Scientific Publications 2005
2005. "Proteome Analysis of Liver Cells Expressing a Full- Length Hepatitis C Virus (HCV) Replicon and Biopsy Specimens of Posttransplantation Liver from HCV-Infected Patients." Journal of Virology 79(12):7558-7569. Abstract The development of a reproducible model system for the study of Hepatitis C virus (HCV) infection has the potential to significantly enhance the study of virus-host interactions and provide future direction for modeling the pathogenesis of HCV. While there are studies describing global gene expression changes associated with HCV infection, changes in the proteome have not been characterized. We report the first large scale proteome analysis of the highly permissive Huh-7.5 cell line containing a full length HCV replicon. We detected > 4,400 proteins in this cell line, including HCV replicon proteins, using multidimensional liquid chromatographic (LC) separations coupled to mass spectrometry (MS). The set of Huh-7.5 proteins confidently identified is, to our knowledge, the most comprehensive yet reported for a human cell line. Consistent with the literature, a comparison of Huh-7.5 cells (+) and (-) the HCV replicon identified expression changes of proteins involved in lipid metabolism. We extended these analyses to liver biopsy material from HCV-infected patients where > 1,500 proteins were detected from 2 g protein lysate using the Huh-7.5 protein database and the accurate mass and time (AMT) tag strategy. These findings demonstrate the utility of multidimensional proteome analysis of the HCV replicon model system for assisting the determination of proteins/pathways affected by HCV infection. Our ability to extend these analyses to the highly complex proteome of small liver biopsies with limiting protein yields offers the unique opportunity to begin evaluating the clinical significance of protein expression changes associated with HCV infection.
2005. "Low-temperature Polymorphs of ZrO2 and HfO2. A Density Functional Theory Study." Physical Review. B, Condensed Matter and Materials Physics 72(14):144107. Abstract We present density functional calculations of the total energies and equations of state of the monoclinic, tetragonal, cubic, orthorhombic-I (Pbca) and orthorhombic-II (cotunnite)-structure phases of zirconia and hafnia in the local density (LDA) and generalized-gradient (GGA) approximations. The accuracy of the LDA approximation is not sufficient and GGA corrections are critical to obtain low-temperature phase transitions under pressure that are consistent with experiment, i.e., (monoclinic‡ orthorhombic-I ‡ cotunnite). The GGA values of the bulk modulus of the cotunnite phase were found to be 251 and 259 GPa for ZrO2 and HfO2, respectively. We developed a new population analysis scheme in which atomic radii are adapted to the actual charge distribution in the material. The results indicate that the effective atomic radius of Hf is smaller than that of Zr, which is a drastic manifestation of the relativistic lanthanide contraction. The population analysis results demonstrate that ionicity: (i) increases from the monoclinic to the cotunnite phase, and (ii) is larger for HfO2 than for ZrO2. This variable ionicity may be the reason why LDA fails to describe the relative stability of different polymorphs. The bandgap and heat of formation are also larger for monoclinic HfO2 than for ZrO2 by 0.6 eV and 0.60 eV/formula unit, respectively. The tetragonal phase, which often exists as a metastable phase at ambient conditions, has a bandgap larger than the monoclinic phase by 0.35 and 0.65 eV for ZrO2 and HfO2, respectively.
2005. "Oxygen Vacancies and Ferromagnetism in CoxTi₁–xO₂–x–y." Journal of Applied Physics 97(7):073908 (6 p.). Abstract Abstract: Cobalt-doped titanium dioxide, or CTO, has emerged in the past two years as a semiconducting, transparent, room-temperature ferromagnet. Very recently it has been shown that the magnetism in CTO often originates in surface nanoparticles or Co-rich regions that have a much-enhanced substitutional Co content up to 40% of Ti sites, so that magnetic CTO is not a true dilute magnetic semiconductor (DMS), but rather a fairly high-density spin system. In this work we describe a computational study of Co-rich CTO using the Generalized Gradient Approximation (GGA) to density functional theory (DFT) within the supercell model. Our total energy calculations show a strong tendency for Co-atom clustering or segregation on Ti sites. There is also a strong tendency for the oxygen vacancies to form complexes with the Co atoms. In addition, we find that the oxygen stoichiometry plays an essential role in determining the system’s magnetic order. The largest ordered moments require at least enough oxygen vacancies to put all of the Co atoms in the +2 charge state, as they indeed appear to be experimentally, so that the conventional DMS mechanism could only apply via n-type carriers. We find a small but not negligible spin density associated with Ti atoms near the vacancy sites, suggesting an F-center-mediated interaction between the much larger Co moments. We also present experimental data showing that the ferromagnetic remanence and coercive field increase with the n-type conductivity.
2005. "CONTROL OF FE(III) SITE OCCUPANCY ON THE RATE AND EXTENT OF MICROBIAL REDUCTION OF FE(III) IN NONTRONITE." Geochimica et Cosmochimica Acta 69(23):5429-5440. doi:10.1016/j.gca.2005.07.008 Abstract A quantitative study was performed to understand how Fe(III) site occupancy controls Fe(III) bioreduction in nontronite by Shewanella putrefaciens CN32. NAu-1 and NAu-2 were nontronites and contained Fe(III) in different structure sites with 16% and 23% total iron (w/w), respectively, with almost all iron as Fe(III). Mössbauer spectroscopy showed that Fe(III) was present in the octahedral site in NAu-1 (with a small amount of goethite), but in both the tetrahedral and the octahedral sites in NAu-2. Mössbauer data further showed that the octahedral Fe(III) in NAu-2 existed in at least two environments- trans (M1) and cis (M2) sites. The microbial Fe(III) reduction in NAu-1 and NAu-2 was studied in batch cultures at a nontronite concentration of 5mg/mL in bicarbonate buffer with lactate as the electron donor. Fe(II) production in inoculated treatments was determined by extraction with 0.5 N HCl and compared to uninoculated controls to establish the extent of biological reduction. The resulting solids were characterized by X-ray diffraction (XRD), Mössbauer spectroscopy, and transmission electron microscopy (TEM). In the presence of an electron shuttle, anthraquinone-2,6-disulfonate (AQDS), the extent of bioreduction was 11-16% for NAu-1 but 28-32% for NAu-2. The extent of reduction in the absence of AQDS was only 5-7% in NAu-1 but 14-18% in NAu-2. The reduction rate was also faster in NAu-2 than that in NAu-1. Mössbauer data of the bioreduced nontronite materials indicated that the Fe(III) reduction in NAu-1 was mostly from the presence of goethite, whereas the reduction in NAu-2 was due to the presence of the tetrahedral and trans-octahedral Fe(III) in the structure. The measured aqueous Fe(II) was negligible [< 2.5% of the total biogenic Fe(II)]. As a result of bioreduction, the average nontronite particle thickness remained nearly the same (from 2.1 to 2.5 nm) for NAu-1, but decreased significantly from 6 to 3.5 nm for NAu-2 with a concomitant change in crystal size distribution. The decrease in crystal size suggests reductive dissolution of nontronite NAu-2, which was supported by aqueous solution chemistry (i.e., aqueous Si). These data suggest that the more extensive Fe(III) bioreduction in NAu-2 was due to the presence of the tetrahedral and the trans-octahedral Fe(III), which was presumed to be more reducible. The biogenic Fe(II) was not associated with biogenic solids such as siderite or green rust or in the aqueous solution. We infer that it may be either adsorbed onto surfaces of nontronite particles/bacteria and in the structure of nontronite. Furthermore, we have demonstrated that natural nontronite clays were capable of supporting cell growth even in non-growth medium, possibly due to presence of naturally existing nutrients in the nontronite clays. These results suggest that crystal chemical environment of Fe(III) is an important determinant in controlling the rate and extent of microbial reduction of Fe(III) in nontronite.
2005. "Anhydrous and Water-Assisted Proton Mobility inPhosphotungstic Acid." Journal of the American Chemical Society 127(14):5238-5245. doi:10.1021/ja042742o Abstract The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. Nonlocal gradient-corrected density functional theoretical calculations were used to determine the energetics associated with proton migration in phosphotungstic acid. The activation energy for anhydrous proton hopping between two oxygen atoms on the exterior of the molecular Keggin unit was calculated to be 103.3 kJ mol-1. The quantum-tunneling effect on the rate of proton movement was determined using semiclassical transition-state theory and was found to be a major contributor to the overall rate of proton movement at temperatures below approximately 350 K. The adsorption of water on an acidic proton decreases the activation barrier for hopping to 11.2 kJ mol-1 by facilitating proton transfer along hydrogen bonds. The overall rate constant for proton hopping was determined as a function of temperature and water partial pressure. Small amounts of water greatly enhance the overall rate of proton movement.
2005. "The Relationship Between Adsorption and Solid Acidityof Heteropolyacids." Catalysis Today 105(1):134-143. doi:10.1016/j.cattod.2005.04.014 Abstract The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. The adsorption energy of a base to a solid acid catalyst is often assumed to correlate with the acid strength of the catalyst. In this study, the influences of adsorbate type, binding configuration and solid acid composition on the adsorption energy are explored using quantum chemical methods. In particular, density functional theory is used to calculate the adsorption energies of functionalized hydrocarbons containing O, N, or S heteroatoms or C C to phosphotungstic (H₃PW₁₂O₄₀) and phosphomolybdic (H₃PMo₁₂O₄₀) acids. The adsorption energies of the different molecules bound to the same solid acid are not easily predicted by the proton affinity of the adsorbate because the stabilization of the protonated adsorbate also varies with composition. Bond order conservation helps to explain the relatively small variance in adsorption energies among reactants of widely varying base strength. The activation barriers to form carbenium-ion transition states from adsorbed olefins are also calculated over the two heteropolyacids. The stronger adsorption of propylene to phosphotungstic acid compared to phosphomolybdic acid results in a higher activation barrier to form the carbenium-ion transition state. These heteropolyacids are predicted to have higher activation barriers than zeolites for carbenium-ion formation, which is typically thought to be the rate controlling step in many hydrocarbon conversion processes. This contrasts with the ranking of acid strength based solely on the magnitude of the adsorption energy.
2005. "Finite Lifetime Effects on the Polarizability Within Time-dependentDensity-functional Theory." Journal of Chemical Physics 122:224115 1-11. doi:10.1063/1.1929740 Abstract The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. We present an implementation for considering finite lifetime of the electronic excited states into linear-response theory within time-dependent density-functional theory. The lifetime of the excited states is introduced by a common phenomenological damping factor. The real and imaginary frequency-dependent polarizabilities can thus be calculated over a broad range of frequencies. This allows for the study of linear-response properties both in the resonance and nonresonance cases. The method is complementary to the standard approach of calculating the excitation energies from the poles of the polarizability. The real and imaginary polarizabilities can then be calculated in any specific energy range of interest, in contrast to the excitation energies which are usually solved only for the lowest electronic states. We have verified the method by investigating the photoabsorption properties of small alkali clusters. For these systems, we have calculated the real and imaginary polarizabilities in the energy range of 1–4 eV and compared these with excitation energy calculations. The results showed good agreement with both previous theoretical and experimental results.
2005. "Experimental and Theoretical Investigation of the Electronic and Geometrical Structures of the Au₃₂ Cluster." Angewandte Chemie International Edition 44(43):7119-7123. doi:10.1002/anie.200502795 Abstract Photoelectron spectroscopy and theoretical calculations are used to elucidate the structure of the Au₃₂- cluster. Although density functional calculations suggest that the high symmetry Ih cage structure of Au₃₂ remains to be the lowest in energy for Au₃₂- at 0 K, the calculated photoelectron spectrum of a low-lying amorphous structure (C1) is found to agree best with the experiment. Free energy calculations show that the C1 structure becomes the most stable isomer at higher temperatures, indicating the importance of entropy in determining the stability of clusters at finite temperatures.
2005. "Experimental and Theoretical Investigation of the Electronic and Geometrical Structures of the Special Au₃₂ Cluster ." Angewandte Chemie International Edition 44(43):7119-7123. doi:10.1002/anie.200502795 Abstract Photoelectron spectroscopy and theoretical calculations are used to elucidate the structure of the Au₃₂ - cluster. Although density functional calculations suggest that the high symmetry Ih cage structure of Au₃₂ remains to be the lowest in energy for Au₃₂ - at 0 K, the calculated photoelectron spectrum of a low-lying amorphous structure (C₁) is found to agree best with the experiment. Free energy calculations show that the C₁ structure becomes the most stable isomer at higher temperatures, indicating the importance of entropy in determining the stability of clusters at finite temperatures.
2005. "Interface structure and perpendicular exchange bias in (Co/Pt)n /FeMn multilayers." Journal of Applied Physics 98(11):116101-1 - 116101-3. doi:10.1063/1.2137878 Abstract We have performed a critical experimental evaluation of the dependence of both perpendicular magnetic anisotropy and exchange bias on the structure of the ferromagnet FM/nonferromagnet and FM/antiferromagnet interfaces of Co/Ptn)and (Co/Ptn) /FeMn multilayers. The growth of these heterostructures by ion-beam sputtering was optimized and the characteristics of their interfaces were systematically controlled by varying the ion-beam energy from 250 to 1500 eV. Calculated effective anisotropy constants and exchange bias fields from hysteresis loops were correlated with both structural roughness and the degree of interdiffusion measured by x-ray reflectivity. Whilst the physical roughness remained unchanged, the degree of interdiffusion was found to increase with higher ion-beam energy – and concurrently the magnetic anisotropy changed from perpendicular to in plane – leading directly to a decrease in exchange bias and coercivity.
2005. "Accumulation and Recovery of Disorder in Au2+-Irradiated Cd2Nb2O7." Nuclear Instruments and Methods in Physics Research. Section B, Beam Interactions with Materials and Atoms 241(1-4):372-376. Abstract Cadmium niobate pyrochlore (Cd2Nb2O7) single crystals have been irradiated at 150, 300, 450 and 600 K using 1.0 MeV Au2+ ions over fluences ranging from 0.01 to 3.5 ions/nm2. The relative disorder on the Cd sublattice in the as-irradiated Cd2Nb2O7 has been analyzed based on in-situ 3.0 MeV He+ Rutherford backscattering spectrometry along the <100>-axial channeling direction. The results show that the crystal can be readily amorphized under the Au2+ irradiation at or below 450 K; however, the relative Cd disorder tends to saturate at 600 K, and full amorphization does not occur at doses up to 5 dpa. Isochronal annealing (20 min) also has been performed at temperatures from 180 to 295 K for samples irradiated at 150 K. Thermal recovery of the disorder has been observed below room temperature.
2005. "Cadmium Nanowire Formation Induced by Ion Irradiation." Advanced Materials 17(13):1602-1606. Abstract One-dimensional nanostructures, such as nanowires, of semiconductors and metals are of great technological interest due to their potential for many advanced technology applications. Utilization of these materials versus their bulk counterparts will not only allow for device miniaturisation, but also may improve device performance or create new functions. Here we report a novel method for the synthesis of crystalline Cd-nanowires without involving either templates or a “seeded” structure. Ion irradiation at low temperatures (≤ 295 K) has been used to induce material decomposition and phase segregation in a cadmium niobate pyrochlore (Cd2Nb2O7) wafer. During the formation and rupture of the gas-filled blisters in the material, soft metallic Cd is extruded/extracted as nanowires through pores in the exfoliated layer. The entire process may be readily controlled by changing the ion irradiation conditions (e.g., ion species, dose and energy) with minimal thermal constraints.
2005. "Erratum to: “Carbon analysis using energetic ion beams” [Nucl. Instr. and Meth. B 222 (2004) 538-546] ." Nuclear Instruments and Methods in Physics Research. Section B, Beam Interactions with Materials and Atoms 227(3):450-451. Abstract This paper corrects the energy calibration for the accelerator system we used for carbon cross section measurements.
2005. "Nitrogen Analysis Using Energetic Ion Beams." Surface and Interface Analysis 37(4):374-378. Abstract As a special case of nuclear reaction analysis (NRA), nuclear elastic scattering analysis (or non-Rutherford scattering analysis) is one of the important methods in ion-beam analysis, and is the preferred technique to analyze light elements in a heavy matrix. Compared to nuclear reaction, nuclear scattering usually has cross sections several orders of magnitude larger, which allows a quantitative analysis of light elements in a quicker and more convenient manner. Similar to NRA, this method complements the analysis of widely used Rutherford backscattering spectrometry. In this study, the scattering cross-sections for 14N(p,p)14N and 14N(alpha,alpha)14N at a laboratory angle of 150 degrees are measured over energy regions from 2.480 to 3.774 MeV using an amorphous film of Si3N4 on Si wafer. Examples for the analysis of lattice disorder on the N sublattice in Au2+-irradiated GaN single crystals will be demonstrated.
2005. "On-line Analysis of Organic Compounds in Diesel Exhaust Using a Proton Transfer Reaction Mass Spectrometer (PTR-MS)." International Journal of Mass Spectrometry 245(1-3):78-89. Abstract Chemical ionization mass spectrometry using H3O+ proton transfer in an ion drift tube (PTR-MS) was used to measure volatile organic compound (VOC) concentrations on-line in diesel engine exhaust as a function on engine load. The purpose of the study was to evaluate the PTR-MS instrument as an analytical tool for diesel engine emissions abatement research. Measured sensitivities determined from gas standards were found to be between 30% and 100% greater than calculated sensitivities. A slight humidity dependent sensitivity was observed for non-polar species, implying that reactions with H+(H2O)2 were important for some organics. The mass spectra of diesel exhaust were complex but displayed a pattern of strong ion signals at 14n+1 (n=3..8) masses, with a relative ion abundance similar to that obtained from electron impact ionization of alkanes. Laboratory experiments verified that C8-C16 n-alkanes and C8-C13 1-alkenes react with H3O+ in dissociative proton transfer reaction resulting in alkyl cation ion products, primarily m/z 41, 43, 57, 71 and 85. Monitoring the sum of these ions signals may be useful for estimating alkane emissions from unburnt diesel fuel. Alkane fragmentation likely simplified the diesel exhaust mass spectrum and reduced potential mass interferences with isobaric aromatic compounds. It is shown that the relative abundances of VOCs changed as a function of engine load. Concentrations of aldehydes and ketones dominated those of aromatic species with formaldehyde and acetaldehyde estimated to be the most abundant VOCs in the PTR-MS mass spectrum at all engine loads. The relative abundances of benzene and toluene increased with engine load indicating their pyrogenic origin. The relative abundance of alkanes, aromatics, aldehydes, and alcohols was broadly consistent with literature publications of diesel exhaust analysis by gas chromatography. About 75% of the organic ion signal could be assigned. On line analysis of diesel exhaust using this technology may be valuable tool for diesel engine emission research.
2005. "Chalcogenide nanowires by evaporation-condensation." Journal of Non-crystalline Solids 351 :1410–1416. Abstract Chalcogenide (arsenic sulfide) nanowires have been successfully synthesized from As2S3 under near-equilibrium conditions via evaporation–condensation process in evacuated glass ampoules. The as-synthesized nanowires were pure, nearly stoichiometric, and amorphous. The nanowires had diameters ranging from 40 to 140 nm and lengths up to a few millimeters. Distinct joints of the crisscrossing nanowires indicate potential for forming structural networks. They have been characterized using scanning electron microscopy (SEM), transmission electron microscopy (TEM), energy dispersive spectroscopy (EDS), Raman spectroscopy, and X-ray diffraction (XRD) to determine their structure, composition, and morphology. Selected area diffraction (SAD) in the TEM and XRD confirmed their amorphous nature. The As–S nanowires could make an ideal system for understanding the carrier transport and photonic properties in nanoscale for this family of materials (IV–V compounds). Chalcogenide nanowires show promise for integrated nanoelectronics and biophotonics.
2005. "Processing of Soot in an Urban Environment: Case Study from the Mexico City Metropolitan Area." Atmospheric Chemistry and Physics 5:3033-3043. Abstract Chemical composition, size, and mixing state of atmospheric particles are critical in determining their e ffects on the environment. There is growing evidence that soot aerosols play a particularly important role in both climate and human health, but still relatively little is known of their physical and chemical nature. In addition, the atmo- 5 spheric residence times and removal mechanisms for soot are neither well understood nor adequately represented in regional and global climate models. To investigate the effect of locality and residence time on properties of soot and mixing state in a polluted urban environment, particles of diameter 0.2–2.0 µm were collected in the Mexico City Metropolitan Area (MCMA) during the MCMA-2003 field campaign from various sites 10 within the city. Individual particle analysis by di fferent electron microscopy methods coupled with energy dispersed X-ray spectroscopy, and secondary ionization mass spectrometry show that freshly-emitted soot particles become rapidly processed in the MCMA. Whereas fresh particulate emissions from mixed-tra ffic are almost entirely carbonaceous, consisting of soot aggregates with liquid coatings suggestive of unburned 15 lubricating oil and water, ambient soot particles which have been processed for less than a few hours are heavily internally mixed, primarily with ammonium sulfate. Single particle analysis suggests that this mixing occurs through several mechanisms that require further investigation. In light of previously published results, the internally-mixed nature of processed soot particles is expected to a ffect heterogeneous chemistry on 20 the soot surface, including interaction with water during wet-removal.
2005. "Investigation of Microstructure and V-defect Formation in InxGa₁-xN/GaN MQW Grown using Temperature-Gradient Metalorganic Chemical Vapor Deposition." Journal of Electronic Materials 34(5):605-611. Abstract Temperature-gradient Organometallic Vapor Phase Epitaxy (OMVPE) was used to deposit InxGa₁-xN/GaN MQW structures with a concentration gradient of In across the wafer. These MQW structures were deposited on low defect density (1.7x10⁸ cm⁻²) GaN template layers for investigation of microstructural properties and V-defect formation. Room temperature (RT) photoluminescence (PL) and photomodulated transmission (PT) were used for optical characterization. Triple-axis X-ray diffraction (TAXRD) and cross-section transmission electron microscopy (XTEM) were used to obtain microstructural properties of different regions across the wafer. Results show that there is a decrease in crystal quality and an increase in V-defect formation with increasing indium concentration. The depth of extension of the V-defects also increases with decreasing growth temperature and increased indium concentration. A direct correlation is found between V-defect density and growth temperature due to increased strain for increasing indium concentration.
2005. "Mid-Infrared Versus Far-Infrared (THz) Relative Intensities of Room-temperature Bacillus Spores." Chemical Physics Letters 403(1-3):152-157. Abstract We have simultaneously recorded the mid-IR and far-IR (sometimes called terahertz, THz) spectra of the sporulated form of five common Bacillus bacteria: Bacillus subtilis ATCC 49760, Bacillus subtilis ATCC 6051, B. thuringiensis subsp. kurstaki ATCC 35866, Bacillus globigii 01, and B. atrophaeus 49337. The 295 K spectra were recorded from ~8 to 6,000 cm-1 of samples deposited onto windows transparent in both the mid- and far-infrared. The results indicate that any room-temperature THz absorption features due to the bacterial spores are at least 28 times weaker (based on p-p noise) than the corresponding mid-IR amide I band.
2005. "Upconversion Luminescence of CdTe Nanoparticles." Physical Review. B, Condensed Matter 71:165304. doi:10.1103/PhysRevB.71.165304 Abstract Efficient upconversion luninescence is observed from CdTe nanoparticles in solution and precipitated as solids. In the solids, the upconversion luminescence spectrum is significantly red-shifted relative to the normal photoluminescence, whereas in solution, there is very little spectral shift. The upconversion luminescence exhibits a near quadratic laser power dependencem, both at room temperature and at 10K. Both the upconversion and photoluminescence show similar decay dynamics with the solid samples showing shorter lifetimes compared to the solutions. This lifetime shortening is attributed to surface states is the likely upconversion excitation mechanism in these particles and that phonon populated defeat do not contribute to the upconversion.