Scientific Publications 2008
2008. "Prediction of the Vibrational Frequencies of UO₂²+ at the CCSD(T) Level." Journal of Physical Chemistry A 112(17):4095-4099. doi:10.1021/jp710334b Abstract Electronic structure calculations at the coupled cluster (CCSD(T)) and density functional theory levels with various relative effective core potentials and basis sets have been used to predict the isolated uranyl ion frequencies. The effects of anharmonicity and spin-orbit corrections on the harmonic frequencies have been calculated. The anharmonic effects are larger than the spin orbit corrections and both are small. The anharmonic effects decrease the frequencies and the spin orbit corrections increase the stretches and decrease the bend. Overall, these corrections decrease the harmonic asymmetric stretch frequency by 6 cm-¹, the symmetric stretch by 3 cm-1 and the bend by 3 cm-¹. The splitting between the asymmetric and symmetric stretch is predicted to be 86 cm-¹, which is consistent with experimental trends for substituted uranyls in solution and in the solid state.
2008. "3D He-3 diffusion MRI as a local in vivo morphometric tool to evaluate emphysematous rat lungs." Journal of Applied Physiology 105:1291-1300. doi:10.1152/japplphysiol.90375.2008 Abstract In this work, we validate 3He magnetic resonance imaging as a non-invasive morphometric tool to assess emphysematous disease state on a local level. Emphysema was induced intratracheally in rats with 25U/100g body weight of porcine pancreatic elastase dissolved in 200 μL saline. Rats were then paired with saline-dosed controls. Nine three-dimensional 3He diffusion-weighted images were acquired at one-, two-, or three-weeks post-dose, after which the lungs were harvested and prepared for histological analysis. Recently introduced indices sensitive to the heterogeneity of the airspace size distribution were calculated. These indices, D1 and D2, were derived from the moments of the mean equivalent airway diameters. Averaged over the entire lung, it is shown that the 3He diffusivity (Dave) and anisotropy (Dan) both correlate with histology (R = 0.85, p < 0.0001 and R = 0.88, p < 0.0001, respectively). By matching small (0.046 cm2) regions in 3He images with corresponding regions in histological slices, Dave and Dan each correlate significantly with both D1 and D2 (R = 0.93, p < 0.0001). It is concluded that 3He MRI is a viable non-invasive morphometric tool for localized in vivo emphysema assessment.
2008. "The effects of shared peptides on protein quantitation in label-free proteomics by LC/MS/MS ." Journal of Proteome Research 7(1):164-169. doi:10.1021/pr0704175 Abstract Assessment of differential protein abundance from the observed properties of detected peptides is an essential part of protein profiling based on shotgun proteomics. However, the abundance observed for degenerate peptides may be due to contributions from multiple proteins that are affected differently by a given treatment. Excluding degenerate peptides eliminates this ambiguity but may significantly decrease the number of proteins for which abundance estimates can be obtained. Peptide degeneracy within a family of biologically related proteins does not cause ambiguity if family members have a common response to treatment. Based on this concept, we have developed an approach for including degenerate peptides in the analysis of differential protein abundance in protein profiling. Data from a recent proteomics study of lung tissue from mice exposed to lipopolysaccharide, cigarette smoke, and a combination of these agents is used to illustrate our method. Starting from data where about half of the protein identifications involved degenerate peptides, 82% of the affected proteins were grouped into families, based on FASTA annotation, with closure on peptide degeneracy. In many cases, a common abundance relative to control was sufficient to explain ion-current peak areas for peptides, both unique and degenerate, that identified biologically-related proteins in a peptide-degeneracy closure group. Based on these results, we propose that peptide-degeneracy closure groups provide a way to include abundance data for degenerate-peptides in quantitative protein profiling by high throughput mass spectrometry.
2008. "Comparative Analysis of Urban Atmospheric Aerosol by Particle-Induced X-ray Emission (PIXE), Proton Elastic Scattering Analysis (PESA), and Aerosol Mass Spectrometry (AMS)." Environmental Science & Technology 42(17):6619-6624. doi:10.1021/es800393e Abstract A multifaceted approach to atmospheric aerosol analysis is often desirable in field studies where an understanding of technical comparability among different measurement techniques is essential. Herein we report quantitative intercomparisons of Particle-Induced X-ray Emission (PIXE) and Proton Elastic Scattering Analysis (PESA), performed off-line under vacuum, with analysis by Aerosol Mass Spectrometry (AMS) carried out in real-time during the MCMA-2003 Field Campaign in the Mexico City Metropolitan Area. Good agreement was observed for mass concentrations of PIXE-measured sulfur (assuming it was dominated by SO42−) and AMS-measured sulfate during the most of the campaign. PESA-measured hydrogen mass was separated into sulfate H and organic H mass fractions assuming the only major contributions were (NH4)2SO4 and organic compounds. Comparison of the organic H mass with AMS organic aerosol measurements indicates that about 75% of the mass of these species evaporated under vacuum. However ~25% of the organics does remain under vacuum, which is only possible with low vapor pressure compounds, and which supports the presence of high molecular weight and/or highly oxidized organics consistent with atmospheric aging. Approximately 10% of the chloride detected by AMS was measured by PIXE, possibly in the form of metal-chloride complexes, while the majority of Cl was likely present as more volatile species including NH4Cl. This is the first comparison of PIXE/PESA and AMS, and to our knowledge also the first report of PESA hydrogen measurements for urban organic aerosols.
2008. "Mineral Precipitation Upgradient from a Zero-Valent Iron Permeable Reactive Barrier." Ground Water Monitoring and Remediation 28(3):56-64. doi:10.1111/j.1745-6592.2008.00203.x Abstract Core samples taken from a zero-valent iron permeable reactive barrier (ZVI PRB) at Cornhusker Army Ammunition Plant, Nebraska, were analyzed for physical and chemical characteristics. Precipitates containing iron and sulfide were present at much higher concentrations in native aquifer materials just upgradient of the PRB than in the PRB itself. Sulfur mass balance on core solids coupled with trends in ground water sulfate concentrations indicates that the average ground water flow after 20 months of PRB operation was approximately twenty fold less than the regional ground water velocity. Transport and reaction modeling of the aquifer PRB interface suggests that, at the calculated velocity, both iron and hydrogen could diffuse upgradient against ground water flow and thereby contribute to precipitation in the native aquifer materials. The initial hydraulic conductivity (K) of the native materials is less than that of the PRB and, given the observed precipitation in the upgradient native materials, it is likely that K reduction occurred upgradient to rather than within the PRB. Although not directly implicated, guar gum used during installation of the PRB is believed to have played a role in the precipitation and flow reduction processes by enhancing microbial activity.
2008. "Electronic Energy Transfer on CaO Surfaces." Journal of Chemical Physics 129(12):124704. doi:10.1063/1.2980049 Abstract We excite low-coordinated surface sites of nanostructured CaO samples using tunable UV laser pulses and observe hyperthermal O-atom emission indicative of an electronic excited-state desorption mechanism. The O-atom yield increases dramatically with photon energy, between 3.75 and 5.4 eV, below the bulk absorption threshold. The peak of the kinetic energy distribution does not increase with photon energy in the range 3.9 to 5.15 eV. These results are analyzed in the context of a laser desorption model developed previously for nanostructured MgO samples. The data are consistent with desorption induced by exciton localization at corner-hole trapped surface sites following either direct corner excitation or diffusion and localization of excitons from higher coordinated surface sites.