Scientific Publications 2010
2010. "Characterization of cation environments in polycrystalline forsterite by Mg-25 MAS, MQMAS, and QCPMG NMR ." American Mineralogist 95(11-12):1601-1607. doi:10.2138/am.2010.3403 Abstract Forsterite (Mg2SiO4) is a silicate mineral frequently studied in the Earth sciences as it has a simple crystal structure and fast dissolution kinetics (elemental release rates under typical conditions on the order of 10-7 mol/m2/s1). During the dissolution process, spectroscopic techniques are often utilized to augment solution chemical analysis and to provide data for determining reaction mechanisms. Nuclear magnetic resonance (NMR) is able to interrogate the local bonding arrangement and coordination of a particular nuclide to obtain in structural information. Although previous NMR studies have focused on the silicon and oxygen environments in forsterite, studies focusing on the two nonequivalent magnesium environments in forsterite are limited to a few single-crystal studies. In this study, we present the results of 25Mg MAS, MQMAS, and static QCMG experiments performed on a powdered sample of pure synthetic forsterite. We also present spectral fits obtained from simulation software packages, which directly provide quadrupolar parameters for 25Mg nuclei occupying each of the two nonequivalent magnesium sites in the forsterite structure. These results are compared to calculations of the electric field gradient tenor conducted in previous ab initio studies to make definitive assignments correlating each peak to their respective magnesium site in the forsterite structure. Although previous NMR investigations of forsterite have focused on single-crystal samples, we have focused on powdered forsterite as the increased surface area of powdered samples makes them more amenable to laboratory-scale dissolution studies and, ultimately, the products from chemical weathering may be monitored an quantified.
2010. "Utilizing High Performance Computing for Chemistry: Parallel Computational Chemistry." Physical Chemistry Chemical Physics. PCCP 12(26):6896-6920. Abstract Parallel hardware has become readily available to the computational chemistry research community. This perspective will review the current state of parallel computational chemistry software utilizing high-performance parallel computing platforms.Hardware and software trends and their effect on quantum chemistry methodologies, algorithms, and software development will also be discussed.
2010. "Microbial communities acclimate to recurring changes in soil redox potential status." Environmental Microbiology 12(12):3137-3149. doi:10.1111/j.1462-2920.2010.02286.x Abstract Rapidly fluctuating environmental conditions can significantly stress organisms, particularly when fluctuations cross thresholds of normal physiological tolerance. Redox potential fluctuations are common in humid tropical soils, and microbial community acclimation or avoidance strategies for survival will in turn shape microbial community diversity and biogeochemistry. To assess the extent to which indigenous bacterial and archaeal communities are adapted to changing in redox potential, soils were incubated under static anoxic, static oxic or fluctuating redox potential conditions, and the standing (DNA-based) and active (RNA-based) communities and biogeochemistry were determined. Fluctuating redox potential conditions permitted simultaneous CO₂ respiration, methanogenesis, N₂O production and iron reduction. Exposure to static anaerobic conditions significantly changed community composition, while 4-day redox potential fluctuations did not. Using RNA: DNA ratios as a measure of activity, 285 taxa were more active under fluctuating than static conditions, compared with three taxa that were more active under static compared with fluctuating conditions. These data suggest an indigenous microbialcommunity adapted to fluctuating redox potential.
2010. "Atomistic Simulation of Water Percolation and Proton Hopping in Nafion Fuel Cell Membrane." Journal of Physical Chemistry B 114(43):13681-13690. doi:10.1021/jp103398b Abstract We have performed a detailed analysis of water clustering and percolation in hydrated Nafion configurations generated by classical molecular dynamics simulations. Our results show that at low hydration levels H2O molecules are isolated and a continuous hydrogen-bonded network forms as the hydration level is increased. Our quantitative analysis has established a hydration level (λ) between 5 and 6 H2O/SO3- as the percolation threshold of Nafion. We have also examined the effect of such a network on proton transport by studying the structural diffusion of protons using the quantum hopping molecular dynamics method. The mean residence time of the proton on a water molecule decreases by two orders of magnitude when the λ value is increased from 5 to 15. The proton diffusion coefficient in Nafion at a λ value of 15 is about 1.1x10-5 cm2/s in agreement with experiment. The results provide quantitative atomic-level evidence of water network percolation in Nafion and its effect on proton conductivity.
2010. "Radiation tolerance of ceramics—Insights from atomistic simulation of damage accumulation in pyrochlores." Energy & Environmental Science 3(10):1551-1559. doi:10.1039/C0EE00066C Abstract We have used molecular dynamics simulations to examine the effects of radiation damage accumulation in two pyrochlore-structured ceramics, namely Gd2Ti2O7 and Gd2Zr2O7. It is well known from experiment that the titanate is susceptible to radiation-induced amorphization, while the zirconate does not go amorphous under prolonged irradiation. Our simulations show that cation Frenkel pair accumulation eventually leads to amorphization of Gd2Ti2O7. Anion disorder occurs with cation disorder. The amorphization is accompanied by a density decrease of about 12.7% and a decrease of about 50% in the elastic modulus. In Gd2Zr2O7, amorphization does not occur, because the residual damage is not sufficiently energetic to drive the material amorphous. Subtle differences in damage accumulation and annealing between the two pyrochlores lead to drastically different radiation response as the damage accumulates.
2010. "Simulation of collision cascades and thermal spikes in ceramics." Nuclear Instruments and Methods in Physics Research. Section B, Beam Interactions with Materials and Atoms 268(19):2857-2862. doi:10.1016/j.nimb.2010.05.047 Abstract Classical molecular dynamics simulations have been employed to examine defect production by energetic recoils in UO2, Gd2Ti2O7, Gd2Zr2O7 and ZrSiO4. These atomistic simulations provide details of the nature and size distribution of defect clusters produced in collision cascades. The accommodation of recoil damage by lower energy cation exchange and greater occupation of anion structural vacancies is a contributing factor for the greater radiation tolerance of Gd2Zr2O7 relative to Gd2Ti2O7. In addition, electronic energy loss processes in UO2 has been modeled in the form of a thermal spike to study the details of track formation and track structure. For thermal spikes with energy deposition of 4 keV/nm in UO2, a track was not formed and mainly isolated Frenkel pairs are produced.
2010. "Multispectrum analysis of the v9 band of 12C2H6: Positions, intensities, self- and N2-broadened half-width coefficients." Journal of Quantitative Spectroscopy and Radiative Transfer 111(9):1234-1251. doi:10.1016/j.jqsrt.2009.10.017 Abstract Line positions, intensities, Lorentz self- and N2-broadened half-width coefficients have been measured for PQ3, PQ2, PQ1, RQ0,RQ1, RQ2, and RQ3 sub-band transitions in the 9 fundamental band of 12C2H6. A multispectrum nonlinear least-squares fitting technique was used to fit up to 17 high-resolution (~0.00156 cm-1), room temperature absorption spectra of pure (99.99% chemical purity) natural sample of ethane and lean mixtures of the high-purity ethane diluted with N2. A Bruker IFS 120HR Fourier transform spectrometer located at the Pacific Northwest National Laboratory (PNNL), in Richland, Washington was used to record the data. A standard Voigt line shape was assumed to fit all the data since no line mixing or other non Voigt line shapes were required to fit any of the spectra used in the analysis. Short spectral intervals (~2 to 2.5 cm-1) of all 17 spectra covering a specific PQ or RQ sub band were fit simultaneously. For the first time in an ethane band, pressure-broadened half-width coefficients were determined for each of the torsional-split components. Constraints were used such that the half-width coefficients of both torsional-split components were identical for a specific broadening gas. No pressure-induced shift coefficients were necessary to fit the spectra to their noise level. The present study revealed for the first time the dependence of self- and N2-broadened half-width coefficients upon the J, K quantum numbers of the transitions in ethane. A number of transitions belonging to the 9+ 4- 4 and the 9+2 4-2 4 hot bands were also observed in the fitted regions and measurements were made when possible.
2010. "Temporal Proteome and Lipidome Profiles Reveal HCV-Associated Reprogramming of Hepatocellular Metabolism and Bioenergetics ." PLoS Pathogens 6(1):Art. No. e1000719. doi:10.1371/journal.ppat.1000719 Abstract Proteomic and lipidomic profiling was performed during multiple time-points of acute HCV infection of cultured Huh-7.5 cells to gain new insights into the intracellular processes influenced by HCV infection. Our proteomic data suggest that HCV induces early perturbations in glycolysis, the pentose phosphate pathway, and the citric acid cycle that favor host biosynthetic activities supporting viral replication and propagation. This is followed by a compensatory shift in metabolism aimed at maintaining energy homeostasis and cell viability during elevated viral replication and increasing cellular stress. Complementary lipidomic analyses identified numerous temporal perturbations in select lipid species (e.g. phospholipids and sphingomyelins) predicted to play an important role in viral replication and down-stream assembly and secretion events. The elevation of lipotoxic ceramide species suggests a potential link between HCV-associated biochemical alterations and the direct cytopathic effect detected in this in vitro system. Using innovative computational modeling approaches we further identified novel topological protein bottlenecks that are essential for HCV-associated metabolic reprogramming. Significantly, these protein bottlenecks represent mitochondrial fatty acid oxidation enzymes present among a subset of host cell metabolism proteins comparably regulated during in vitro infection and in liver tissue from HCV-infected patients with histological evidence of fibrosis. Collectively, these data suggest that HCV-associated targeting of bottleneck proteins functioning in mitochondrial fatty acid oxidation may play a key role in regulating the temporal alterations in cellular metabolic homeostasis that occur during infection and that related physiological disruptions may contribute to liver disease progression.
2010. "Genome Sequence of the Deltaproteobacterial Strain NaphS2 and Analysis of Differential Gene Expression during Anaerobic Growth on Naphthalene." PLoS One 5(11):Article No. e14072. doi:10.1371/journal.pone.0014072 Abstract Anaerobic polycyclic hydrocarbon (PAH) degradation coupled to sulfate reduction may be an important mechanism for in situ remediation of contaminated sediments. Steps involved in the anaerobic degradation of 2-methylnaphthalene have been described in the sulfate reducing strains NaphS3, NaphS6 and N47. Evidence from N47 suggests that naphthalene degradation involves 2-methylnaphthalene as an intermediate, whereas evidence in NaphS2, NaphS3 and NaphS6 suggests a mechanism for naphthalene degradation that does not involve 2-methylnaphthalene. To further characterize pathways involved in naphthalene degradation in NaphS2, the draft genome was sequenced, and gene and protein expression examined.
2010. "Non-stoichiometric material transfer in the pulsed laser deposition of LaAlO3." Applied Physics Letters 97(12):124105. doi:10.1063/1.3487778 Abstract Inequivalent angular distributions have been found for La and Al in the ablation plume from LaAlO3 single crystal targets using a KrF laser during pulsed laser deposition. Angular distributions and stoichiometries in the condensate were measured and reveal decidedly non-stoichiometric transfer from target to substrate over most of the angular range. Composition varied dramatically for plume angles parallel to the long axis of the laser spot with the on-axis position exhibiting a peak in the La/Al atom ratio at ~1.5. The distributions were more diffuse in the perpendicular direction. Stoichiometric LaAlO3 was found in the condensate only at an extreme off-axis position.
2010. "Sensitive Immunosensor for Cancer Biomarker Based on Dual Signal Amplification Strategy of Graphene Sheets and Multi-Enzyme Functionalized Carbon Nanospheres ." Analytical Chemistry 82(7):2989-2995. doi:10.1021/ac100036p Abstract A novel electrochemical immunosensor for sensitive detection of cancer biomarker α fetoprotein (AFP) is described that uses a graphene sheet sensor platform and functionalized carbon nanospheres (CNSs) labeling with horseradish peroxidase-secondary antibodies (HRP-Ab2). Greatly enhanced sensitivity for the cancer biomarker is based on a dual signal amplification strategy: first, the synthesized CNSs yielded a homogeneous and narrow size distribution, which allowed several binding events of HRP-Ab2 on each nanosphere. Enhanced sensitivity was achieved by introducing the multi-bioconjugates of HRP-Ab2-CNSs onto the electrode surface through sandwich immunoreactions. Secondly, functionalized graphene sheets used for the biosensor platform increased the surface area to capture a large amount of primary antibodies (Ab1), thus amplifying the detection response. This amplification strategy is a promising platform for clinical screening of cancer biomarkers and point-of-care diagnostics.
2010. "Formation of O Adatom Pairs and Charge Transfer upon O-2 Dissociation on Reduced TiO2(110)." Physical Chemistry Chemical Physics. PCCP 12(24):6337-6344. Abstract Scanning tunneling microscopy and density functional theory have been used to investigate the details of O2 dissociation leading to the formation of oxygen adatom (Oa) pairs at terminal Ti sites. An intermediate, metastable Oa-Oa configuration with two nearest-neighbor O atoms is observed after O2 dissociation at 300 K. The nearest-neighbor Oa pairs are destabilized by Coulomb repulsion of charged Oa’s that separate further along the Ti row into energetically more favorable second-nearest neighbor configuration. The potential energy profile calculated for O2 dissociation on Ti rows and following Oa’s separation strongly supports the experimental observations. Furthermore, our results suggest that the itinerant electrons associated with the O vacancies are being utilized in the O2 dissociation process at the Ti row, whereas at least two oxygen vacancies per O2 molecule are required in order for this process to become viable.
2010. "Water Interactions with Terminal Hydroxyls on TiO2 (110)." Journal of Physical Chemistry C 114(40):17080-17084. doi:10.1021/jp1036876 Abstract A combination of scanning tunneling microscopy and density functional theory has been used to investigate the interactions between water molecules and terminal hydroxyls (OHt’s) adsorbed on the TiO2(110) surface at 300 K. We show that OHt’s have a significant effect on the water reactivity. Two distinctive reaction pathways are unraveled depending on the whether H2O and OHt are on the same or adjacent Ti rows. The underlying reaction mechanisms involve proton transfer from H2O to OHt leading to the formation of new H2O molecules, accompanied by O scrambling and along- or across-row apparent motion of OHt’s.