and the channel remains in the open conformation, whereas when His-235 is deprotonated, the hydrogen bond dissociates, and the channel closes. Mutations of the proximal Tyr-263, which also links TM α-helices 2 and 3 via a hydrogen bond, alter proton sensitivity over a 1.5 pH unit range. MD simulations show that mutations of Tyr-263 alter the hydrogen bonding capacity of His-235. The overall findings show that His-235 in the TM region of GLIC is a novel proton binding site linked to channel activation. PMID:22084238

  14. Streamlined Approach for Environmental Restoration Plan for Corrective Action Unit 484: Surface Debris, Waste Sites, and Burn Area, Tonopah Test Range, Nevada

    SciTech Connect

    Bechel Nevada

    2004-05-01

    This Streamlined Approach for Environmental Restoration plan details the activities necessary to close Corrective Action Unit (CAU) 484: Surface Debris, Waste Sites, and Burn Area (Tonopah Test Range). CAU 484 consists of sites located at the Tonopah Test Range, Nevada, and is currently listed in Appendix III of the Federal Facility Agreement and Consent Order. CAU 484 consists of the following six Corrective Action Sites: (1) CAS RG-52-007-TAML, Davis Gun Penetrator Test; (2) CAS TA-52-001-TANL, NEDS Detonation Area; (3) CAS TA-52-004-TAAL, Metal Particle Dispersion Test; (4) CAS TA-52-005-TAAL, Joint Test Assembly DU Sites; (5) CAS TA-52-006-TAPL, Depleted Uranium Site; and (6) CAS TA-54-001-TANL, Containment Tank and Steel Structure

  15. Heavy metal contamination of surface soil in electronic waste dismantling area: site investigation and source-apportionment analysis.

    PubMed

    Jinhui Li; Huabo Duan; Pixing Shi

    2011-07-01

    The dismantling and disposal of electronic waste (e-waste) in developing countries is causing increasing concern because of its impacts on the environment and risks to human health. Heavy-metal concentrations in the surface soils of Guiyu (Guangdong Province, China) were monitored to determine the status of heavy-metal contamination on e-waste dismantling area with a more than 20 years history. Two metalloids and nine metals were selected for investigation. This paper also attempts to compare the data among a variety of e-waste dismantling areas, after reviewing a number of heavy-metal contamination-related studies in such areas in China over the past decade. In addition, source apportionment of heavy metal in the surface soil of these areas has been analysed. Both the MSW open-burning sites probably contained invaluable e-waste and abandoned sites formerly involved in informal recycling activities are the new sources of soil-based environmental pollution in Guiyu. Although printed circuit board waste is thought to be the main source of heavy-metal emissions during e-waste processing, requirement is necessary to soundly manage the plastic separated from e-waste, which mostly contains heavy metals and other toxic substances.

  16. An ionizable active-site tryptophan imparts catalase activity to a peroxidase core.

    PubMed

    Loewen, Peter C; Carpena, Xavi; Vidossich, Pietro; Fita, Ignacio; Rovira, Carme

    2014-05-21

    Catalase peroxidases (KatG's) are bifunctional heme proteins that can disproportionate hydrogen peroxide (catalatic reaction) despite their structural dissimilarity with monofunctional catalases. Using X-ray crystallography and QM/MM calculations, we demonstrate that the catalatic reaction of KatG's involves deprotonation of the active-site Trp, which plays a role similar to that of the distal His in monofunctional catalases. The interaction of a nearby mobile arginine with the distal Met-Tyr-Trp essential adduct (in/out) acts as an electronic switch, triggering deprotonation of the adduct Trp.

  17. Adsorption and characterization of MCPA on DDTMA- and raw-montmorillonite: Surface sites involved.

    PubMed

    Santiago, Cintia C; Fernández, Mariela A; Torres Sánchez, Rosa M

    2016-01-01

    The 4-chloro-2-methylphenoxy acid (MCPA) is an herbicide widely used in agriculture, which generates a great concern about contamination of surface water and serious consequences for human health and the environment. In this work, the adsorption of MCPA on an Argentine montmorillonite (MMT) and its organo-montmorillonite product (OMMT) with different dodecyl trimethyl ammonium loading was investigated. MCPA adsorption on OMMT increases at least 3 times, with respect to the amount determined for MMT. X-ray diffraction and zeta potential analyses indicated the inner (interlayer) and outer surface participate as adsorption sites. Changes in surface electric charge and also interlayer expansion suggest that dimethyl amine (MCPA counterion) was also surface-adsorbed. The larger aggregates of OMMT, without and with MCPA, obtained compared to those of MMT samples, generate an improvement in the coagulation efficiency. This property, particularly after MCPA retention, allows an easier separation of the solids from the solution and enables a simple technological process application. PMID:26786275

  18. Stable U(IV) complexes form at high-affinity mineral surface sites.

    PubMed

    Latta, Drew E; Mishra, Bhoopesh; Cook, Russell E; Kemner, Kenneth M; Boyanov, Maxim I

    2014-01-01

    Uranium (U) poses a significant contamination hazard to soils, sediments, and groundwater due to its extensive use for energy production. Despite advances in modeling the risks of this toxic and radioactive element, lack of information about the mechanisms controlling U transport hinders further improvements, particularly in reducing environments where U(IV) predominates. Here we establish that mineral surfaces can stabilize the majority of U as adsorbed U(IV) species following reduction of U(VI). Using X-ray absorption spectroscopy and electron imaging analysis, we find that at low surface loading, U(IV) forms inner-sphere complexes with two metal oxides, TiO2 (rutile) and Fe3O4 (magnetite) (at <1.3 U nm(-2) and <0.037 U nm(-2), respectively). The uraninite (UO2) form of U(IV) predominates only at higher surface loading. U(IV)-TiO2 complexes remain stable for at least 12 months, and U(IV)-Fe3O4 complexes remain stable for at least 4 months, under anoxic conditions. Adsorbed U(IV) results from U(VI) reduction by Fe(II) or by the reduced electron shuttle AH2QDS, suggesting that both abiotic and biotic reduction pathways can produce stable U(IV)-mineral complexes in the subsurface. The observed control of high-affinity mineral surface sites on U(IV) speciation helps explain the presence of nonuraninite U(IV) in sediments and has important implications for U transport modeling.

  19. Detecting Local Ligand-Binding Site Similarity in Non-Homologous Proteins by Surface Patch Comparison

    PubMed Central

    Sael, Lee; Kihara, Daisuke

    2012-01-01

    Functional elucidation of proteins is one of the essential tasks in biology. Function of a protein, specifically, small ligand molecules that bind to a protein, can be predicted by finding similar local surface regions in binding sites of known proteins. Here, we developed an alignment free local surface comparison method for predicting a ligand molecule which binds to a query protein. The algorithm, named Patch-Surfer, represents a binding pocket as a combination of segmented surface patches, each of which is characterized by its geometrical shape, the electrostatic potential, the hydrophobicity, and the concaveness. Representing a pocket by a set of patches is effective to absorb difference of global pocket shape while capturing local similarity of pockets. The shape and the physicochemical properties of surface patches are represented using the 3D Zernike descriptor, which is a series expansion of mathematical 3D function. Two pockets are compared using a modified weighted bipartite matching algorithm, which matches similar patches from the two pockets. Patch-Surfer was benchmarked on three datasets, which consist in total of 390 proteins that bind to one of 21 ligands. Patch-Surfer showed superior performance to existing methods including a global pocket comparison method, Pocket-Surfer, which we have previously introduced. Particularly, as intended, the accuracy showed large improvement for flexible ligand molecules, which bind to pockets in different conformations. PMID:22275074

  20. Noctis Landing: A Proposed Landing Site/Exploration Zone for Human Missions to the Surface of Mars

    NASA Technical Reports Server (NTRS)

    Lee, Pascal; Acedillo, Shannen; Braham, Stephen; Brown, Adrian; Elphic, Richard; Fong, Terry; Glass, Brian; Hoftun, Christopher; Johansen, Brage W.; Lorber, Kira; Mittlefehldt, David; Takagi, Yuta; Thomas, Peter; West, Michael; West, Stephen; Zolensky, Michael

    2015-01-01

    ) offer many such outcrop options. -­- Identifiable stratigraphic contacts and cross-cutting relationships from which relative ages can be determined. In place and collapsed canyon walls in NL, TC, and IC offer such opportunities. -­- Other types of ROIs include access points to surrounding plateau top areas for longer term regional exploration. A key attribute of the proposed Noctic Landing site is its strategic location to allow the shortest possible surface excusions to Tharsis and Valles Marineris (VM). VM is the feature and region on Mars that exposes the longest record of Mars' geology and evolution through time. Tharsis is the region of Mars that has experienced the longest and most extensive volcanic history, and might still be volcanically active. Some of the youngest lava flows on Mars have been identified on the western flanks of the Tharsis Bulge, i.e., within driving range of future longrange (500 - 1000 km) pressurized rover traverses. The proposed site also contains ROIs that offer the following Resources (incl. Civil Engineering) characteristics: -­- Access to raw material that exhibits the potential to (1) be used as feedstock for water-generating in situ resource utilization (ISRU) processes and (2) yield significant quantities (greater than 100 MT) of water. The raw material is likely in the form of hydrated minerals, and possibly ice/regolith mix. The top of the raw material deposit is at the surface. -­- Access to a region where infrastructure can be emplaced or constructed. This region is less than 5 km from the LS and contains flat, stable terrain. The region exhibits evidence for an abundant source of loose regolith. Several deep pits in the area combined with the availability of sand suggests that some natural terrain features can be adapted for construction purposes. -­- Access to raw material that exhibits the potential to be used as metal feedstock for ISRU and construction purposes. Iron and sulfur-rich mineral surface deposits have been

  1. Insight into both coverage and surface structure dependent CO adsorption and activation on different Ni surfaces from DFT and atomistic thermodynamics.

    PubMed

    Hao, Xiaobin; Wang, Baojun; Wang, Qiang; Zhang, Riguang; Li, Debao

    2016-06-29

    CO adsorption and activation on Ni(100), (110) and (111) surfaces have been systematically investigated to probe the effect of coverage and surface structure on CO adsorption and activation. Herein, dispersion-corrected density functional theory calculations (DFT-D) were employed, and the related thermodynamic energies at 523 K were calculated by including the zero-point energy, thermal energy and entropic corrections; the results show that the saturated coverage of CO on the Ni(111), (100) and (110) surfaces correspond to 8/9, 9/12 and 9/9 ML, respectively. As the coverage increases, the stepwise adsorption free energies decrease on the flat (111) and (100) surfaces, whereas small changes occur on the corrugated (110) surface. CO migrates from the three-fold hollow site to the top site on the (111) surface, and from the four-fold hollow to the two-fold bridge site on the (100) surface, while all the CO molecules remain at the short-bridge site on the (110) surface. As a result, the obtained intermolecular CO-CO repulsive interactions on the flat surface are stronger than the interactions on the corrugated surface. Furthermore, the computed CO vibrational frequencies at different levels of coverage over the Ni surfaces agree well with the experimental results. On the other hand, kinetic analyses were utilized to compare the stepwise CO desorption with the dissociation at different degrees of coverage on the three Ni surfaces. CO desorption is more favorable than its dissociation at all coverage levels on the most exposed Ni(111) surface. Analogously, CO desorption becomes more favorable than its dissociation on the Ni(110) surface at higher coverage, except for coverage of 1/9 ML, in which CO desorption competes with its dissociation. However, on the Ni(100) surface, CO dissociation is more favorable than its desorption at 1/12 ML; when the coverage increases from 2/12 to 3/12 ML, equilibrium states exist between dissociation and desorption over the surface; when

  2. Nuclear Site Security in the Event of Terrorist Activity

    SciTech Connect

    Thomson, M.L.; Sims, J.

    2008-07-01

    This paper, presented as a poster, identifies why ballistic protection should now be considered at nuclear sites to counter terrorist threats. A proven and flexible form of multi purpose protection is described in detail with identification of trial results that show its suitability for this role. (authors)

  3. Active Finger Recognition from Surface EMG Signal Using Bayesian Filter

    NASA Astrophysics Data System (ADS)

    Araki, Nozomu; Hoashi, Yuki; Konishi, Yasuo; Mabuchi, Kunihiko; Ishigaki, Hiroyuki

    This paper proposed an active finger recognition method using Bayesian filter in order to control a myoelectric hand. We have previously proposed a finger joint angle estimation method based on measured surface electromyography (EMG) signals and a linear model. However, when we estimate 2 or more finger angles by this estimation method, the estimation angle of the inactive finger is not accurate. This is caused by interference of surface EMG signal. To solve this interference problem, we proposed active finger recognition method from the amplitude spectrum of surface EMG signal using Bayesian filter. To confirm the effectiveness of this recognition method, we developed a myoelectric hand simulator that implements proposed recognition algorithm and carried out real-time recognition experiment.

  4. Geomagnetic activity and polar surface air temperature variability

    NASA Astrophysics Data System (ADS)

    Seppälä, A.; Randall, C. E.; Clilverd, M. A.; Rozanov, E.; Rodger, C. J.

    2009-10-01

    Here we use the ERA-40 and ECMWF operational surface level air temperature data sets from 1957 to 2006 to examine polar temperature variations during years with different levels of geomagnetic activity, as defined by the A p index. Previous modeling work has suggested that NO x produced at high latitudes by energetic particle precipitation can eventually lead to detectable changes in surface air temperatures (SATs). We find that during winter months, polar SATs in years with high A p index are different than in years with low A p index; the differences are statistically significant at the 2-sigma level and range up to about ±4.5 K, depending on location. The temperature differences are larger when years with wintertime Sudden Stratospheric Warmings (SSWs) are excluded. We take into account solar irradiance variations, unlike previous analyses of geomagnetic effects in ERA-40 and operational data. Although we cannot conclusively show that the polar SAT patterns are physically linked by geomagnetic activity, we conclude that geomagnetic activity likely plays a role in modulating wintertime surface air temperatures. We tested our SAT results against variation in the Quasi Biennial Oscillation, the El Niño Southern Oscillation and the Southern Annular Mode. The results suggested that these were not driving the observed polar SAT variability. However, significant uncertainty is introduced by the Northern Annular Mode, and we cannot robustly exclude a chance linkage between sea surface temperature variability and geomagnetic activity.

  5. Active Flow Control Strategies Using Surface Pressure Measurements

    NASA Technical Reports Server (NTRS)

    Kumar, Vikas; Alvi, Farrukh S.

    2010-01-01

    Evaluate the efficacy of Microjets Can we eliminate/minimize flow separation? Is the flow unsteadiness reduced? Guidelines for an active control Search for an appropriate sensor. Examine for means to develop a flow model for identifying the state of flow over the surface Guidelines toward future development of a Simple and Robust control methodology

  6. Field Summary Report for Remedial Investigation of Hanford Site Releases to the Columbia River, Hanford Site, Washington, Collection of Surface Water, River Sediments, and Island Soils

    SciTech Connect

    L. C. Hulstrom

    2009-09-28

    This report has been prepared in support of the remedial investigation of Hanford Site Releases to the Columbia River and describes the 2008/2009 data collection efforts. This report documents field activities associated with collection of sediment, river water, and soil in and adjacent to the Columbia River near the Hanford Site and in nearby tributaries.

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

    SciTech Connect

    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.

  8. Active Layer and Moisture Measurements for Intensive Site 0 and 1, Barrow, Alaska

    DOE Data Explorer

    John Peterson

    2015-04-17

    These are measurements of Active Layer Thickness collected along several lines beginning in September, 2011 to the present. The data were collected at several time periods along the Site0 L2 Line, the Site1 AB Line, and an ERT Monitoring Line near Area A in Site1.

  9. Discovering the active sites for C3 separation in MIL-100(Fe) by using operando IR spectroscopy.

    PubMed

    Wuttke, Stefan; Bazin, Philippe; Vimont, Alexandre; Serre, Christian; Seo, You-Kyong; Hwang, Young Kyu; Chang, Jong-San; Férey, Gérard; Daturi, Marco

    2012-09-17

    A reducible MIL-100(Fe) metal-organic framework (MOF) was investigated for the separation of a propane/propene mixture. An operando methodology was applied (for the first time in the case of a MOF) in order to shed light on the separation mechanism. Breakthrough curves were obtained as in traditional separation column experiments, but monitoring the material surface online, thus providing evidences on the adsorption sites. The qualitative and quantitative analyses of Fe(II) and, to some extent, Fe(III) sites were possible, upon different activation protocols. Moreover, it was possible to identify the nature and the role of the active sites in the separation process by selective poisoning of one family of sites: it was clearly evidenced that the unsaturated Fe(II) sites are mainly responsible for the separation effect of the propane/propene mixture, thanks to their affinity for the unsaturated bonds, such as the C=C entities in propene. The activity of the highly concentrated Fe(III) sites was also highlighted.

  10. [Aluminum coordination and active sites on aluminas, Y-zeolites and pillared layered silicates]. Progress report

    SciTech Connect

    Fripiat, J.J.

    1994-02-01

    This report is organized in four sections. In the first the authors will outline structural features which are common to all fine grained alumina, as well as to non-framework alumina in zeolites. This section will be followed by a study of the surface vs. bulk coordination of aluminum. The third section will deal with measurement of the number of acid sites and the scaling of their strength. The fourth and last section will describe three model reactions: the isomerization of 1-butene and of 2 cis-butene; the isomerization and disproportionation of oxtho-xylene; and the transformation of trichloroethane into vinyl chloride followed by the polymerization of the vinyl chloride. The relationship between chemical activity and selectivity and what is known of the local structure of the active catalytic sites will be underlined. Other kinds of zeolites besides Y zeolite have been studied. Instead of the aluminum pillared silicates they found it more interesting to study the substitution of silicon by aluminum in a layered structure containing a permanent porosity (aluminated sepiolite).

  11. Active Site, Catalytic Cycle, and Iodination Reactions of Vanadium Iodoperoxidase: A Computational Study.

    PubMed

    Pacios, Luis F; Gálvez, Oscar

    2010-05-11

    A combined computational study using molecular surfaces and Poisson-Boltzmann electrostatic potentials for proteins and quantum calculations on complexes representing the vanadate cofactor throughout the catalytic cycle is employed to study the activity of vanadium iodoperoxidase (VIPO) from alga Laminaria digitata . A model structure of VIPO is compared with available crystal structures of chloroperoxidases (VClPOs) and bromoperoxidases (VBrPOs) focusing on properties of the active site that concern halogen specificity. It is found that VIPO displays distinctive features regarding electrostatic potentials at the site cavity and the local topography of the cavity entrance. Quantum calculations on cofactor stages throughout the catalytic cycle reveal that, while steps involving binding of hydrogen peroxide and halide oxidization agree with available data on VBrPO, final formation and subsequent release of hypohalous acid could follow a different pathway consisting of His476-assisted protonation of bonded hypoiodite and further displacement by a water molecule. Ab initio free energies of reaction computed to explore iodination of organic substrates predict strongly exoergonic reactions with HOI, whereas other possible iodination reagents give thermodynamically disfavored reactions.

  12. Evaluating Nonpolar Surface Area and LC/MS Response: An Application for Site Occupancy Measurements for Enzyme Intermediates in Polyketide Biosynthesis

    PubMed Central

    Randall, Shan M.; Koryakina, Irina; Williams, Gavin J.; Muddiman, David C.

    2014-01-01

    RATIONALE Site occupancy measurements using LC/MS are reported throughout the literature. However, site occupancy quantification suffers from ionization bias between modified and unmodified peptides containing the active site. In this study, we explore the MS signal as a function of nonpolar surface area (NPSA) in order to better understand this bias in electrospray response. The correlation between hydrophobicity and LC/MS response was evaluated and applied to study enzyme intermediates in polyketide synthases. METHODS Site occupancy methods were developed to study acyltransferase activity. To further evaluate these methods, several standard peptides containing one cysteine residue were modified with alkylation reagents of increasing hydrophobicity to study the MS signal as a function of nonpolar surface area. RESULTS A consistent trend in MS response was observed which is dependent on the NPSA of the analyte. An optimal NPSA zone was observed for the peptides studied. CONCLUSIONS Nonpolar surface area can be used as metric to determine relative LC/MS response for peptides and evaluate site occupancy measurements. PMID:25366398

  13. Analysis of multi-temporal landsat satellite images for monitoring land surface temperature of municipal solid waste disposal sites.

    PubMed

    Yan, Wai Yeung; Mahendrarajah, Prathees; Shaker, Ahmed; Faisal, Kamil; Luong, Robin; Al-Ahmad, Mohamed

    2014-12-01

    This studypresents a remote sensing application of using time series Landsat satellite images for monitoring the Trail Road and Nepean municipal solid waste (MSW) disposal sites in Ottawa, Ontario, Canada. Currently, the Trail Road landfill is in operation; however, during the 1960s and 1980s, the city relied heavily on the Nepean landfill. More than 400 Landsat satellite images were acquired from the US Geological Survey (USGS) data archive between 1984 and 2011. Atmospheric correction was conducted on the Landsat images in order to derive the landfill sites' land surface temperature (LST). The findings unveil that the average LST of the landfill was always higher than the immediate surrounding vegetation and air temperature by 4 to 10 °C and 5 to 11.5 °C, respectively. During the summer, higher differences of LST between the landfill and its immediate surrounding vegetation were apparent, while minima were mostly found in fall. Furthermore, there was no significant temperature difference between the Nepean landfill (closed) and the Trail Road landfill (active) from 1984 to 2007. Nevertheless, the LST of the Trail Road landfill was much higher than the Nepean by 15 to 20 °C after 2007. This is mainly due to the construction and dumping activities (which were found to be active within the past few years) associated with the expansion of the Trail Road landfill. The study demonstrates that the use of the Landsat data archive can provide additional and viable information for the aid of MSW disposal site monitoring. PMID:25150051

  14. RAFT microemulsion polymerization with surface-active chain transfer agent

    NASA Astrophysics Data System (ADS)

    El-Hedok, Ibrahim Adnan

    The work described in this dissertation focuses on enhancing the polymer nanoparticle synthesis using RAFT (reversible-addition fragmentation chain transfer) in microemulsion polymerization in order to achieve predetermined molecular weight with narrow molecular weight polydispersity. The hypothesis is that the use of an amphiphilic chain transfer agent (surface-active CTA) will confine the CTA to the surface of the particle and thermodynamically favor partitioning of the CTA between micelles and particles throughout the polymerization. Thus, the CTA diffusion from micelles to polymer particles would be minimized and the breadth of the CTA per particle distribution would remain low. We report the successful improved synthesis of poly(butyl acrylate), poly(ethyl acrylate), and poly(styrene) nanoparticles using the RAFT microemulsion polymerization with surface-active CTA. The polymerization kinetics, polymer characteristics and latex size experimental data are presented. The data analysis indicates that the CTA remains partitioned between the micelles and particles by the end of the polymerization, as expected. We also report the synthesis of well-defined core/shell poly(styrene)/poly(butyl acrylate) nanoparticle, having polydispersity index value of 1.1, using semi-continuous microemulsion polymerization with the surface-active CTA. The surface-active CTA restricts the polymerization growth to the surface of the particle, which facilitates the formation of a shell block co-polymers with each subsequent second monomer addition instead of discrete homopolymers. This synthesis method can be used to create a wide range of core/shell polymer nanoparticles with well-defined morphology, given the right feeding conditions.

  15. Influence of surface charge, binding site residues and glycosylation on Thielavia terrestris cutinase biochemical characteristics.

    PubMed

    Shirke, Abhijit N; Basore, Danielle; Holton, Samantha; Su, An; Baugh, Evan; Butterfoss, Glenn L; Makhatadze, George; Bystroff, Christopher; Gross, Richard A

    2016-05-01

    Cutinases are esterases of industrial importance for applications in recycling and surface modification of polyesters. The cutinase from Thielavia terrestris (TtC) is distinct in terms of its ability to retain its stability and activity in acidic pH. Stability and activity in acidic pHs are desirable for esterases as the pH of the reaction tends to go down with the generation of acid. The pH stability and activity are governed by the charged state of the residues involved in catalysis or in substrate binding. In this study, we performed the detailed structural and biochemical characterization of TtC coupled with surface charge analysis to understand its acidic tolerance. The stability of TtC in acidic pH was rationalized by evaluating the contribution of charge interactions to the Gibbs free energy of unfolding at varying pHs. The activity of TtC was found to be limited by substrate binding affinity, which is a function of the surface charge. Additionally, the presence of glycosylation affects the biochemical characteristics of TtC owing to steric interactions with residues involved in substrate binding. PMID:26758295

  16. Structural mechanism of RuBisCO activation by carbamylation of the active site lysine

    PubMed Central

    Stec, Boguslaw

    2012-01-01

    Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is a crucial enzyme in carbon fixation and the most abundant protein on earth. It has been studied extensively by biochemical and structural methods; however, the most essential activation step has not yet been described. Here, we describe the mechanistic details of Lys carbamylation that leads to RuBisCO activation by atmospheric CO2. We report two crystal structures of nitrosylated RuBisCO from the red algae Galdieria sulphuraria with O2 and CO2 bound at the active site. G. sulphuraria RuBisCO is inhibited by cysteine nitrosylation that results in trapping of these gaseous ligands. The structure with CO2 defines an elusive, preactivation complex that contains a metal cation Mg2+ surrounded by three H2O/OH molecules. Both structures suggest the mechanism for discriminating gaseous ligands by their quadrupole electric moments. We describe conformational changes that allow for intermittent binding of the metal ion required for activation. On the basis of these structures we propose the individual steps of the activation mechanism. Knowledge of all these elements is indispensable for engineering RuBisCO into a more efficient enzyme for crop enhancement or as a remedy to global warming. PMID:23112176

  17. Methanol Synthesis over Cu/ZnO/Al2O3: The Active Site in Industrial Catalysis

    SciTech Connect

    Behrens, Malte

    2012-03-28

    Unlike homogeneous catalysts, heterogeneous catalysts that have been optimized through decades are typically so complex and hard to characterize that the nature of the catalytically active site is not known. This is one of the main stumbling blocks in developing rational catalyst design strategies in heterogeneous catalysis. We show here how to identify the crucial atomic structure motif for the industrial Cu/ZnO/Al{sub 2}O{sub 3} methanol synthesis catalyst. Using a combination of experimental evidence from bulk-, surface-sensitive and imaging methods collected on real high-performance catalytic systems in combination with DFT calculations. We show that the active site consists of Cu steps peppered with Zn atoms, all stabilized by a series of well defined bulk defects and surface species that need jointly to be present for the system to work.

  18. Using catalytic atom maps to predict the catalytic functions present in enzyme active sites.

    PubMed

    Nosrati, Geoffrey R; Houk, K N

    2012-09-18

    Catalytic atom maps (CAMs) are minimal models of enzyme active sites. The structures in the Protein Data Bank (PDB) were examined to determine if proteins with CAM-like geometries in their active sites all share the same catalytic function. We combined the CAM-based search protocol with a filter based on the weighted contact number (WCN) of the catalytic residues, a measure of the "crowdedness" of the microenvironment around a protein residue. Using this technique, a CAM based on the Ser-His-Asp catalytic triad of trypsin was able to correctly identify catalytic triads in other enzymes within 0.5 Å rmsd of the CAM with 96% accuracy. A CAM based on the Cys-Arg-(Asp/Glu) active site residues from the tyrosine phosphatase active site achieved 89% accuracy in identifying this type of catalytic functionality. Both of these CAMs were able to identify active sites across different fold types. Finally, the PDB was searched to locate proteins with catalytic functionality similar to that present in the active site of orotidine 5'-monophosphate decarboxylase (ODCase), whose mechanism is not known with certainty. A CAM, based on the conserved Lys-Asp-Lys-Asp tetrad in the ODCase active site, was used to search the PDB for enzymes with similar active sites. The ODCase active site has a geometry similar to that of Schiff base-forming Class I aldolases, with lowest aldolase rmsd to the ODCase CAM at 0.48 Å. The similarity between this CAM and the aldolase active site suggests that ODCase has the correct catalytic functionality present in its active site for the generation of a nucleophilic lysine. PMID:22909276

  19. Using Catalytic Atom Maps to Predict the Catalytic Functions Present in Enzyme Active Sites

    PubMed Central

    Nosrati, Geoffrey R.; Houk, K. N.

    2012-01-01

    Catalytic Atom Maps (CAMs) are minimal models of enzyme active sites. The structures in the Protein Data Bank (PDB) were examined to determine if proteins with CAM-like geometries in their active sites all share the same catalytic function. We combined the CAM-based search protocol with a filter based on the weighted contact number (WCN) of the catalytic residues, a measure of the “crowdedness” of the microenvironment around a protein residue. Using this technique, a CAM based on the Ser-His-Asp catalytic triad of trypsin was able to correctly identify catalytic triads in other enzymes within 0.5 Å RMSD of the Catalytic Atom Map with 96% accuracy. A CAM based on the Cys-Arg-(Asp/Glu) active site residues from the tyrosine phosphatase active site achieved 89% accuracy in identifying this type of catalytic functionality. Both of these Catalytic Atom Maps were able to identify active sites across different fold types. Finally, the PDB was searched to locate proteins with catalytic functionality similar to that present in the active site of orotidine 5′-monophosphate decarboxylase (ODCase), whose mechanism is not known with certainty. A CAM, based on the conserved Lys-Asp-Lys-Asp tetrad in the ODCase active site, was used to search the PDB for enzymes with similar active sites. The ODCase active site has a geometry similar to that of Schiff base-forming Class I aldolases, with lowest aldolase RMSD to the ODCase CAM at 0.48 Å. The similarity between this CAM and the aldolase active site suggests that ODCase has the correct catalytic functionality present in its active site for the generation of a nucleophilic lysine. PMID:22909276

  20. Site-specific patterning of highly ordered nanocrystal superlattices through biomolecular surface confinement.

    PubMed

    Noh, Hyunwoo; Choi, Chulmin; Hung, Albert M; Jin, Sungho; Cha, Jennifer N

    2010-09-28

    With the increasing demand in recent years for high-performance devices for both energy and health applications, there has been extensive research to direct the assembly of nanoparticles into meso- or macroscale single two- and three-dimensional crystals of arbitrary configuration or orientation. Inorganic nanoparticle arrays can have intriguing physical properties that differ from either individual nanoparticles or bulk materials. For most device applications, it is necessary to fabricate two-dimensional nanoparticle superlattices at programmed sites on a surface. However, it has remained a significant challenge to generate patterned arrays with long-range positional order because most highly ordered close-packed nanocrystal arrays are typically obtained by kinetically driven evaporation processes. In this report, we demonstrate a method to generate patterned nanocrystal superlattices by confining nanoparticles to geometrically defined 2-D DNA sites on a surface and using associative biomolecular interparticle interactions to produce thermodynamically stable arrays of hexagonally packed nanocrystals with significant long-range order observed over 1-2 μm. We also demonstrate the role of chemical and geometrical confinement on particle packing and obtaining long-range order. Finally, we also demonstrate that the formation of DNA-mediated nanocrystal superlattices requires both interparticle DNA hybridization and solvent-less thermal annealing.