Showing papers by "Environmental Molecular Sciences Laboratory published in 2006"

Advances, Applications and Performance of the Global Arrays Shared Memory Programming Toolkit

Abstract: This paper describes capabilities, evolution, performance, and applications of the Global Arrays (GA) toolkit. GA was created to provide application programmers with an inteface that allows them to distribute data while maintaining the type of global index space and programming syntax similar to that available when programming on a single processor. The goal of GA is to free the programmer from the low level management of communication and allow them to deal with their problems at the level at which they were originally formulated. At the same time, compatibility of GA with MPI enables the programmer to take advatage of the existing MPI software/libraries when available and appropriate. The variety of applications that have been implemented using Global Arrays attests to the attractiveness of using higher level abstractions to write parallel code.

Characterization of ambient aerosols in Mexico City during the MCMA-2003 campaign with Aerosol Mass Spectrometry: results from the CENICA Supersite

Abstract: An Aerodyne Aerosol Mass Spectrometer (AMS) was deployed at the CENICA Supersite, during the Mexico City Metropolitan Area field study (MCMA-2003) from 31 March-4 May 2003 to investigate particle concentrations, sources, and processes The AMS provides real time in- formation on mass concentration and composition of the non-refractory species in particulate matter less than 1 µm (NR-PM1) with high time and size-resolution In order to account for the refractory material in the aerosol, we also present estimates of Black Carbon (BC) using an aethalome- ter and an estimate of the aerosol soil component obtained from Proton-Induced X-ray Emission Spectrometry (PIXE) analysis of impactor substrates Comparisons of AMS + BC + soil mass concentration with other collocated particle instruments (a LASAIR Optical Particle Counter, a PM25 Tapered Element Oscillating Microbalance (TEOM), and a PM25 DustTrak Aerosol Monitor) show that the AMS + BC + soil mass concentration is consistent with the total PM25 mass concentration during MCMA-2003 within the combined uncertainties In Mexico City, the organic fraction of the estimated PM25 at CENICA represents, on average, 546% (standard deviation =10%) of the mass, with the rest consisting of inorganic compounds (mainly ammonium ni- trate and sulfate/ammonium salts), BC, and soil Inorganic compounds represent 275% of PM25 ( =10%); BC mass concentration is about 11% ( =4%); while soil represents

Advances in Proteomics Data Analysis and Display Using an Accurate Mass and Time Tag Approach

Abstract: Proteomics has recently demonstrated utility for increasing the understanding of cellular processes on the molecular level as a component of systems biology approaches and for identifying potential biomarkers of various disease states. The large amount of data generated by utilizing high efficiency (e.g., chromatographic) separations coupled with high mass accuracy mass spectrometry for high-throughput proteomics analyses presents challenges related to data processing, analysis, and display. This review focuses on recent advances in nanoLC-FTICR-MS-based proteomics approaches and the accompanying data processing tools that have been developed to display and interpret the large volumes of data being produced.

A Component Architecture for High-Performance Scientific Computing

Abstract: The Common Component Architecture (CCA) provides a means for software developers to manage the complexity of large-scale scientific simulations and to move toward a plug-and-play environment for high-performance coputing. In the scientific computing context, component models also promote collaboration using independently developed software, thereby allowing particular individals or groups to focus on the aspects of greatest interest to them. The CCA supports parallel and distributed coputing as well as local high-performance connections between components in a language-independent manner. The design places minimal requirements on components and thus facilitates the integration of existing code into the CCA environment. The CCA model imposes minimal ovehead to minimize the impact on application performance. The focus on high performance distinguishes the CCA from most other component models. The CCA is being applied within an increasing range of disciplines, including cobustion research, global climate simulation, and computtional chemistry.

An IMS−IMS Analogue of MS−MS

Abstract: The development of a new ion mobility/mass spectrometry instrument that incorporates a multifield drift tube/ion funnel design is described. In this instrument, individual components from a mixture of ions can be resolved and selected on the basis of mobility differences prior to collisional activation inside the drift tube. The fragment ions that are produced can be dispersed again in a second ion mobility spectrometry (IMS) region prior to additional collisional activation and MS analysis. The result is an IMS-IMS analogue of MS-MS. Here, we describe the preliminary instrumental design and experimental approach. We illustrate the approach by examining the highly characterized bradykinin and ubiquitin systems. Mobility-resolved fragment ions of bradykinin show that b-type ions are readily discernible fragments, because they exist as two easily resolvable structural types. Current limitations and future directions are briefly discussed.

Preparation of ultrafine chalcopyrite nanoparticles via the photochemical decomposition of molecular single-source precursors.

Abstract: The synthesis and characterization of ultrafine CuInS2 nanoparticles are described. Ultraviolet irradiation was used to decompose a molecular single source precursor, yielding organic soluble ∼2 nm sized nanoparticles with a narrow size distribution. UV−vis absorption, 1H and 31P{1H} NMR, and fluorescence spectroscopies and mass spectrometry were used to characterize decomposition of the precursors and nanoparticle formation. The nanoparticles were characterized by high-resolution transmission electron microscopy (HRTEM), scanning electron microscopy energy dispersive X-ray spectroscopy, powder X-ray diffraction (XRD), electron diffraction, inductively coupled plasma analysis, UV−vis absorption spectroscopy, and fluorescence spectroscopy. They have a wurzite-type crystal structure with a copper-rich composition. The hypsochromic shift in their emission band due to quantum confinement effects is consistent with the size of the nanocrystals indicated in the HRTEM and XRD analyses.

Characterization of the Mouse Brain Proteome Using Global Proteomic Analysis Complemented with Cysteinyl-Peptide Enrichment

Abstract: We report a global proteomic approach for analyzing brain tissue and for the first time a comprehensive characterization of the whole mouse brain proteome. Preparation of the whole brain sample incorporated a highly efficient cysteinyl-peptide enrichment (CPE) technique to complement a global enzymatic digestion method. Both the global and the cysteinyl-enriched peptide samples were analyzed by SCX fractionation coupled with reversed phase LC-MS/MS analysis. A total of 48,328 different peptides were confidently identified (>98% confidence level), covering 7792 nonredundant proteins ( approximately 34% of the predicted mouse proteome). A total of 1564 and 1859 proteins were identified exclusively from the cysteinyl-peptide and the global peptide samples, respectively, corresponding to 25% and 31% improvements in proteome coverage compared to analysis of only the global peptide or cysteinyl-peptide samples. The identified proteins provide a broad representation of the mouse proteome with little bias evident due to protein pI, molecular weight, and/or cellular localization. Approximately 26% of the identified proteins with gene ontology (GO) annotations were membrane proteins, with 1447 proteins predicted to have transmembrane domains, and many of the membrane proteins were found to be involved in transport and cell signaling. The MS/MS spectrum count information for the identified proteins was used to provide a measure of relative protein abundances. The mouse brain peptide/protein database generated from this study represents the most comprehensive proteome coverage for the mammalian brain to date, and the basis for future quantitative brain proteomic studies using mouse models. The proteomic approach presented here may have broad applications for rapid proteomic analyses of various mouse models of human brain diseases.

Facile syntheses of monodisperse ultrasmall Au clusters.

Abstract: During our effort to synthesize the tetrahedral Au20 cluster, we found a facile synthetic route to prepare monodisperse suspensions of ultrasmall Au clusters AuN (N < 12) using diphosphine ligands. In our monophasic and single-pot synthesis, a Au precursor ClAu(I)PPh3 (Ph = phenyl) and a bidentate phosphine ligand P(Ph)2(CH2)(M)P(Ph)2 are dissolved in an organic solvent. Au(I) is reduced slowly by a borane-tert-butylamine complex to form Au clusters coordinated by the diphosphine ligand. The Au clusters are characterized by both high-resolution mass spectrometry and UV-vis absorption spectroscopy. We found that the mean cluster size obtained depends on the chain length M of the ligand. In particular, a single monodispersed Au11 cluster is obtained with the P(Ph)2(CH2)3P(Ph)2 ligand, whereas P(Ph)2(CH2)(M)P(Ph)2 ligands with M = 5 and 6 yield Au10 and Au8 clusters. The simplicity of our synthetic method makes it suitable for large-scale production of nearly monodisperse ultrasmall Au clusters. It is suggested that diphosphines provide a set of flexible ligands to allow size-controlled synthesis of Au nanoparticles.

Integrated Molecular Signature of Disease: Analysis of Influenza Virus-Infected Macaques through Functional Genomics and Proteomics

Abstract: Recent outbreaks of avian influenza in humans have stressed the need for an improved nonhuman primate model of influenza pathogenesis. In order to further develop a macaque model, we expanded our previous in vivo genomics experiments with influenza virus-infected macaques by focusing on the innate immune response at day 2 postinoculation and on gene expression in affected lung tissue with viral genetic material present. Finally, we sought to identify signature genes for early infection in whole blood. For these purposes, we infected six pigtailed macaques (Macaca nemestrina) with reconstructed influenza A/Texas/36/91 virus and three control animals with a sham inoculate. We sacrificed one control and two experimental animals at days 2, 4, and 7 postinfection. Lung tissue was harvested for pathology, gene expression profiling, and proteomics. Blood was collected for genomics every other day from each animal until the experimental endpoint. Gross and microscopic pathology, immunohistochemistry, viral gene expression by arrays, and/or quantitative real-time reverse transcription-PCR confirmed successful yet mild infections in all experimental animals. Genomic experiments were performed using macaque-specific oligonucleotide arrays, and high-throughput proteomics revealed the host response to infection at the mRNA and protein levels. Our data showed dramatic differences in gene expression within regions in influenza virus-induced lesions based on the presence or absence of viral mRNA. We also identified genes tightly coregulated in peripheral white blood cells and in lung tissue at day 2 postinoculation. This latter finding opens the possibility of using gene expression arrays on whole blood to detect infection after exposure but prior to onset of symptoms or shedding.

Density-functional global optimization of gold nanoclusters

Abstract: The structure of gas-phase gold clusters of size $\ensuremath{\sim}20$ is studied by density-functional global optimization in the full configuration space. The putative global minimum of ${\mathrm{Au}}_{20}$ is confirmed to be a tetrahedron $({T}_{d})$ independently of the choice of the exchange-correlation functional, whereas the structure of the low-lying excited states depends on the theoretical approach. The peculiar stability of ${T}_{d}$ is rationalized in terms of the synergic effects of $s\text{\ensuremath{-}}d$ hybridization and electronic shell closure. Calculations on ${\mathrm{Au}}_{16}$ and ${\mathrm{Au}}_{18}$ show that ${T}_{d}$ ${\mathrm{Au}}_{20}$ possibly represents a ``unicum'' in the sequence of gold clusters.

Proteome analysis of mitochondrial outer membrane from Neurospora crassa.

Abstract: The mitochondrial outer membrane mediates numerous interactions between the metabolic and genetic systems of mitochondria and the rest of the eukaryotic cell. We performed a proteomic study to discover novel functions of components of the mitochondrial outer membrane. Proteins of highly pure outer membrane vesicles (OMV) from Neurospora crassa were identified by a combination of LC-MS/MS of tryptic peptide digests and gel electrophoresis of solubilized OMV proteins, followed by their identification using MALDI-MS PMF. Among the 30 proteins found in at least three of four separate analyses were 23 proteins with known functions in the outer membrane. These included components of the import machinery (the TOM and TOB complexes), a pore-forming component (porin), and proteins that control fusion and fission of the organelle. In addition, proteins playing a role in various biosynthetic pathways, whose intracellular location had not been established previously, could be localized to the mitochondrial outer membrane. Thus, the proteome of the outer membrane can help in identifying new mitochondria-related functions.

Reactivity of Sulfide Mineral Surfaces

Abstract: In the preceding chapter, the fundamental nature of sulfide mineral surfaces has been discussed, and the understanding we have of the ways in which the surface differs from a simple truncation of the bulk crystal structure reviewed. This naturally leads on to considering our understanding of sulfide surface chemistry, in the sense of how sulfide surfaces interact and react, particularly with gases and liquids. As noted elsewhere in this volume, research on sulfide mineral surfaces and surface reactivity is a relatively recent concern of mineralogists and geochemists, partly prompted by the availability of new imaging and spectroscopic methods, powerful computers and new computer algorithms. There has been a significantly longer history of sulfide mineral surface research associated with technologists working with, or within, the mining industry. Here, electrochemical methods, sometimes combined with analytical and spectroscopic techniques, have been used to probe surface chemistry. The motivation for this work has been to gain a better understanding of the controls of leaching reactions used to dissolve out metals from ores, or to understand the chemistry of the froth flotation systems used in concentrating the valuable (usually sulfide) minerals prior to metal extraction. The need for improved metal extraction technologies is still a major motivation for research on sulfide surfaces, but in the last couple of decades, new concerns have become important drivers for such work. In particular, much greater awareness of the negative environmental impact of acid and toxic metal-bearing waters derived from breakdown of sulfide minerals at former mining operations has prompted research on oxidation reactions, and on sorption of metals at sulfide surfaces. At the interface between fundamental geochemistry and industrial chemistry, the role of sulfide substrates in catalysis, and in the self-assembly and functionalization of organic molecules, has become an area of significant interest. Such work ranges in its …

On the structure and chemical bonding of tri-tungsten oxide clusters W3On- and W3On (n=7-10): W3O8 as a potential molecular model for O-deficient defect sites in tungsten oxides.

Abstract: Electronic and structural properties of a series of tri-tungsten oxide clusters, W3On- and W3On (n=7-10), are investigated using photoelectron spectroscopy and density functional theory (DFT) calculations. Both W 5d and O 2p detachment features are observed for n=7-9, whereas only detachment features from O 2p-type orbitals are observed for W3O10- at high electron binding energies (>7 eV). A large energy gap (approximately 3.4 eV) is observed for the stoichiometric W3O9 cluster, which already reaches the bulk value, suggesting that W3O9 can be viewed as the smallest molecular model for bulk WO3. DFT calculations are carried out to locate the most stable structures for both the anion and neutral clusters; time-dependent DFT method is used to predict the vertical detachment energies and to compare with the experimental data. It is shown that W3O9 possesses a D3h structure, in which each W atom is tetrahedrally coordinated with two bridging O atoms and two terminal O atoms. W3O8 and W3O7 can be viewed as removing one and two terminal O atoms from W3O9, respectively, whereas W3O1) can be viewed as replacing a terminal O in W3O9 by a peroxo O2 unit. We show that W3O8 contains a localized W4+ site, which can readily react with O2 to form the W3O10 clusters with a calculated O2 adsorption energy of -78 kcal/mol. It is suggested that the W3O8 cluster can be viewed as a molecular model for O-deficient site in tungsten oxides.

Experimental and Theoretical Characterization of Superoxide Complexes [W2O6(O2−)] and [W3O9(O2−)]: Models for the Interaction of O2 with Reduced W Sites on Tungsten Oxide Surfaces

Abstract: Two O-rich tungsten oxide clusters, W2O8- and W3O11-, were produced and investigated by photoelectron spectroscopy and density functional theory calculations. The two anions are best considered as W2O6(O2-) and W3O9(O2-), respectively, each containing a side-on bound superoxide ligand, whereas the neutral clusters W2O8 and W3O11 are shown to involve O2 physisorbed to the W2O6 or W3O9 stoichiometric cluster. The current study indicates that the extra electron in W2O6- and W3O9- are capable of activating dioxygen by non-dissociative electron transfer (W 5d - O2 -*), and the two anionic clusters can be viewed as models for reduced defect sites on tungsten oxide surfaces for the chemisorption of O2.

Ferromagnetism and structure of epitaxial Cr-doped anatase TiO 2 thin films

Abstract: The materials and magnetic properties of Cr-doped anatase ${\mathrm{TiO}}_{2}$ thin films deposited on ${\mathrm{LaAlO}}_{3}(001)$ and ${\mathrm{SrTiO}}_{3}(001)$ substrates by oxygen-plasma-assisted molecular beam epitaxy have been studied in detail to elucidate the origin of ferromagnetic ordering. Cr substitution for Ti in the anatase lattice, with no evidence of Cr interstitials, segregation, or secondary phases, was independently confirmed by transmission electron microscopy with energy dispersive x-ray spectroscopy, extended x-ray absorption fine structure, and Rutherford backscattering spectrometry in the channeling geometry. Epitaxial films deposited at $\ensuremath{\sim}0.1\phantom{\rule{0.3em}{0ex}}\mathrm{\AA{}}∕\mathrm{s}$ were found to have a highly defected crystalline structure, as quantified by high-resolution x-ray diffraction (XRD). These films were also ferromagnetic at room temperature with a moment of $\ensuremath{\sim}0.5{\ensuremath{\mu}}_{B}∕\mathrm{Cr}$, Curie temperatures in the range of $400\text{--}700\phantom{\rule{0.2em}{0ex}}\ifmmode^\circ\else\textdegree\fi{}\mathrm{C}$, and exhibited shape and in-plane magnetocrystalline anisotropy. However, no free carrier spin polarization was observed by Hall effect measurements, raising questions about the mechanism of magnetism. Films deposited slowly $(\ensuremath{\sim}0.015\phantom{\rule{0.3em}{0ex}}\mathrm{\AA{}}∕\mathrm{s})$ possessed a nearly perfect crystalline structure as characterized by XRD. Contrary to expectations, these films exhibited negligible ferromagnetism at all Cr concentrations. Annealing in vacuum to generate additional oxygen defects and free carrier electrons did not significantly increase the ferromagnetic ordering in either fast- or slow-grown films. These results contradict both oxygen-vacancy-derived free-carrier-mediated exchange and F-center-mediated bound magnetic polaron exchange mechanisms, and instead indicate the primary role of extended structural defects in mediating the ferromagnetic ordering in doped anatase films.

Molecular dynamics simulations of the interaction between the surfaces of polar solids and aqueous solutions

Abstract: Molecular dynamics (MD) simulations were performed on the interaction of two solid surfaces, namely the (001) hematite and (104) calcite surfaces, in contact with aqueous electrolyte solutions containing different concentrations of dissolved NaCl The structure and a number of properties of the interface were investigated The size and amount of statistics needed for convergence of these calculations required the use of high performance computers The two surfaces show different bonding mechanisms with the water, but both result in a distinctive layering of the water, which in turn modifies a range of surface behaviour including diffusivity and charge distribution We find that the resulting charge distribution from the solvent has a greater control of the disposition of dissolved ions than either surface charge or ionic strength, within reasonable limits Thus we see a characteristic double layer at neutral surfaces and the charge distribution oscillates into the bulk Finally, preliminary work on calculating the free energy of dissolution of ions from the surface to the aqueous solution suggests that the presence of dissolved ions makes a small but significant reduction to the dissolution free energies

Soft-Landing of Peptides onto Self-Assembled Monolayer Surfaces

Abstract: Mass-selected peptide ions produced by electrospray ionization were deposited as ions by soft-landing (SL) onto fluorinated and hydrogenated self-assembled monolayer (FSAM and HSAM) surfaces using a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) specially designed for studying collisions of large ions with surfaces. Analysis of modified surfaces was performed in situ by combining 2 keV Cs+ secondary ion mass spectrometry with FT-ICR detection of the sputtered ions (FT-ICR-SIMS). Similar SIMS spectra obtained following SL at different collision energies indicate that peptide fragmentation occurred in the analysis step (SIMS) rather than during ion deposition. The effect of the surface on SL was studied by comparing the efficiencies of SL on gold, FSAM, HSAM, and COOH-terminated SAM surfaces. It was found that FSAM surfaces are more efficient in retaining ions than their HSAM analogues, consistent with their larger polarizability. The efficiency of soft-landing of different peptides...

Characterization of the Human Pancreatic Islet Proteome by Two-Dimensional LC/MS/MS

Abstract: The pancreatic beta-cell plays a central role in the maintenance of glucose homeostasis and in the pathogenesis of both type 1 and type 2 diabetes mellitus. Elucidation of the insulin secretory defects observed in diabetes first requires a better understanding of the complex mechanisms regulating insulin secretion, which are only partly understood. While there have been reports detailing proteomic analyses of islet cell lines or isolated rodent islets, the information gained is not always applicable to humans. Therefore, definition of the human islet proteome could contribute to a better understanding of islet biology and lead to more effective treatment strategies. We have applied a two-dimensional LC-MS/MS-based analysis to the characterization of the human islet proteome, resulting in the confident identification of 29,021 different tryptic peptides covering 3,365 proteins (≥ 2 unique peptide identifications per protein). As expected, the three major islet hormones (insulin, glucagon, and somatostatin) were detected, as well as various beta-cell enriched secretory products, ion channels, and transcription factors. In addition, significant proteome coverage of metabolic enzymes and cellular pathways was observed, including the integrin signaling cascade and the MAP kinase, NF-κβ, and JAK/STAT pathways. The resulting peptide reference library provides a resource for future higher throughput and quantitative studies of islet biology.

Automated derivation and parallel computer implementation of renormalized and active-space coupled-cluster methods

Abstract: Our recent efforts that have led to an automated derivation and computer implementation of the renormalized and active-space coupled-cluster (CC) methods with Tensor Contraction Engine (TCE) are summarized. The TCE-generated renormalized and active-space CC computer codes are parallel and applicable to closed- and open-shell references, enabling accurate calculations of potential energy surfaces along bond-breaking coordinates and excited states displaying a significant multi-reference character. The effectiveness of the new codes in describing electronic quasi-degeneracies is illustrated by the renormalized CC calculations of the potential energy curve of HCl and the active-space CC calculations for the low-lying excited states of the Be3 system. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006