Scientific Publications 2010
2010. "Molecular investigations into a globally important carbon pool: permafrost-protected carbon in Alaskan soils." Global Change Biology 16(9):2543-2554. doi:10.1111/j.1365-2486.2009.02141.x Abstract The fate of carbon (C) contained within permafrost in boreal forest environments is an important consideration for the current and future carbon cycle as soils warm in northern latitudes. Currently, little is known about the microbiology or chemistry of permafrost soils that may affect its decomposition once soils thaw. We tested the hypothesis that low microbial abundances and activities in permafrost soils limit decomposition rates compared with active layer soils. We examined active layer and permafrost soils near Fairbanks, AK, the Yukon River, and the Arctic Circle. Soils were incubated in the lab under aerobic and anaerobic conditions. Gas fluxes at -5 and 5ºC were measured to calculate temperature response quotients (Q₁₀). The Q₁₀ was lower in permafrost soils (average 2.7) compared with active layer soils (average 7.5). Soil nutrients, leachable dissolved organic C (DOC) quality and quantity, and nuclear magnetic resonance spectroscopy of the soils revealed that the organic matter within permafrost soils is as labile, or even more so, than surface soils. Microbial abundances (fungi, bacteria, and subgroups: methanogens and Basidiomycetes) and exoenzyme activities involved in decomposition were lower in permafrost soils compared with active layer soils, which, together with the chemical data, supports the reduced Q₁₀ values. CH₄ fluxes were correlated with methanogen abundance and the highest CH₄ production came from active layer soils. These results suggest that permafrost soils have high inherent decomposability, but low microbial abundances and activities reduce the temperature sensitivity of C fluxes. Despite these inherent limitations, however, respiration per unit soil C was higher in permafrost soils compared with active layer soils, suggesting that decomposition and heterotrophic respiration may contribute to a positive feedback to warming of this eco region.
2010. "Green Rust Reduction of Chromium Part 2: Comparison of Heterogeneous andHomogeneous Chromate Reduction." Journal of Physical Chemistry C 114(39):16408-16415. doi:10.1021/jp1021328 Abstract White and green rusts are the active chemical reagents of buried scrap iron pollutant remediation. In this work, a comparison of the initial electron-transfer step for the reduction of CrO4-2 by Fe₂+(aq) and Fe(OH)₂(s)is presented. Using hybrid density functional theory and Hartree-Fock cluster calculations for the aqueous reaction, the rate constant for the homogeneous reduction of chromium by ferrous iron was determined to be 5 × 10¯² M¯¹s¯¹ for the initial electron transfer. Using a combination of Hartree-Fock slab and cluster calculations for the heterogeneous reaction, the initial electron transfer for the heterogeneous reduction of chromium by ferrous iron was determined to be 1 × 10² s ¯¹. The difference in rates is driven by the respective free energies of reaction: 33.4 vs -653.2 kJ/mol. This computational result is apparently the opposite of what has been observed experimentally, but further analysis suggests that these results are fully convergent with experiment. The experimental heterogeneous rate is limited by surface passivation from slow intersheet electron transfer, while the aqueous reaction may be an autocatalytic heterogeneous reaction involving the iron oxyhydroxide product. As a result, it is possible to produce a clear model of the pollutant reduction reaction sequence for these two reactants.
2010. "In-situ Transmission Electron Microscopy and Spectroscopy Studies of Interfaces in Li-ion Batteries: Challenges and Opportunities." Journal of Materials Research 25(8):1541-1547. doi:10.1557/JMR.2010.0198 Abstract The critical challenge facing the lithium ion battery development is the basic understanding of the structural evolution during the cyclic operation of the battery and the consequence of the structural evolution on the properties of the battery. Although transmission electron microscopy (TEM) and spectroscopy have been evolved to a stage such that it can be routinely used to probe into both the structural and chemical composition of the materials with a spatial resolution of a single atomic column, a direct in-situ TEM observation of structural evolution of the materials in lithium ion battery during the dynamic operation of the battery has never been reported. This is related to three factors: high vacuum operation of a TEM; electron transparency requirement of the region to be observed, and the difficulties dealing with the liquid electrolyte of lithium ion battery. In this paper, we report the results of exploring the in-situ TEM techniques for observation of the interface in lithium ion battery during the operation of the battery. A miniature battery was fabricated using a nanowire and an ionic liquid electrolyte. The structure and chemical composition of the interface across the anode and the electrolyte was studied using TEM imaging, electron diffraction, and electron energy loss spectroscopy. In addition, we also explored the possibilities of carrying out in-situ TEM studies of lithium ion batteries with a solid state electrolyte.
2010. "Core-Shell Structured Magnetic Ternary Nanocubes." Journal of the American Chemical Society 132(50):17686-17689. doi:10.1021/ja1091084 Abstract While transition metal-doped ferrite nanoparticles constitute an important class of soft magnetic nanomaterials with spinel structures, the ability to control the shape and composition would enable a wide range of applications in homogeneous or heterogeneous reactions such as catalysis and magnetic separation of biomolecules. This report describes novel findings of an investigation of core-shell structured MnZn ferrite nanocubes synthesized in organic solvents by manipulating the reaction temperature and capping agent composition in the absence of the conventionally-used reducing agents. The core-shell structure of the highly-monodispersed nanocubes (~20 nm) are shown to consist of an Fe3O4 core and an (Mn0.5Zn0.5)(Fe0.9, Mn1.1)O4 shell. In comparison with Fe3O4 and other binary ferrite nanoparticles, the core-shell structured nanocubes were shown to display magnetic properties regulated by a combination of the core-shell composition, leading to a higher coercivity (~350 Oe) and field-cool/zero-field-cool characteristics drastically different from many regular MnZn ferrite nanoparticles. The findings are discussed in terms of the unique core-shell composition, the understanding of which has important implication to the exploration of this class of soft magnetic nanomaterials in many potential applications such as magnetic resonance imaging, fuel cells, and batteries.
2010. "Highly efficient blue organic light emitting devices with indium-free transparent anode on flexible substrates." Organic Electronics 11(9):1555-1560. doi:10.1016/j.orgel.2010.06.018 Abstract Indium-free transparent conducting oxides may provide a lower cost solution for the transparent anode in flexible displays and energy efficient solid state lighting. We report herein a near room temperature sputtering process for generating an indium-free transparent conductive oxide (TCO) coating on a flexible substrate. Specifically, we deposited gallium-doped zinc oxide (GZO) uniformly over a 12” diameter area at room temperature on polyethylene terephthalate (PET). During deposition, the system heats to about 60oC due to the energetic sputtering conditions, without any noticeable damage to the PET substrate. The GZO films exhibit excellent physical, optical and electrical properties: roughness ~7 nm, transmittance >85% and resistivity ~ 10-3 ohm• cm. Phosphorescent blue organic light-emitting devices (OLEDs) were fabricated on these substrates with comparable performance (16% external quantum efficiency and 33 lm/W power efficiency at 1mA/cm2) to that of devices fabricated on GZO (or ITO) deposited on glass substrates, suggesting flexible GZO/PET substrates may be used instead of high-cost and rigid ITO and glass for flexible displays and solid state lighting.
2010. "Hydrolysis of TiCl₄: Initial Steps in the Production of TiO₂." Journal of Physical Chemistry A 114(28):7561-7570. doi:10.1021/jp102020h Abstract The hydrolysis of titanium tetrachloride (TiCl₄) to produce titanium dioxide (TiO₂)nanoparticles has been studied to provide insight into the mechanism for forming these nanoparticles. We provide calculations of the potential energy surfaces, the thermochemistry of the intermediates, and the reaction paths for the initial steps in the hydrolysis of TiCl₄. We assess the role of the titanium oxychlorides (TiₓOyClz; x ) 2-4, y ) 1,3-6, and z ) 2, 4, 6) and their viable reaction paths. Using transition-state theory and RRKM theory, we predicted rate constants including the effect of tunneling. Heats of formation at 0 and 298 K are predicted for TiCl₄, TiCl₃OH, TiOCl₂, TiOClOH, TiCl₂(OH)₂, TiCl(OH)₃, Ti(OH)₄, and TiO₂ using the CCSD(T) method with correlation consistent basis sets extrapolated to the complete basis set limit and compared with the available experimental data. Clustering energies and heats of formation are calculated for neutral clusters. The calculated heats of formation were used to study condensation reactions that eliminate HCl or H₂O. The reaction energy is substantially endothermic if more than two HCl molecules are eliminated. The results show that the mechanisms leading to formation of TiO₂ nanoparticles and larger ones are complicated and will have a strong dependence on the experimental conditions.
2010. "Electron Affinities and Electronic Structures of o-, m-, and p- Hydroxyphenoxyl Radicals: A Combined Low-Temperature Photoelectron Spectroscopic and Ab initio Calculation Study." Journal of Physical Chemistry A 114(34):9083-9089. Abstract Hydroxyl substituted phenoxide, o-, m-, p- HO(C6H4)O– and the corresponding neutral radicals are important species, in particularly, the p- isomer pair is directly involved in the proton-coupled electron transfer in biological photosynthetic centers. Here we report the first spectroscopic study of these species in the gas phase by means of low-temperature photoelectron spectroscopy (PES) and ab initio calculations. Vibrationally resolved PES spectra were obtained at 70 K and several photon energies for each anion, directly yielding electron affinity (EA) and electronic structure information of the corresponding hydroxyphenoxyl radical. The EAs are found to vary with OH positions, from 1.990 ± 0.010 eV (p-) to 2.315 ± 0.010 (o-) and 2.330 ± 0.010 (m-). Theoretical calculations were carried out to identify the optimized molecular structures for both anions and neutral radicals. The electron binding energies and excited state energies were also calculated to compare with experimental data. Excellent agreement is found between calculations and experiments. Molecular orbital analyses indicate strong OH anti-bonding interaction with the phenoxide moiety for o- as well as p- isomers, whereas such interaction is largely missing for the m- anion. The variance of EAs among three isomers is interpreted primarily due to the interplay between two competing factors: the OH anti-bonding interaction and H-bonding stabilization (existed only in the o- anion).
2010. "Photoelectron Spectroscopy of C60Fn- and C60Fm2- (n=17,33,35,43,45,47;m=34,46) in the Gas Phase and the Generation and Characterization of C1-C60F47- and D2-C60F44 in Solution." Journal of Physical Chemistry A 114(4):1756-1765. Abstract A photoelectron spectroscopy investigation of the fluorofullerene anions C60Fn− (n = 17, 33, 35, 43, 45, 47) and the doubly-charged anions C60F342− and C60F462− is reported. The electron affinities for the corresponding neutral molecules, C60Fn, were directly measured and were found to increase as n increased, reaching the extremely high value of 5.66 ± 0.10 eV for C60F47. Density functional calculations suggest that the experimentally observed species C60F17−, C60F35−, and C60F47− were each formed by reductive-defluorination of the parent fluorofullerene, C3v-C60F18, C60F36 (a mixture of isomers), and D3-C60F48, respectively, without rearrangement of the remaining fluorine atoms. The DFT-predicted stability of C60F47− was verified by its generation by chemical reduction from D3-C60F48 in chloroform solution at 25 °C and its characterization by mass spectrometry and 19F NMR spectroscopy. Further reductive-defluorination of C60F47− in solution resulted in the selective generation of a new fluorofullerene, D2-C60F44, which was also characterized by mass spectrometry and 19F NMR spectroscopy.
2010. "Stepwise hydration of the cyanide anion: A temperature-controlled photoelectron spectroscopy and ab initio computational study of CN-(H2O)n(n=2-5)." Journal of Chemical Physics 132(12):124306/1-10. doi:10.1063/1.3360306 Abstract We report the study of microsolvated CN-(H2O)n (n = 1-5) clusters in the gas phase using a combination of experimental and computational approaches. The hydrated cyanide clusters were produced by electrospray and their structural and energetic properties were probed using temperature-controlled photoelectron spectroscopy (PES) and ab initio electronic structure calculations. Comparison between the low temperature (T = 12 K) and the room-temperature (RT) spectra shows a 0.25 eV spectral blue shift in the binding energy of the n = 1 cluster and a significant spectral sharpening and blue shift for n = 2 and 3. The experimental results are complemented with ab initio electronic structure calculations at the MP2 and CCSD(T) levels of theory that identified several isomers on the ground state potential energy function (PEF) arising from the ability of CN- to form hydrogen bonds with water via both the C and N ends. In all cases the N end seems to be the preferred hydration site. The excellent agreement between the low temperature measured PES spectra and the basis set- and correlation-corrected (at the CCSD(T) level of theory) calculated vertical detachment energies, viz. 3.85 vs. 3.84 eV (n = 0), 4.54 vs. 4.54 eV (n = 1), 5.20 vs. 5.32 eV (n = 2), 5.58 vs. 5.50 eV (n = 3) and 5.89 vs. 5.87 eV (n = 4), allow us to firmly establish the global minimum structures for all the hydrated cyanide clusters. The microsolvation pattern was found to be similar to the halide anions (Cl-, Br- and I-), adopting structures in which CN- resides on the surface of a water network. While at T = 12 K the clusters adopt structures that are close to the minimum energy configurations, at room temperature it is expected that other isomers (lying within ~0.6 kcal/mol above the global minima) are also populated, resulting in the broadening of the PES spectra.
2010. "Nitrogen-Doped Graphene and its Application in Electrochemical Biosensing." ACS Nano 4(4):1790-1798. Abstract Chemical doping with foreign atoms is an effective method to intrinsically modify the properties of host materials. Among them, nitrogen (N) doping plays a critical role in regulating the electronic properties of carbon materials. Recently, graphene as a true 2-dimensional carbon material has shown fascinating applications in bioelectronics and biosensors. In this paper, we report a facile strategy to prepare N-doped graphene by using plasma treatment of pristine graphene synthesized via chemical method. Meanwhile, a possible schematic diagram has been proposed to detail the structure of N-doped graphene. By controlling the exposure time, N percentage in host grapheme can be regulated ranging from 0.11% to 1.35%. Moreover, the as prepared N-doped graphene has displayed high electrocatalytic activity to hydrogen peroxide and further been used for glucose biosensing with concentration as low as 0.01 mM in the presence of interferences.
2010. "Photoelectron Imaging and Spectroscopy of MI2- (M = Cs, Cu, Au): Evolution from Ionic to Covalent Bonding." Journal of Physical Chemistry A 114(42):11244-11251. doi:10.1021/jp103173d Abstract We reporta combined experimental and theoretical investigation on MI2 – (M = Cs, Cu, Ag, Au) to explore the chemical bonding in the group IA and IB di-iodide complexes. Both photoelectron imaging and low-temperature photoelectron spectroscopy are applied to MI2 – (M = Cs, Cu, Au), yielding vibrationally resolved spectra for CuI2 – and AuI2 – and accurate electron affinities, 4.52 ± 0.02, 4.256 ± 0.010, and 4.226 ± 0.010 eV for CsI2, CuI2, and AuI2, respectively. Spin-orbit coupling is found to be important in all the di-iodide complexes and ab initio calculations including spin-orbit effects allow quantitative assignments of the observed photoelectron spectra. A variety of chemical bonding analyses (charge population, bond order, and electron localization functions) have been carried out, revealing a gradual transition from the expected ionic behavior in CsI2 – to strong covalent bonding in AuI2 –. Both relativistic effects and electron correlation are shown to enhance the covalency in the gold di-iodide complex.
2010. "Vibrationally Resolved Photoelectron Spectroscopy of Di-Gold Carbonyl Clusters Au2(CO)n-(n=1-3): Experiment and Theory." Journal of Physical Chemistry A 114(3):1247-1254. doi:10.1021/jp903558v Abstract We report vibrationally-resolved photoelectron spectroscopy (PES) of Au2(CO)n- (n = 1-3), in combination with relativistic density functional theory (DFT) and ab initio calculations. The ground state transition in the spectrum of Au2CO- is broad, containing vibrational structures both in the bending and CO stretching modes and suggesting a large structural change from Au2CO- to Au2CO. The ground state transitions for both n = 2 and 3 display a well resolved vibrational progression in the CO stretching mode with frequencies of 2110 - 40 and 2160 - 40 cm-1, respectively. The PES data show that chemisorption of the first two CO’s each induces a significant red-shift in the electron binding energies. The third CO is physisorbed, inducing only a slight increase in electron binding energies relative to Au2(CO)2-. Relativistic DFT and ab initio calculations are performed to determine the ground-state structures for Au2(CO)n- and Au2(CO)n and the results agree well with the experiment. Au2(CO), Au2(CO)2, and Au2(CO)2- are all found to be linear, while Au2(CO)-- is bent due to the Renner-Teller effect. A strong spin-orbit effect is found in Au2(CO)2- that quenches the Renner-Teller effect, keeping the linear structure for this anion. The physisorption in Au2(CO)3- is borne out in CCSD(T) calculations. However, a wide range of DFT methods used fail to correctly predict the relative energies of physisorbed versus chemisorbed isomers for Au2(CO)3-.
2010. "Direct Observation of Site Specific Molecular Chemisorption of O2 on TiO2 (110)." The Journal of Physical Chemistry Letters 1(24):3524-3529. doi:10.1021/jz101535f Abstract Molecularly chemisorbed O2 species were directly imaged on reduced TiO2(110) at 50 K with high-resolution scanning tunneling microscopy (STM). Two different O2 adsorption channels, one at bridging oxygen vacancies (VO) and another at five-fold coordinated terminal titanium atoms (Ti5c), have been identified. While O2 species at Ti5c site appears as a single protrusion centered on the Ti5c row, the O2 at VO manifests itself by a disappearance of the VO feature. It is found that STM tip can easily dissociate O2 species, unless extremely low magnitudes of the tunneling parameters are used. The O2 molecules chemisorbed at low temperatures at these two distinct sites are the most likely precursors for the two previously established O2 dissociation channels, observed at temperatures above 150 and 230 K at the VO and Ti5c sites, respectively.
2010. "Nanoscale Alloying, Phase-Segregation, and Core-Shell Evolution of Gold-Platinum Nanoparticles and Their Electrocatalytic Effect on Oxygen Reduction Reaction." Chemistry of Materials 22(14):4282-4294. Abstract The design and preparation of active and robust bimetallic catalysts require the understanding of the nanoscale alloying and phase-segregation structures. While platinum-based bimetallic catalysts have been widely explored for oxygen reduction reaction in fuel cells, little has been established for the correlation between the nanoscale phase structures and the catalytic properties. Here we describe new findings of the correlation between the nanoscale phase structures and the electrocatalytic properties of gold-platinum nanoparticles. The alloying and partial or complete phase-segregation were probed as a function of composition, size, thermal treatment temperature and duration by X-ray diffraction, X-ray photoelectron spectroscopy, high-resolution transmission electron microscopy, electrochemical characterization, and density functional theory modeling. The unprecedented thermal control of the alloying and phase segregation provided the basis for establishing the nanostructure−catalysis correlation, which has immediate implications to the design and nanoengineering of a wide variety of advanced bimetallic functional nanostructures.
2010. "Thermal Treatment of PtNiCo Electrocatalysts: Effects of Nanoscale Strain and Structure on the Activity and Stability for the Oxygen Reduction Reaction." Journal of Physical Chemistry C 114(41):17580-17590. doi:10.1021/jp106843k Abstract The ability to control the nanoscale size, composition, phase, and facet of multimetallic catalysts is important for advancing the design and preparation of advanced catalysts. This report describes the results of an investigation of the thermal treatment temperature on nanoengineered platinum-nickel-cobalt catalysts for oxygen reduction reaction, focusing on understanding the effects of lattice strain and surface properties on activity and stability. The thermal treatment temperatures ranged from 400 to 926 °C. The catalysts were characterized by microscopic, spectroscopic, and electrochemical techniques for establishing the correlation between the electrocatalytic properties and the catalyst structures. The composition, size, and phase properties of the trimetallic nanoparticles were controllable by our synthesis and processing approach. The increase in the thermal treatment temperature of the carbon-supported catalysts was shown to lead to a gradual shrinkage of the lattice constants of the alloys and an enhanced population of facets on the nanoparticle catalysts. A combination of the lattice shrinkage and the surface enrichment of nanocrystal facets on the nanoparticle catalysts as a result of the increased temperature was shown to play a major role in enhancing the electrocatalytic activity for catalysts. Detailed analyses of the oxidation states, atomic distributions, and interatomic distances revealed a certain degree of changes in Co enrichment and surface Co oxides as a function of the thermal treatment temperature. These findings provided important insights into the correlation between the electrocatalytic activity/stability and the nanostructural parameters (lattice strain, surface oxidation state, and distribution) of the nanoengineered trimetallic catalysts.
2010. "High-Performance, Superparamagnetic, Nanoparticle-Based Heavy Metal Sorbents for Removal of Contaminants from Natural Waters." ChemSusChem 3(6):749-757. doi:10.1002/cssc.201000027 Abstract We describe the synthesis and characterization of superparamagnetic iron oxide nanoparticle based heavy metal sorbents with various surface chemistries that demonstrate an excellent affinity for the separation of heavy metals in contaminated water systems (i.e. spiked Columbia river water). The magnetic nanoparticle sorbents are prepared from an easy to synthesize iron oxide precursor, followed by a simple, one-step ligand exchange technique to introduce the organic surface functionality of interest chosen to target either specific or broader classes of heavy metals. Functionalized superparamagnetic nanoparticles are excellent sorbent materials for the extraction of heavy metal contaminants from environmental and clinical samples since they are easily removed from the media once bound to the contaminant by simply applying a magnetic field. These engineered magnetic nanoparticle sorbents have an inherently high active surface area (often > 100 m2/g), allowing for increased binding capacity. To demonstrate the potential sorbent performance of each of the surface modified magnetic nanoparticles, river water was spiked with Hg, Pb, Cd, Ag, Co, Cu, and Tl and exposed to low concentrations of the functionalized nanoparticles. The samples were analyzed to determine the metal content before and after exposure to the magnetic nanoparticle sorbents. In almost all cases reported here the nanoparticles were found to be superior to commercially available sorbents binding a wide range of different heavy metals with extremely high affinity. Detailed characterization of the functionalized magnetic nanoparticle sorbents including FT-IR, BET surface analysis, TGA, XPS and VSM as well as the heavy metal removal experiments are presented.
2010. "Combined Statistical Analyses of Peptide Intensities and Peptide Occurrences Improves Identification of Significant Peptides from MS-based Proteomics Data." Journal of Proteome Research 9(11):5748-5756. Abstract Liquid chromatography-mass spectrometry-based (LC-MS) proteomics uses peak intensities of proteolytic peptides to infer the differential abundance of peptides/proteins. However, substantial run-to-run variability in peptide intensities and observations (presence/absence) of peptides makes data analysis quite challenging. The missing abundance values in LC-MS proteomics data are difficult to address with traditional imputation-based approaches because the mechanisms by which data are missing are unknown a priori. Data can be missing due to random mechanisms such as experimental error, or non-random mechanisms such as a true biological effect. We present a statistical approach that uses a test of independence known as a G-test to test the null hypothesis of independence between the number of missing values and the experimental groups. We pair the G-test results evaluating independence of missing data (IMD) with a standard analysis of variance (ANOVA) that uses only means and variances computed from the observed data. Each peptide is therefore represented by two statistical confidence metrics, one for qualitative differential observation and one for quantitative differential intensity. We use two simulated and two real LC-MS datasets to demonstrate the robustness and sensitivity of the ANOVA-IMD approach for assigning confidence to peptides with significant differential abundance among experimental groups.
2010. "Irradiation-induced defect clustering and amorphization in silicon carbide." Journal of Materials Research 25(12):2349-2353. Abstract Previous computer simulations of multiple 10 keV Si cascades in 3C-SiC demonstrated that many damage-state properties exhibit relatively smooth, but noticeably different, dose dependencies. Recent analysis of these archived damage-state properties reveals more complex relationships between system energy, swelling, energy per defect, relative disorder, elastic modulus and elastic constant, C11. These relationships provide evidence for the onset of defect clustering and amorphization processes, both of which appear to be driven by local energy and elastic instabilities from the accumulation of defects. The results provide guidance on experimental approaches to reveal the onset of these processes.
2010. "Global Proteomics Reveal An Atypical Strategy for Carbon/Nitrogen Assimilation by a Cyanobacterium Under Diverse Environmental Perturbations." Molecular & Cellular Proteomics. MCP 9(12):2678-89. doi:10.1074/mcp.M110.000109 Abstract Cyanobacteria, the only prokaryotes capable of oxygenic photosynthesis, are present in diverse ecological niches and play crucial roles in global carbon and nitrogen cycles. To proliferate in nature, cyanobacteria utilize a host of stress responses to accommodate periodic changes in environmental conditions. A detailed knowledge of the composition of, as well as the dynamic changes in, the proteome is necessary to gain fundamental insights into such stress responses. Toward this goal, we have performed a largescale proteomic analysis of the widely studied model cyanobacterium Synechocystis sp. PCC 6803 under 33 different environmental conditions. The resulting high-quality dataset consists of 22,318 unique peptides corresponding to 1,955 proteins, a coverage of 53% of the predicted proteome. Quantitative determination of protein abundances has led to the identification of 1,198 differentially regulated proteins. Notably, our analysis revealed that a common stress response under various environmental perturbations, irrespective of amplitude and duration, is the activation of atypical pathways for the acquisition of carbon and nitrogen from urea and arginine. In particular, arginine is catabolized via putrescine to produce succinate and glutamate, sources of carbon and nitrogen, respectively. This study provides the most comprehensive functional and quantitative analysis of the Synechocystis proteome to date, and shows that a significant stress response of cyanobacteria involves an uncommon mode of acquisition of carbon and nitrogen. Oxygenic phototrophic prokaryotes, the progenitors of the chloroplast, are crucial to global oxygen production and worldwide carbon and nitrogen cycles. These microalgae are robust organisms capable carbon neutral biofuel production. Synechocystis sp. PCC 6803 has historically been a model cyanobacterium for photosynthetic research and is emerging as a promising biofuel platform. Cellular responses are severely modified by environmental conditions, such as temperature and nutrient availability. However the global protein responses of Synechocystis 6803 under physiological relevant environmental stresses have not been characterized. Here we present the first global proteome analysis of a photoautotrophic bacteria and the most complete coverage to date of a photosynthetic prokaryotic proteome. To obtain a more complete description of the protein components of Synechocystis 6803, we have performed an in-depth proteome analysis of this organism utilizing the Accurate Mass and Time (AMT) tag approach1 utilizing 33 growth conditions and timepoints. The resulting proteome consists of 22,318 unique peptides, corresponding to 2,369 unique proteins, covering 65% of the predicted proteins. Quantitative analysis of protein abundance ratios under nutrient stress revealed that Synechocystis 6803 resorts to a universal mechanism for nitrogen utilization under phosphate, sulfate, iron, and nitrogen depletion. Comparison of this proteomic data with previously published microarray studies under similar environmental conditions showed that the general response predicted by both types of analyses are common but that the actual levels of protein expression can not be inferred from gene expression data. Our results demonstrate a global nitrogen response to multiple stressors that may be similar to that used by other cyanobacteria under various stress conditions. We anticipate that this protein expression data will be a foundation for the photosynthetic and biofuel communities to better understand metabolic changes under physiological conditions relevant to global productivity. Further more, this comparison of correlation between gene and protein expression data provides deeper insight into the ongoing debate as to whether gene expression can be used to infer cellular response.
2010. "A REVIEW OF NON-INVASIVE IMAGING METHODS AND APPLICATIONS IN CONTAMINANT HYDROGEOLOGY RESEARCH." Journal of Contaminant Hydrology 113(1-4):1-24. doi:10.1016/j.jconhyd.2010.01.001 Abstract Contaminant hydrogeological processes occurring in porous media are typically not amenable to direct observation. As a result, indirect measurements (e.g., contaminant breakthrough at a fixed location) are often used to infer processes occurring at different scales, locations, or times. To overcome this limitation, non-invasive imaging methods are increasingly being used in contaminant hydrogeology research. The most common methods, and the subjects of this review, are optical imaging using UV or visible light, dual-energy gamma-radiation, X-ray microtomography, and magnetic resonance imaging (MRI). Non-invasive imaging techniques have provided valuable insights into a variety of complex systems and processes, including porous media characterization, multiphase fluid distribution, fluid flow, solute transport and mixing, colloidal transport and deposition, and reactions. In this paper we review the theory underlying these methods, applications of these methods to contaminant hydrogeology research, and methods’ advantages and disadvantages. As expected, there is no perfect method or tool for non-invasive imaging. However, optical methods generally present the least expensive and easiest options for imaging fluid distribution, solute and fluid flow, colloid transport, and reactions in artificial two-dimensional (2D) porous media. Gamma radiation methods present the best opportunity for characterization of fluid distributions in 2D at the Darcy scale. X-ray methods present the highest resolution and flexibility for three-dimensional (3D) natural porous media characterization, and 3D characterization of fluid distributions in natural porous media. And MRI presents the best option for 3D characterization of fluid distribution, fluid flow, colloid transport, and reaction in artificial porous media. Obvious deficiencies ripe for method development are the ability to image transient processes such as fluid flow and colloid transport in natural porous media in three-dimensions, the ability to image many reactions of environmental interest in artificial and natural porous media, and the ability to image selected processes over a range of scales in artificial and natural porous media.
2010. "Using Dispersivity Values to Quantify the Effects of Pore-Scale Flow Focusing on Enhanced Reaction along a Transverse Mixing Zone." Advances in Water Resources 33(4):525-535. doi:10.1016/j.advwatres.2010.02.004 Abstract A key challenge for predictive modeling of transverse mixing and reaction of solutes in groundwater is to determine values of transverse dispersivity (T) in heterogeneous flow fields that accurately describe mixing and reaction at the pore scale. We evaluated the effects of flow focusing in high permeability zones on mixing enhancement using experimental micromodel flow cells and pore-scale lattice Boltzmann - finite volume model (LB-FVM) simulation. Micromodel results were directly compared to LB-FVM simulations using two different pore structures, and excellent agreement was obtained. Six different flow focusing pore structures were then systematically tested using LB-FVM, and both analytical solutions and a two-dimensional (2D) continuum-scale model were used to fit T values to pore-scale results. Pore-scale results indicate that the overall rate of mixing-limited reaction increased by up to 40% when flow focusing occurred, and it was greater in pore structures with longer flow focusing regions and greater porosity contrast. For each pore structure, T values from analytical solutions of transverse concentration profiles or total product at a given longitudinal location showed good agreement for nonreactive and reactive solutes, and values determined in flow focusing zones were always smaller than those downgradient after the flow focusing zone. Transverse dispersivity values from the 2D continuum model were between values within and downgradient from the flow focusing zone determined from analytical solutions. Also, total product and transverse concentration profiles along the entire pore structure from the 2D continuum model matched pore scale results. These results indicate that accurate quantification of pore-scale flow focusing with transverse dispersion coefficients is possible only when the entire flow and concentration fields are considered.
2010. "Coarse-Grained Molecular Dynamics Study of Permeability Enhancement in DPPC Bilayers by Incorporation of Lysolipid." Journal of Physical Chemistry B 114(15):5053-5060. Abstract The enhanced permeability of flat lipid bilayer membranes at their gel to liquid-crystalline (LC) phase transition has been explored using coarse-grained molecular dynamics. The phase transition temperature, Tm, is deduced by monitoring the area per lipid, the lipid lateral diffusion constant, and the lipid-lipid radial distribution function. We find that a peak in the permeability coincides with the phase transition from the gel to LC state when lysolipid is present. This peak in permeability correlates with a jump in the area per lipid near the same temperature as well as increased fluctuations in the lipid bilayer free volume. At temperatures above Tm, the permeability is only slightly dependent on the amount of lysolipid present. The increased free volume due to the “missing tail” of the lysolipid is partially compensated for by a decrease in area per lipid as the amount of lysolipid increases. We also found that in the coarse-grained model a small amount (e15 mol %) of lysolipid stabilizes the gel phase and increases the phase transition temperature, while a larger amount of lysolipid (20 mol %) reduces Tm back to that for pure DPPC, and bilayers consisting of g30 mol % lysolipid did not form a gel phase but still exhibited a peak in permeability near Tm for pure DPPC.