Showing papers by "Pacific Northwest National Laboratory published in 1995"
TL;DR: In this paper, a method for finding free energy barriers for transitions in high-dimensional classical and quantum systems is presented and used to calculate the dissociative sticking probability of H 2 on a metal surface within the transition state theory.
1,880 citations
TL;DR: The measurement of dipolar contributions to the splitting of 15N resonances of 1H-15N amide pairs in multidimensional high-field NMR spectra of field-oriented cyanometmyoglobin is reported and implications as an additional source of information for protein structure determination in solution are discussed.
Abstract: The measurement of dipolar contributions to the splitting of 15N resonances of 1H-15N amide pairs in multidimensional high-field NMR spectra of field-oriented cyanometmyoglobin is reported. The splittings appear as small field-dependent perturbations of normal scalar couplings. Assignment of more than 90 resonances to specific sequential sites in the protein allows correlation of the dipolar contributions with predictions based on the known susceptibility and known structure of the protein. Implications as an additional source of information for protein structure determination in solution are discussed.
750 citations
TL;DR: In this article, the authors detected communities of autotrophic methanogenesis in deep crystalline rock aquifers within the Columbia River Basalt Group (CRB) and found that the ground waters contained up to 60 μM dissolved H 2 and autotrophs outnumbered heterotrophic microorganisms.
Abstract: Bacterial communities were detected in deep crystalline rock aquifers within the Columbia River Basalt Group (CRB). CRB ground waters contained up to 60 μM dissolved H 2 and autotrophic microorganisms outnumbered heterotrophs. Stable carbon isotope measurements implied that autotrophic methanogenesis dominated this ecosystem and was coupled to the depletion of dissolved inorganic carbon. In laboratory experiments, H 2 , a potential energy source for bacteria, was produced by reactions between crushed basalt and anaerobic water. Microcosms containing only crushed basalt and ground water supported microbial growth. These results suggest that the CRB contains a lithoautotrophic microbial ecosystem that is independent of photosynthetic primary production.
683 citations
TL;DR: In this paper, a comprehensive review of radiation effects due to γ-, β- and α-decay events, as well as from actinide doping experiments and particle irradiations, on nuclear waste form glasses and crystalline ceramics was provided.
582 citations
TL;DR: In this paper, a series of kinetic-batch studies was conducted to determine the capability of zero-valent iron (Fe0) to remove a wide range of highly mobile contaminants in groundwater.
367 citations
TL;DR: Suggested approaches to the modelling include the application of a number of powerful techniques, such as percolation theory, fractal analysis, lattice-based microstructure models, the renormalization group, neural networks, and fuzzy logic.
Abstract: This review contains a description of modelling studies relative to functionally graded materials (FGMs). Two principal topics are covered: models for microstructure-dependent thermophysical properties, and models for the design, processing, and performance of FGMs. The former is a particularly important input to FGM modelling because of the wide variety of microstructures that can exist across the graded direction of a single material. Based on the work described in this review, recommendations are made regarding areas in which additional modelling studies would be beneficial. Suggested approaches to the modelling include the application of a number of powerful techniques, such as percolation theory, fractal analysis, lattice-based microstructure models, the renormalization group, neural networks, and fuzzy logic.
321 citations
TL;DR: In this article, the authors proposed that zircon be used as a waste form for the disposal of the more than 100 metric tons of plutonium that will result from the dismantling of nuclear weapons.
Abstract: Zircon, ZrSiO4, is a well-characterized, naturally occurring phase that is extremely durable. Zircon has been synthesized with Pu-concentrations up to 10 wt. % and radiation-damage effects studied to saturation doses of nearly 0.8 displacements per atom. We propose that zircon be used as a waste form for the disposal of the more than 100 metric tons of plutonium that will result from the dismantling of nuclear weapons. There are already several demonstrated processing technologies, of which hot pressing offers the most potential. This highly durable material, even under hydrothermal conditions, with its high waste loading and smaller volume allows deep, permanent disposal of the weapons plutonium in geologic environments in which the borosilicate waste-form glass would not be stable.
290 citations
TL;DR: In this paper, the authors used X-ray diffraction, Raman Spectroscopy, Atomic Force Microscopy, optical transmission and ellipsometry measurements to characterize zinc oxide films with respect to crystalline phase and phase stability.
270 citations
TL;DR: In this article, a site-binding model was applied that treated SWy-1 as an aggregate of fixed-charge sites and edge sites analogous to gibbsite and silica, and results were modeled to identify likely surface complexation reactions responsible for removal ofuranyl from solution.
Abstract: Adsorption of uranyl to SWy- 1 montmorillonite was evaluated experimentally and results were modeled to identify likely surface complexation reactions responsible for removal ofuranyl from solution. Uranyl was contacted with SWy- 1 montmorillonite in a NaC104 electrolyte solution at three ionic strengths (I = 0.001, 0.01, 0.1), at pH 4 to 8.5, in a N2~) atmosphere. At low ionic strength, adsorption decreased from 95% at pH 4 to 75% at pH 6.8. At higher ionic strength, adsorption increased with pH from initial values less than 75%; adsorption edges for all ionic strengths coalesced above a pH of 7. A site-binding model was applied that treated SWy-1 as an aggregate of fixed-charge sites and edge sites analogous to gibbsite and silica. The concentration of fixed-charge sites was estimated as the cation exchange capacity, and non-preference exchange was assumed in calculating the contribution of fixed-charge sites to total uranyl adsorption. The concentration of edge sites was estimated by image analysis of transmission electron photomicrographs. Adsorption constants for uranyl binding to gibbsite and silica were determined by fitting to experimental data, and these adsorption constants were then used to simulate SWy-1 adsorption results. The best simulations were obtained with an ionization model in which A1OH2 + was the dominant aluminol surface species throughout the experimental range in pH. The pH-dependent aqueous speciation of uranyl was an important factor determining the magnitude of uranyl adsorption. At low ionic strength and low pH, adsorption by fixed-charge sites was predominant. The decrease in adsorption with increasing pH was caused by the formation of monovalent aqueous uranyl species, which were weakly bound to fixed-charge sites. At higher ionic strengths, competition with Na + decreased the adsorption of UOz 2+ to fixed-charge sites. At higher pH, the most significant adsorption reactions were the binding of UP22+ to A1OH and of(UO2)3(OH)5 + tO SiOH edge sites. Near-saturation of A1OH sites by UOz 1+ allowed significant contributions of SiOH sites to uranyl adsorption.
257 citations
TL;DR: A review of the hydrogen permeation barriers which can be applied to the structural metals used in fusion power plants is presented in this article, where the need for barriers appears strongest in Pb-17Li blanket designs, although barriers are also necessary for other blanket and coolant systems.
234 citations
TL;DR: The 2D computation reveals insight into the lifetime behaviors and provides guidance for nonperturbative spectroscopic measurements with NSOM, capable of predicting molecular emission properties in front of a metal/dielectric interface of arbitrary geometry.
Abstract: In near-field scanning optical microscopy (NSOM), the measured fluorescence lifetime of a single dye molecule can be shortened or lengthened, sensitively dependent on the relative position between the molecule and aluminum coated fiber tip. The modified lifetimes and other emission characteristics are simulated by solving Maxwell equations with the finite-difference time-domain (FDTD) method. The 2D computation reveals insight into the lifetime behaviors and provides guidance for nonperturbative spectroscopic measurements with NSOM. This new methodology is capable of predicting molecular emission properties in front of a metal/dielectric interface of arbitrary geometry.
TL;DR: The results indicate that bacteria within the genus Sphingomonas are present in Southeast Coastal Plain subsurface sediments and that the capacity for degrading a broad range of substituted aromatic compounds appears to be common among Spindingomonas species from this environment.
Abstract: An obligately aerobic chemoheterotrophic bacterium (strain F199) previously isolated from Southeast Coastal Plain subsurface sediments and shown to degrade toluene, naphthalene, and other aromatic compounds (J. K. Fredrickson, F. J. Brockman, D. J. Workman, S. W. Li, and T. O. Stevens, Appl. Environ. Microbiol. 57:796-803, 1991) was characterized by analysis of its 16S rRNA nucleotide base sequence and cellular lipid composition. Strain F199 contained 2-OH14:0 and 18:1 omega 7c as the predominant cellular fatty acids and sphingolipids that are characteristic of the genus Sphingomonas. Phylogenetic analysis of its 16S rRNA sequence indicated that F199 was most closely related to Sphingomonas capsulata among the bacteria currently in the Ribosomal Database. Five additional isolates from deep Southeast Coastal Plain sediments were determined by 16S rRNA sequence analysis to be closely related to F199. These strains also contained characteristic sphingolipids. Four of these five strains could also grow on a broad range of aromatic compounds and could mineralize [14C]toluene and [14C]naphthalene. S. capsulata (ATCC 14666), Sphingomonas paucimobilis (ATCC 29837), and one of the subsurface isolates were unable to grow on any of the aromatic compounds or mineralize toluene or naphthalene. These results indicate that bacteria within the genus Sphingomonas are present in Southeast Coastal Plain subsurface sediments and that the capacity for degrading a broad range of substituted aromatic compounds appears to be common among Sphingomonas species from this environment.
TL;DR: In this article, the adsorption of liquid and vapor water on defective and nearly defect-free TiO 2 (110) surfaces has been studied using X-ray photoelectron spectroscopy (XPS) and ultraviolet photoemission spectrum analysis (UPS).
TL;DR: In this paper, it was shown that hydrophobic adsorption, rather than phase partitioning, is the primary sorption mechanism for neutral organic molecules on these particle coatings and that mineral-bound humic materials may, therefore, provide a major sink for the removal of contaminants in groundwater.
TL;DR: In this article, the Hartree-Fock and correlated levels of theory using the correlation consistent sequence of basis sets were used to estimate the degree of convergence in the computed properties with respect to the complete basis set limit.
Abstract: Ionic clusters comprised of a single alkali metal cation and up to eight water molecules were studied at the Hartree–Fock and correlated levels of theory using the correlation consistent sequence of basis sets. Estimates of the degree of convergence in the computed properties with respect to the complete basis set limit were facilitated by the underlying systematic manner in which the correlation consistent sets approach completeness. In favorable cases, improved property values could be obtained by fitting finite basis set results with a simple analytical expression in order to extrapolate to the complete basis set limit. The sensitivity of structures and binding energies were analyzed with regard to the inclusion of valence and core‐valence correlation recovery at the MP2, MP4, and CCSD(T) levels of theory. The replacement of metal core electrons and the introduction of relativistic contributions via effective core potentials was compared to corresponding all‐electron results.
TL;DR: The work demonstrates that ESI-MS has significant potential for measuring relative binding affinities and characterizing the structures of ligands associated noncovalently to proteins and should be widely useful in medicinal chemistry.
Abstract: We report a method based on mass spectrometry for the characterization of noncovalent complexes of proteins with mixtures of ligands; this method is relevant to the study of drug leads and may be useful in screening libraries for tight-binding compounds. This study describes the competitive binding of inhibitors derived from para-substituted benzenesulfonamides to bovine carbonic anhydrase II (BCAII, EC 4.2.1.1) using this technique. Relative binding constants and structural information for a mixture of inhibitors can be obtained in a single experiment using ESI-FTICR-MS. The work demonstrates that ESI-MS has significant potential for measuring relative binding affinities and characterizing the structures of ligands associated noncovalently to proteins. We have detected noncovalent complexes in the gas phase for ligands having values of K{sub b} as low as 1.7 x 10{sup 6} M{sup -1} in solution. The technique also allowed identification of tightbinding ligands from small libraries. The structures of inhibitors having similar masses can be identified by the high-resolution and multistep dissociation mass spectrometry of which FTICR is uniquely capable. This range of capabilities for ESI-FTICR-MS should be widely useful in medicinal chemistry. 22 refs., 2 figs.
TL;DR: In this article, the crystal structures of MgAl 2 O 4 spinel single crystals irradiated to high neutron fluences (> 5 x 10 26 n/m 2 (E n > 0.1 MeV)), were examined by neutron diffraction.
TL;DR: In this article, high-soluble amphiphilic materials are shown to form aggregates in supercritical CO{sub 2}. The strategy for synthesis of these materials involves incorporating CO-sub 2-philic segments that, for example, are perfluorinated alkyl chains.
Abstract: Highly soluble amphiphilic materials are shown to form aggregates in supercritical CO{sub 2}. The strategy for synthesis of these amphiphilic molecules involves incorporating CO{sub 2}-philic segments that, for this study, are perfluorinated alkyl chains. These CO{sub 2} -philic regions function like the hydrocarbon tails of conventional surfactant molecules used in liquid organic solvents. Synthesis and characterization of three different CO{sub 2} amphiphiles are reported. Subsequent small angle X-ray scattering (SAXS) measurements were used to characterize the aggregation of these materials in supercritical CO{sub 2}. Each of the three amphiphiles studied showed a different type of aggregation behavior. A graft copolymer consisting of a CO{sub 2}-philic backbone and CO{sub 2}-phobic grafts associated into a micellar structure in the presence of water to promote hydrogen bonding. These aggregates contain approximately 600 grafts in the core. The commercially available surfactant perfluoroalkylpoly( ethylene oxide), or F(CF{sub 2}){sub 6-10}CH{sub 2} CH{sub 2}O(CH{sub 2}CH{sub 2}O){sub 3-8}H, forms classic reverse micelle structures having radii of about 84 A under the conditions of high pressure required to solubilize the material. A third amphiphile, the semifluorinated alkane diblock molecule F(CF{sub 2}){sub 10}(CH{sub 2}){sub 10}H, may form small aggregates of at most 4 unimers per aggregate. 41 refs., 10 figs.,more » 1 tab.« less
TL;DR: In this article, a number of central improvements are discussed in a prioritized manner, with consideration of the key progress necessary to include feedback processes between meteorology and chemistry, aerosol formation, in cloud development with subsequent effects on wet removal, dry deposition and surface exchange processes.
TL;DR: In this article, the same defect creation and healing processes were also observed on a nearly defect-free thermally annealed single-crystal surface using XPS, which was used to confirm the defect type and to quantify the density of Ti3+ defects created.
TL;DR: Results demonstrate the capabilities of polymer-coated SAW sensor arrays for analyzing of solvent vapor mixtures and the advantages of the EDPCR-Monte Carlo method for predicting and optimizing performance.
Abstract: A method for determining the optimal set of polymer sensor coatings to include in a surface acoustic wave (SAW) sensor array for the analysis of organic vapors is described. The method combines an extended disjoint principal components regression (EDPCR) pattern recognition analysis with Monte Carlo simulations of sensor responses to rank the various possible coating selections and to estimate the ability of the sensor array to identify any set of vapor analytes. A data base consisting of the calibrated responses of 10 polymer-coated SAW sensors to each of six organic solvent vapors from three chemical classes was generated to demonstrate the method. The predicted rate of vapor identification (87%) was experimentally verified, and the vapor concentrations were estimated within 10% of experimental values in most cases. The majority of errors in identification occurred when an individual vapor could not be differentiated from a mixture of the same vapor with a much lower concentration of a second component. The selection of optimal coating sets for several ternary vapor mixtures is also examined. Results demonstrate the capabilities of polymer-coated SAW sensor arrays for analyzing of solvent vapor mixtures and the advantages of the EDPCR-Monte Carlo method for predicting and optimizing performance. 30more » refs., 5 figs., 11 tabs.« less
TL;DR: In this article, the Fourier transform method is used to do the multiple convolutions required to calculate molecular isotope distributions, which can be used to produce peak profiles of finite resolution and can be adjusted to match that of an experimental apparatus.
Abstract: A new method is presented for calculating isotope distributions starting from a molecular formula and elemental isotopic abundances. The algorithm uses Fourier transform methods to do the multiple convolutions required to calculate molecular isotope distributions. In contrast to `infinite resolution` methods based on expansion of a polynomial expression, the present method produces peak profiles of finite resolution, and the peak profile function can be adjusted to match that of an experimental apparatus. The method is very fast, accurate, and economical in its use of computer memory and can be applied to extremely large molecules. In a sample calculation applied to a DNA oligomer of molecular mass > 123 kDa, the calculation completed in <1 s at a resolution of approximately 400 000 while an array size of only 4096 double precision points was used. Calculation of the moments of the resulting distribution showed that the average molecular weight of the distribution was accurate to 0.013 parts per million and the standard deviation was accurate to 0.15 parts per million. 10 refs., 3 figs.
TL;DR: The purification of a 3-chlorobenzoate-reductive dehalogenase from the cytoplasmic membrane of D. tiedjei DCB-1 was reported, which was yellow and probably a heme protein and able to complex with carbon monoxide.
Abstract: Although reductive dehalogenation by anaerobic microorganisms offers great potential for the degradation of halocarbons, little is known about the biochemical mechanisms involved. It has previously been demonstrated that the dehalogenase activity involved in 3-chlorobenzoate dehalogenation by Desulfomonile tiedjei DCB-1 is present in the membrane fraction of the cell extracts. We report herein the purification of a 3-chlorobenzoate-reductive dehalogenase from the cytoplasmic membrane of D. tiedjei DCB-1. The dehalogenase activity was monitored by the conversion of 3-chlorobenzoate to benzoate with reduced methyl viologen as a reducing agent. The membrane fraction of the cell extracts was obtained by ultracentrifugation, and the membrane proteins were solubilized with either the detergent CHAPS (3-[(3-cholamidopropyl)-dimethyl-ammonio]-1-propanesulfonate) or Triton X-100 in the presence of glycerol. The solubilized dehalogenase was purified by ammonium sulfate fractionation and a combination of anion exchange, hydroxyapatite, and hydrophobic interaction chromatographies. This procedure yielded about 7% of the total dehalogenase activity with a 120-fold increase in specific activity. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed that the purified dehalogenase consisted of two subunits with molecular weights of 64,000 and 37,000. The enzyme converted 3-chlorobenzoate to benzoate at its highest specific activity in 10 mM potassium phosphate buffer (pH 7.2) at 38 degrees C. The enzyme was yellow and probably a heme protein. The enzyme had an adsorbance peak at 408 nm. The dithionite-reduced enzyme displayed absorbance peaks at 416, 522, and 550 nm. The dithionite-reduced enzyme was able to complex with carbon monoxide. The nature of the heme chromophore is currently unknown.
TL;DR: An extended mass-to-charge ratio range quadrupole mass spectrometer was employed to examine the effects of harsher conditions in the ESI atmosphere-vacuum interface region on the streptavidin tetramer.
TL;DR: Preliminary results are presented which demonstrate the feasibility of using the CE-ESI-FTICR combination as a high-performance detection scheme for the analysis of cellular proteins acquired directly from small populations of intact living cells.
Abstract: The combination of capillary electrophoresis (CE) with electrospray ionization (ESI) mass spectrometry has proven to be broadly applicable to a wide range of biologically important compounds. When combined with Fourier transform ion cyclotron resonance (FTICR) mass spectrometry, the combined method, in addition to high-resolution separations, affords high-resolution precision mass measurements for analytes separated from complex mixtures. Direct chemical analysis of single cells has received considerable attention in recent years; the single cell approach provides a major step toward answering important questions in the field of cellular biochemistry. In this work we present preliminary results which demonstrate the feasibility of using the CE-ESI-FTICR combination as a high-performance detection scheme for the analysis of cellular proteins acquired directly from small populations (i.e., 5-10) of intact living cells. The human erythrocyte was chosen as a model system owing to its availability, relatively homogeneous composition, and thorough documentation of contents by previous researchers. In this work we demonstrate the on-line acquisition of high-resolution mass spectra (average resolution >45 000 fwhm) of both the {alpha} and the {beta} chains of hemoglobin acquired from the injection of 10 human erythrocytes. 33 refs., 3 figs.
TL;DR: In this article, a subgrid-scale parameterization of the influence of topography on clouds, precipitation, and land surface hydrology is proposed to bridge the gap between what is required and what is resolved.
Abstract: Estimates of the impact of global climate change on land surface hydrology require climate information on spatial scales far smaller than those explicitly resolved by global climate models of today and the foreseeable future. To bridge the gap between what is required and what is resolved, we propose a subgrid-scale parameterization of the influence of topography on clouds, precipitation, and land surface hydrology. The parameterization represents subgrid variations in surface elevation in terms of probability distributions of discrete elevation classes. Separate cloud, radiative, and surface processes are calculated for each elevation class. Rainshadow effects are not treated by the parameterization; they have to be explicitly resolved by the host model. The simulated surface temperature, precipitation, and snow cover for each elevation class are distributed to different geographical locations according to the spatial distribution of surface elevation within each grid cell. The subgrid parameterization has been implemented in the Pacific Northwest Laboratory's climate version of the Penn State/NCAR Mesoscale Model. The scheme is evaluated by driving the regional climate model with observed lateral boundary conditions for the Pacific Northwest and comparing simulated fields with surface observations. The method yields more realistic spatial distributions of precipitation and snow cover in mountainous areas and is considerably more computationally efficient than achieving high resolution by the use of nesting in the regional climate model.
10 Oct 1995
TL;DR: An electronic nose is described, some results from a prototype electronic nose are shown, and applications of electronic noses in the environmental, medical, and food industries are discussed.
Abstract: Electronic/artificial noses are being developed as systems for the automated detection and classification of odors, vapors, and gases. An electronic nose is generally composed of a chemical sensing system (e.g., sensor array or spectrometer) and a pattern recognition system (e.g., artificial neural network). We are developing electronic noses for the automated identification of volatile chemicals for environmental and medical applications. In this paper, we briefly describe an electronic nose, show some results from a prototype electronic nose, and discuss applications of electronic noses in the environmental, medical, and food industries.
TL;DR: The present model quantitatively describes the onset of phase locking as well as the general trends in frequency shifts and measured abundances just before phase locking.
Abstract: This work investigates the cyclotron motion of two Coulombically interacting ion clouds with different mass-to-charge ratios. Trap geometry as well as the shape of each ion cloud determines the maximum number of ions that can be confined in a Penning-like ion trap. We consider the two important cases of either spherically or cylindrically shaped ion clouds. These models exhibit the most important space charge effects in Fourier-transform ion cyclotron resonance mass spectrometry including frequency shifts, amplitude and phase modulation, and phase locking. Both positive and negative frequency shifts are possible for spherical ion clouds when their cyclotron radii differ. Due to the Coulombic ineraction between ion clouds, both cyclotron-radius and phase modulation occur. This modulation increases inversely to the cyclotron frequency difference. Cyclotron phase locking results when two ion clouds have similar mass-to-charge ratios and a sufficiently large ion population, at which point a mass spectrum shows only a single peak. Spherical ion clouds are usually more likely to phase lock than cylindrically shaped clouds. The phase-locking threshold sets limits on the maximum resolution, mass accuracy, and dynamic range achievable by mass spectrometry. Phase locking is treated in detail and our results are compared to previously published experimental data. The present model quantitatively describes the onset of phase locking as well as the general trends in frequency shifts and measured abundances just before phase locking.
TL;DR: In this paper, the authors used MP2 methods for multireference wave functions for the Cope rearrangement and simultaneously found that the CASSCF wave function overestimates the diradical character of the wave function.
Abstract: Earlier calculations on the Cope rearrangement based on a CASSCF wave function for the six electrons in the rearranging bonds gave reasonable energies at most places on the potential surface except in the crucial region around the chair transition state. Recently developed MP2 methods for multireference wave functions yield greatly improved energies. Using our version of this method, we simultaneously find that the CASSCF wave function overestimates the diradical character of the wave function. When this error is corrected, the Dewar-type diradicaloid stable intermediate no longer occurs as a minimum in the potential surface and the aromatic transition state moves to shorter bond lengths.
TL;DR: Electrospray ionization-mass spectrometry (ESI-MS) shows potential for the study of small molecule-oligonucleotide duplex interactions and determination ofSmall molecule binding stoichiometry.