Scientific Publications 2005
2005. "Support Effects on Bronsted acid site densities and alcohol dehydration turnover rates on tungsten oxide domains." Journal of Catalysis 227:479-491. Abstract Initial activity and acid site density of several WAl, WSi (MCM41) and one WSn sample were determined. Trans/cis 2-butene selectivity is dependent on the support. Presumably, these differences are due to subtle differences in base strengths. 2-Butanol dehydration rates (per W-atom) reached maximum values at intermediate WOx surface densities on WAl, as reported for 2-butanol dehydration reactions on WZr. Titration results indicate that Bronsted acid sites are required for 2-butanol dehydration on WAl, WSi and WSn. UV-visible studies suggest that WAl is much more difficult to reduce than WZr. The detection of reduced centers on WAl, the number of which correlates to Bronsted acid site density and catalyst activity, as well as the temperature dependence of Bronsted acid site density indicate the in-situ formation of these active sites. We infer that this mechanism is common among all supported WOx samples described in this study. Turnover rates are a function of Bronsted acid site density only. High acid site densities lead to high turnover rates. Higher active site densities may cause stronger conjugate bases, as a higher electron density has to be stabilized, and thus weaker acidity, enabling a faster rate of product desorption. The maximum achievable active site density is dependent on the support. WZr reaches a higher active site density than WAl.
2005. "Misfit Dislocations at the Single Crystal Fe₂O₃/Al₂O₃ Interface ." Physical Review. B, Condensed Matter and Materials Physics 72(7):Article number 075403. doi:10.1103/PhysRevB.72.075403 Abstract The buried interface of epitaxially-grown ⍺-Fe₂O₃(0001)/ ⍺-Al₂O₃(0001) has been studied recently using ion scattering techniques and high resolution transmission electron microscopy (HRTEM) recently. The results reveal the existence of disordering at the interface attributed to misfit dislocations associated with lattice mismatch between the substrate and the film. Molecular dynamics (MD) calculations were carried out to understand the formation of misfit dislocations and the interface structural features. The calculations show that misfit dislocations form in the Al₂O₃ substrate and terminate at the interface, consistent with the experimental observations. Snapshots of the atomic positions generated by the MD calculations were used in Monte Carlo simulations of the ion channelling experiments. The hitting probabilities determined from these simulations are compared with the experimental surface and interface peaks obtained from the aligned RBS spectra. Combination of MD and the ion scattering simulations with RBS and HRTEM measurements show promising results in understanding the interface structures of this single crystal Fe₂O₃/Al₂O₃.
2005. "NMR methods for in-situ biofilm metabolism studies." Journal of Microbiological Methods 62(3):337-344. Abstract Novel procedures and instrumentation are described for nuclear magnetic resonance (NMR) spectroscopy and imaging studies of live, in situ microbial films. A perfused NMR/optical microscope sample chamber containing a planar biofilm support was integrated into a recirculation/dilution flow loop growth reactor system and used to grow in situ Shewanella oneidensis strain MR-1 biofilms. Localized NMR techniques were developed and used to non-invasively monitor time-resolved metabolite concentrations and to image the biomass volume and distribution. As a first illustration of the feasibility of the methodology an initial 13C-labeled lactate metabolic pathway study was performed, yielding results consistent with existing genomic data for MR-1. These results represent progress toward our ultimate goal of correlating time- and depth-resolved metabolism and mass transport with gene expression in live in situ biofilms using combined NMR/optical microscopy techniques.
2005. "NMR methods for in-situ biofilm metabolism studies: spatial and temporal resolved measurements." Water Science and Technology 52(7):7-12. Abstract We are developing nuclear magnetic resonance (NMR) microscopy, spectroscopy and combined NMR/optical techniques to the study of biofilms. Objectives include: time and depth-resolved metabolite concentrations with isotropic spatial resolution on the order of 10 microns, metabolic pathways and flux rates, mass transport and ultimately their correlation with gene expression by optical microscopy in biofilms. These methods are being developed with Shewanella oneidensis MR-1 as a model system, but are equally applicable to other biofilm systems of interest. Thus, spatially resolved NMR of biofilms is expected to contribute significantly to the understanding of adherent cell metabolism.
2005. "The High-Resolution Infrared Spectrum of 10BF3 from 400 to 4600 cm-1." Journal of Molecular Structure 742:3-20. doi:10.1016/j.molstruc.2004.11.089 Abstract High-resolution infrared spectra of boron trifluoride, enriched to 99.5 atom % 10B, have been measured from 400 cm-1. In that region we have identified and analyzed 17 absorption bands including three fundamentals. In addition, 3 hot bands associated with v2 were analyzed, 7 hot bands associated with v4, two with v1+v4 and one hot band each associated with the v3 and v1+v2 bands. The spectral resolution of the measurements varied from 0.0015 cm -1 at the lowest wavenumber to 0.0035 cm -1 at the highest wavenumber. This study resulted in the first direct characterization of the v1 state via two routes, one through the combined analysis of the 110000-000000 and 110000-100000 vibrational transitions and the other through the analysis of the 001100-000000 and 001100-100000 transitions. All of the quadratic vibrational anharmonic constants have been determined except x23. An improved set of ground state rotational constants has been determined for 10BF3. With corrections through most but not all of the quadratic rotational terms we have found that Be=0.346170 ± 0.000003 cm-1 and Ce = 0.173038 ± 0.000006 cm-1. These give a B-F bond distance of re = 130.731 ± 0.010 pm. The effects of l-type resonance were used to locate certain vibrational states that could not be directly observed through infrared transitions from the ground state. The splitting of the A1´ and A2´ components of v3+v4 was found to be quite large, 6.131 ± 0.007 cm-1. Several other resonances were also found including the weak vibrational interaction, which had been overlooked by earlier workers, between 2v2 and the A1´ vabrational state 3v4.
2005. "A role for Pareto optimality in mining performance data." Concurrency and Computation. Practice & Experience 17(1):27-48. doi:10.1002/cpe.877 Abstract Improvements in performance modeling and identification of computational regimes within software libraries is a critical first step in developing software libraries that are truly agile with respect to the application as well as to the hardware. It is shown here that Pareto ranking, a concept from multi-objective optimization, can be an effective tool for mining large performance datasets. The approach is illustrated using software performance data gathered using both the public domain LAPACK library and an asynchronous communication library based on IBM LAPI active message library.
2005. "Peptide identification via constrained multi-objective optimization: Pareto-based genetic algorithms ." Concurrency and Computation. Practice & Experience 17(14):1687-1704. Abstract Automatic data-base independent peptide identification from collision-induced dissociation tandem mass spectrometry data is made difficult by large plateaus in the fitness landscapes of scoring functions and the fuzzy nature of the constraints that is due to noise in the data. Two different scoring functions are combined into a parallel multi-objective optimization framework.
2005. "Uranium removal by sulfate reducing biofilms in the presence of carbonates ." Water Science and Technology 52(7):49-55. Abstract Hexavalent uranium [U(VI)] was immobilized in biofilms composed of the sulfate reducing bacteria (SRB), Desulfovibrio desulfuricans G20. The biofilms were grown in two flat-plate, continuous-flow reactors using lactate as the electron donor and sulfate as the electron acceptor. The growth medium contained uranium U(VI) and the pH was maintained constant using bicarbonate buffer. The reactors were operated for 5 months, and during that time biofilm activity and uranium removal were evaluated. The efficiency of uranium removal strongly depended on the concentration of uranium in the influent, and was estimated to be 30.4% in the reactor supplied with 3 mg/L of U(VI) and 73.9% in the reactor supplied with 30 mg/L of U(VI). TEM and SAED analysis showed that uranium in both reactors accumulated mostly on microbial cell membranes and in the periplasmic space. The deposits had amorphous or poor nanocrystalline structures.
2005. "Analysis of Precipitates from Reactions of Hyperalkaline Solutions with Soluble Silica." Applied Geochemistry 20(7):1357-1367. Abstract Cancrinite, sodalite, and zeolite A have been found to form upon contacting hyperalkaline simulated tank waste (STW) with vadose zone sediments from the Hanford Reservation. Here, we use soluble silica and STW to study mineral formation and transformation. We also used two Hanford sediment fractions (diameters < 50 µm and > 50 µm instead of soluble silica) as silica sources for comparison. A series of batch experiments at 50_C and 25 days duration were conducted by reacting 0.026 mol/kg soluble Si with six different STW solutions. The STW solutions differed in NaOH and Al concentrations. Cancrinite, sodalite, and zeolite A formed when soluble Si was used as the Si source. The minerals were characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), and 27Al and 29Si magic-angle spinning nuclear magnetic resonance (MAS-NMR). Larger NaOH and Al concentrations favored formation of the more compact structures of cancrinite and sodalite. At larger NaOH concentration more Al for Si substitution occurred in the tetrahedral sites. A greater Al(4)/Al(6) ratio in the solids was found for the higher Si/Al ratio solutions based on NMR results. Mixtures of cancrinite and sodalite were characterized by particles with lepispheric morphology. At low Al concentration, increasing NaOH resulted in distinct hexagonal, prismatic particles common to crystalline cancrinite. At low Al/Si ratio, we observed the characteristic cubic morphology of zeolite in addition to cancrinite and sodalite.
2005. "The High-Resolution Infrared Spectrum of 11BF3 From 400 to 1650 cm-1." Journal of Molecular Spectroscopy 234(1):122-136. Abstract High-resolution infrared spectra of boron trifluoride, enriched to 99.5 atom % 11B, have been measured from 400 cm-1 to 1650 cm-1. In that region we have identified and analyzed 16 absorption bands attributed to the three fundamental bands, two combination bands, ten hot bands and one difference band. All possible states were accessed in this region through direct transitions either from the ground state or as hot bands from thermally populated levels. The spectral resolution of the measurements varied from 0.0015 cm-1 to 0.0020 cm-1. An improved set of ground state rotational constants and rovibrational constants for the infrared active fundamental vibrations have been determined from over 31,000 assigned transitions. This study resulted in the first direct characterization of the infrared inactive v1 state of 11BF3 leading to values for v1, v1B and v1C of 885.843 221(22), 0.000 505 242(26) and 0.000 678 567(55) cm-1, respectively. The Fermi resonance perturbation between the Ev3 states v3 and 3v4 (l=+1) was further elucidated by observation of hot band transitions to both the 3v4(l=+1)and 3v4(l=v3) states. Several other resonances were also found including the weak rotational interaction, between the A1v state 2v2 and the E' state of v1+v4.
2005. "Functionalized TiO2 nanoparticles for use for in-situ anion immobilization." Environmental Science and Technology 39(18):7306-7310. Abstract 40-60 nm anatase nanoparticles were coated with an organosilane monolayer terminated with an ethylenediamine (EDA) ligand. This functionalized nanoparticle (FNP) was then treated with an aqueous solution of Cu(II) to create a cationic Cu-EDA complex bound to the nanoparticle surface. The Cu-EDA FNP was then studied for its binding affinity for pertechnetate anion from a Hanford groundwater matrix. The Cu-EDA FNP was also evaluated for its injectability into a porous medium for possible application as a subsurface semi-permeable reactive barrier. Injection was readily accomplished, and resulted in a highly uniform distribution of the FNP sorbent in the test column.
2005. "One-step, non-denaturing isolation of an RNA polymerase enzyme complex using an improved multi-use affinity probe resin." Molecular Biosystems 1(1):53-56. doi:10.1039/b500950b Abstract The rapid isolation of protein complexes is critical to the goal of interpreting genomic information in the context of cellular function. High-throughput methods for identifying protein binding partners in a way suitable for mass spectrometric identification and structural analysis are sought after and small molecule/peptide interactions may provide the key. We have now shown that a newly synthesized resin derivatized with a bisarsenical dye can be used to isolate the Shewanella oneidensis RNA polymerase core enzyme, using the tetracysteine-tagged RNA polymerase A as bait protein. A critical advantage of this method is the ability to release the intact complex using a mild, one-step procedure with a competing dithiol. In addition to the identification of the core subunit complex, potential additional regulatory factors, including universal stress protein, were identified. These results provide a path forward to identifying how changes in critical protein complexes over time modulate cell function
2005. "Unusual aggregates from the oxidation of alkene self-assembled monolayers: a previously unrecognized mechanism for SAM ozonolysis?" Physical Chemistry Chemical Physics. PCCP 7:3605-3609. doi:10.1039/b508147e Abstract Airborne particles are important in climate, visibility, human health and atmospheric reactions. Organics associated with airborne particles are thought to be oxidized to polar, hygroscopic species with enhanced cloud-nucleating properties. We show that ozone oxidation of unsaturated organics on silica as a proxy for airborne dust leads to the formation of hydrophobic polymer balls which do not increase the uptake of water as previously assumed. We propose that atmospheric formation of hydrophobic polymers is generally controlled by the availability of water rather than acid, and hence is much more common in the lower atmosphere than previously recognized.
2005. "Production, purification, and characterization of human scFv antibodies expressed in Saccharomyces cerevisiae, Pichia pastoris, and Escherichia coli. ." Protein expression and purification 42(2):255-267. Abstract Single chain (scFv) antibodies are used as affinity reagents for diagnostics, therapeutics, and proteomic analyses. The antibody discovery platform we use to identify novel antigen binders involves discovery, characterization, and production. The discovery and characterization components have previously been characterized but in order to fully utilize the capabilities of affinity reagents from our yeast surface display library, efforts were focused on developing a production component to obtain purified, soluble, and active scFvs. Instead of optimizing conditions to achieve maximum yield, efforts were focused on using a system that could quickly and easily produce and process hundreds of scFv antibodies. Heterologous protein expression in Saccharomyces cerevisiae, Pichia pastoris, and Escherichia coli were evaluated for their ability to rapidly, efficaciously, and consistently produce scFv antibodies for use in downstream proteomic applications. Following purification, the binding activity of several scFv antibodies were quantified using a novel Biacore assay. All three systems produced soluble scFv antibodies which ranged in activity from 0-99%. scFv antibody yields from Saccharomyces, Pichia, and E. coli were 1.5-4.2, 0.4-7.3, and 0.63-16.4 mg L-1 culture, respectively. For our purposes, expression in E. coli proved to be the quickest and most consistent way to obtain and characterize purified scFv for downstream applications. The E. coli expression system was also used to compare scFv production levels from the periplasm, inclusion bodies, and culture media. The E. coli production system was then used to produce variants of several scFv to determine structure function relationships.
2005. "T2-Shortening of 3He Gas by Magnetic Microspheres." Journal of Magnetic Resonance 173(1):90-96. Abstract In the interconnected pores of a material like the lung the transverse relaxation time (T2) for 3He gas is shortened by the deposition of magnetic microspheres and rapid molecular diffusion through induced field distortions. Here, this unique relaxation process is described theoretically and predicted T2-shortening is validated using pressurized 3He gas in a foam model of lung tissue. Results demonstrate that – 1) significant T2-shortening is induced by microsphere deposition, 2) shortened T2’s are accurately predicted, and 3) measured relaxation times are exploitable for quantifying the local volume fraction of magnetic microspheres deposited in gas-filled spaces.
2005. "Interior and Interfacial Aqueous Solvation of Benzene Dicarboxylate Dianions and Their Methylated Analogues: A Combined Molecular Dynamics and Photoelectron Spectroscopy Study." Journal of Physical Chemistry A 109(23):5042-5049. Abstract Aqueous solvation of benzene dicarboxylate dianions (BCD2-) was studied by means of photoelectron spectroscopy and molecular dynamics simulations. Photoelectron spectra of hydrated ortho-, and para-BCD2- with up to 25 water molecules were obtained. An even-odd effect was observed for the p-BCD2- system as a result of the alternate solvation of the two negative charges. However, the high polarizability of the benzene ring makes the two carboxylate groups interact with each other in p-BCD2-, suppressing the strength of this even-odd effect compared with the linear dicarboxylate dianions linked by an aliphatic chain. No even-odd effect was observed for the o-BCD2- system, because each solvent molecule can interact with the two carboxylate groups at the same time due to their proximity. For large solvated clusters, the spectral features of the solute decreased while the solvent features became dominant, suggesting that both o- and p-BCD2- are situated in the center of the solvated clusters. Molecular dynamics simulations with both non-polarizable and polarizable force fields confirmed that all three isomers (o-, m-, and p-BCD2-) solvate in the aqueous bulk. However, upon methylation the hydrophobic forces overwhelm electrostatic interactions and, as a result, the calculations predict that the tetra-methyl o-BCD2- is located at the water surface with the carboxylate groups anchored in the liquid and the methylated benzene ring tilted away from the aqueous phase.
2005. "Cesium Incorporation and Diffusion in Cancrinite, Soalite, Zeolite, and Allophane." Microporous and Mesoporous Materials 86(1-3):277-286. Abstract At the US Department of Energy’s Hanford site, high level nuclear waste has leaked from under4 ground storage tanks. The waste consists of hyperalkaline solutions, which upon contact with the 5 sediments, caused dissolution of silicate minerals and precipitation of secondary aluminosilicate min6 erals. Cancrinite, sodalite, LTA zeolite, and allophane have been identified as the new mineral phases 7 in laboratory simulations. Cesium, the major radionulide in the waste solutions, may be incorporated 8 into the structural framework of the precipitates. The objectives of this study were to determine the 9 resistance of incorporated Cs to ion exchange and the mobility and diffusion coefficient of Cs in the 10 minerals. The minerals were synthesized in solutions mimicking the tank waste and were washed with 11 deionized water. Two sets of experiments were conducted to test the resistance of Cs to ion exchange. 12 In the first set, Cs was exchanged three times at 80 C by 0.5 N Na, K, or Ca. The Cs remaining in 13 minerals was quantified after acid digestion. In the second set, we studied the Cs desorption kinetics 14 by using 0.1 M Na as ion exchanger. Cesium concentration in the solution phase was measured as a 15 function of time for 23 days. Cesium incorporated in sodalite and cancrinite was far more difficult to 16 replace than that in LTA zeolite and allophane. Most of the incorporated Cs (94–99%) in LTA zeolite 17 and allophane was readily exchangeable with Na or K; less than 20% of Cs in sodalite and <55% of Corresponding author. E-mail: email@example.com; FAX: 509-335-8674 (M. Flury) 2 Cs in cancrinite could be exchanged. The fraction of desorbed Cs was also affected by the exchangin18 g 19 ions; the ion with lowest dehydration energy (K) was the most effective in replacing Cs. The results 20 of the desorption kinetics experiments showed that Cs desorbed quickly from LTA zeolite and the Cs 21 diffusion coefficient was close to that in solution; i.e., about 10−9 m2/s. Solid-state NMR analysis 22 supported the high mobility of Cs in LTA zeolite. Cesium desorption from cancrinite, sodalite, and 23 allophane, however, was slow, suggesting that Cs was trapped in cages and channels of these minerals. 24 Effective diffusion coefficients for Cs in cancrinite and sodalite were near 10−14 m2/s. 25 Key words: Cesium, ion exchange, desorption, feldspathoids, zeolite, allophane, intraparticle diffusion
2005. "Effects of Ionizing Radiation in Nonirradiated Cells." Proceedings of the National Academy of Sciences of the United States of America 102(40):14127-14128. Abstract Implicit in understanding the biological effects of ionizing radiation and subsequent risks associated with such exposure is that only cells “hit” by the radiation are likely to carry the legacy of radiation damage. When a cell is “hit” the deposition of energy can result in direct damage to the genetic material or indirect damage to critical nuclear targets through the radiolysis of water (Figure 1). The subsequent action of DNA repair processes either removes the lesion(s), or fixes the induced damage such that all surviving progeny of an irradiated cell carry the burden of radiation exposure, e.g., a gene mutation and/or a chromosomal rearrangement (Figure 1A). This central tenet in our understanding of the biological effects of ionizing radiation has now been called into question by the description of a number of non-targeted effects associated with radiation exposure. These effects can occur in the progeny of irradiated cells generations after the initial exposure, and/or in cells that were not directly traversed by ionizing radiation, but were some distance from the “hit” cells (reviewed in 1, 2) (Figure 1B). The work of Belyakov and colleagues in this issue of PNAS demonstrates for the first time non-targeted bystander responses in a three-dimensional human tissue model system (3). The investigators use a microbeam to deliver defined numbers of charged particles, in this case alpha particles - the type of radiation associated with radon decay, with high accuracy to precise locations (4, 5). A defined area of cells was irradiated in a thin vertical plane, ~two cell diameters, to bisect the tissue sample. Because of the inherent nature of the alpha particles there is very little radiation scatter. Consequently cells more than a few microns away from the plane of irradiated cells receive zero radiation dose. At 72 hours post irradiation, the tissues were formalin fixed, paraffin embedded, and sectioned in strips at increasing distances parallel to the plane of irradiated cells. This allowed analysis of tissue slices containing only non-irradiated cells at known distances from the plane of irradiated cells. Unirradiated cells up to 1 mm away from the irradiated cells, ~50-75 cell diameters distant, showed a significant enhancement in the measured fractions of apoptotic and micronucleated cells.