Doping Golden Buckyballs: Cu@Au₁₆- and Cu@Au₁₇- Cluster Anions

LM Wang,^(a) S Bulusu,^(b) HJ Zhai,^(c) XC Zeng,^(b) and LS Wang,^(a)

(a) Washington State University Tri-Cities, Richland Washington
(b) University of Nebraska, Lincoln, Nebraska

Figure 1. Photoelectron spectra of the cluster anions CuAu₁₆- and CuAu₁₇- (Figures 1b and 1d), compared to the parent gold clusters Au₁₆- and Au₁₇- (Figures 1a and 1c). Full image [png 62kb]

Figure 2. Simulated photoelectron spectra for two endohedral structures each for Cu@Au₁₆- and Cu@Au₁₇- along with those for Au₁₆- and Au₁₇-. Full image [png 148kb]

Clusters are groups of a small number of atoms that often have chemical and physical properties that are different than the corresponding bulk materials. Understanding the underlying physical and structural reasons for these unique properties may allow for improved materials for electronics, sensors, and catalysis.

The discovery of the unique catalytic effects of gold nanoparticles on oxide substrates has stimulated a flurry of research into the structures and properties of free gold nanoclusters, which may hold the key to elucidating the catalytic mechanisms of supported gold clusters. One of the most remarkable results has been the discovery of planar gold cluster anions (Auη-) of up to 12 gold atoms and the two- to three-dimensional transition for clusters with n larger than 12. Among larger gold clusters, Au₂₀ has been found to be a perfect tetrahedron. A more recent study of the structures of Auη- cluster anions in the medium size range (n=15-19) has shown that clusters with n=16-18 possess unprecedented empty cage structures. In particular, the Au₁₆- cluster anion has an interesting tetrahedral structure with an inner diameter of about 5.5 Å and can be compared to the fullerenes (buckyballs). The cage structures of the cluster anions Au₁₆- and Au₁₇- have recently been confirmed by electron diffraction, and thus, they are the first experimentally confirmed and the smallest possible gold cages. The large empty space inside these cage clusters immediately suggested that they can be doped with a foreign atom to produce a new class of endohedral gold cages that are analogous to endohedral fullerenes.

A gold cage containing a central atom first was predicted for a series of icosahedral clustersM@Au₁₂ (M=W, Ta-, Re+) based on the 18-electron rule and subsequently was confirmed experimentally. However, because Au12 itself does not possess a cage structure, the dopant atom with the appropriate electron count must play an essential role in maintaining the integrity of the cage. Bimetallic gold clusters have been studied experi-mentally as they offer new opportunities to fine tune the electronic and structural properties of gold nano-clusters. Following the discovery of the hollow gold cages, two recent theoretical studies that focused on doping the cages with a foreign atom have appeared. Because the parent Au16- and Au17- cluster anions are empty cages, many different types of atoms could be used as dopants to form new endohedral gold clusters. In this highlight, we report the first use of photoelectron spectroscopy (PES) analysis and density functional theory (DFT) calculations to observe and characterize Au₁₆- and Au₁₇- doped with a Cu atom (Cu@Au₁₆- and Cu@Au₁₇).

Figure 1 shows the spectra of CuAu₁₆- and CuAu₁₇- ions along with the of the parent gold clusters. First, we focus on the CuAu₁₆- ion (Figure 1b), whose PE spectrum is remarkably similar to that of its parent gold cluster Au₁₆- (Figure 1a). The similarity between the spectra of these two species suggests that Cu doping does not alter the geometric and electronic structures of the Au₁₆- cluster anion significantly, which is only possible if the Cu is trapped inside the Au₁₆- cage.

The spectrum of the doped cluster anion CuAu₁₇- is also very similar to that of the parent gold cluster Au₁₇, except that there is one low-binding-energy peak followed by a large energy gap in the spectrum of the Cu doped cluster (Figures1 c and d). This spectral similarity again suggests that the Cu dopant induces very little structural change in the Au17 cage except that it donates one electron. Au₁₇ is a closed-shell species with 18 valence electrons; therefore, the extra electron is expected to enter its lowest occupied molecular orbital and give rise to the low-binding-energy peak (X) in the PE spectrum of the CuAu₁₇- cluster anion (Figure 1d). All these observations again imply that Cu stays in the center of the Au₁₇- ion cage (Cu@+Au₁₇2-) and does not perturb the electronic and geometric structures of the cage significantly.

We carried out theoretical studies to confirm these observations. The results revealed that the endohedral Cu@Au₁₆- and Cu@Au₁₇- cluster anions are overwhelmingly favored over any other structure with the Cu atom on the outside of the cage. Figure 2 shows the simulated PE spectra for two endohedral structures each for the Cu@Au₁₆- and Cu@ Au₁₇- cluster anions along with those of the parent clusters. In one structure, the Cu atom is located in the center of the cages, and in the other structure, it is displaced slightly from the center. The energy differences between the two isomers are very small, and their simulated PE spectra are also very similar to each other. The calculated vertical detachment energies for the Cu@Au₁₆- and Cu@Au₁₇ cluster anions also are in good agreement with the experimental values. Overall, the excellent agreement between theory and experiment unequivocally confirms the endohedral structures of these Cu-doped gold cages.

Doping gold clusters could be a powerful way to tune their chemical and physical properties, and the results reported in this highlight suggest that a new class of endohedral gold cages is indeed viable. In these examples, the cage structures of Au16- and Au17- cluster anions are maintained simply by changing the dopants, which is reminiscent of the behavior of endohedral fullerenes. It would be particularly interesting to dope transition-metal atoms inside these gold cages to create magnetic gold clusters as the resulting material may exhibit new, physical, chemical, and catalytic properties that are distinct from the pure gold clusters.

This exciting work was published online in the April 13, 2007, edition of the journal Angewandte Chemie (Wang et al. 2007).

Citation

Wang LM, S Bulusu, HJ Zhai, XC Zeng, and LS Wang. 2007. "Doping Golden Buckyballs: Cu@Au₁₆- and Cu@ Au₁₇- Cluster Anions." Angewandte Chemie 46(16):2915-2918.

Solid-State NMR Characterization of CdS Nanoparticle/Polymer Interfaces

MP Espe,^(a) S Ortiz,^(a) and SD Burton,^(b)

(a) University of Akron, Akron, Ohio
(b) W.R. Wiley Environmental Molecular Sciences Laboratory, Richland, Washington.

Figure 1. Parts per million (ppm) 113Cd of CdS as synthesized, DP (bottom, d1=60 sec, ct=1146, lb=200, ss 5 KHz) and CP (top, d1=2sec, cp=1ms, ct=13660, lb=200, ss 5 KHz). Full Image [png 3kb]

Figure 2. 1H-113Cd heteronuclear correlation experiment on CdS precipitated with ethanol. Full Image [png 6kb]

Semiconducting nanopoarticles made from cadmium chalcogenide have unique optical, catalytic and energy transfer properties stemming from their size and morphology. To better understand the physical properties created during the processing of these nanopartical materials, nuclear magnetic resonance (NMR) spectrometry is one of the tools used to investigate atomic structure and substrate-surface interactions.

Cadmium chalcogenide (CdX; X = S, Se, Te) semiconducting (II-VI) nanoparticles are currently of significant interest because the properties of the nanoparticles are intermediate to those of molecular and bulk materials, which have a diverse number of realized and potential applications. Several of these applications include organic/inorganic light-emitting diodes, electroluminescence devices, nanoelectronics, quantum-dot LASERs, photovoltaic solar cells, catalysts, materials for imaging, and assaying bio-systems. In most of these systems, the critical property of the nanoparticle is its photoluminescence, for which the emission wavelength can be varied by varying the particle size. The photoluminescent properties are highly dependent on the surface structure of the nanoparticle, with high defect numbers producing more trapped-state luminescence. The surface defect sites can be electronically passivated by coating the CdX nanoparticle surfaces with capping agents, such as phosphine oxides, thiols, and amines. These passivated particles luminesce predominantly through band-edge emissions, resulting in longer excitation lifetimes and higher luminescent intensities.

Solid-state NMR is the ideal technique for the study of the structure of CdX nanomaterials as both the bulk and surface structures of the NMR active nuclei can be probed. In addition, the interaction between the nanoparticles and the surface passivation materials can be characterized. NMR studies of the CdX materials benefit from the presence of an array of ideal NMR active nuclei, including 113Cd (12.26 percent natural abundance [n.a.], spin=1/2), 77Se (7.6 percent n.a., spin=1/2), 125Te (7 percent n.a., spin=1/2), and 13C (1.1 percent n.a., spin=1/2).

The materials analyzed using capabilities in the EMSL High Field Magnetic Resonance Facility were cadmium sulfide (CdS) nanoparticles synthesized using two different capping agents: 1-thioglycerol and 4-bromophenylethenyl phosphonic acid (4BrEPPA). In summary, the cadmium chemical shift shows the successful formation of cadmium nanoparticles resulting from the resultant chemical shift and a wide line caused by structural heterogeneity. The lower spectrum shown in Figure 1 represents all the cadmium present in the sample, while the top spectrum of these represents that cadmium at the surface of the nanoparticles. The spectral editing was generated using a H-Cd cross polarization magic-angle spinning technique that uses protons on the surface to enhance the surface cadmium signal. There is a small fraction of cadmium at the surface compared to the whole sample.

A two-dimensional heteronuclear correlation experiment was performed on the CdS precipitated with ethanol. In that experiment, the correlation between the protons (F1 dimension) and the cadmium (F2 dimension) in the sample was observed (see Figure 2). The two protons were observed to have a strong correlation with the cadmium of the CdS nanoparticles, one at approxunately 4 ppm representing correlation with protons of CH2 close to the sulfur and the CH and the other at about 8 ppm, possibly resulting from protons of the OH groups at the surface of the CdS.

These and additional results, which discussed synthesis, further analysis, and the effects of hydration on the surface, were presented July 22, 2008, at the NMR Symposium during the Rocky Mountain Analytical Conference, in Breckenridge Colorado.

Bio-Stimulation of Iron Reduction and Subsequent Oxidation of Sediment Containing Fe-Silicates and Fe-Oxides: Effects of Redox Cycling on Fe(III) Bio-Reduction

J Komlos,^(a) RK Kukkadapu,^(b) JM Zachara,^(a), and PR Jaffé^(a)

(a) Princeton University, Princeton, New Jersey
(b) W.R. Wiley Environmental Molecular Sciences Laboratory, Richland, Washington
(c) Pacific Northwest National Laboratory, Richland, Washington

Figure 1. Mössbauer spectra (12K) of the (a) pristine sediment, (b) bio-reduced sediment, and (c) re-oxidized sediment. Full Image [png 15kb]

Effective bio-remediation depends on the durability of bio-reduced sediments to trap contaminants. This study determined that iron silicates in sediments can be repeatedly bio-reduced and re-oxdized, thus forming a cyclical means of sequestering contaminants in the environment.

Figure 1. Mössbauer spectra (12K) of the (a) pristine sediment, (b) bio-reduced sediment, and (c) re-oxidized sediment. Sediment containing a mixture of iron(Fe)-phases, including Fe-oxides and Fe-silicates, was bio-reduced in a long-term flow-through column experiment followed by re-oxidation with dissolved oxygen. This study de-termined the nature of the re-oxidized Fe(III) and how redox cycling of Fe would affect subsequent Fe(III) bio-availability. In addition, the effect of manganese (Mn) on Fe(III) reduction was explored. 57Fe-Mössbauer spectroscopy measurements showed that bio-stimulation resulted in partial reduction (20 percent) of silicate Fe(III) to silicateFe(II), while the reduction of Fe-oxides was negligible. Furthermore, the reduction of Fe in the sediment was uniform throughout the column, suggesting that Fe is not mobilized. As shown in Figure 1, the Mössbauer spectra of the re-oxidized sample were similar to that of pristine sediment implying that Fe-mineralogy of the re-oxidized sediment was mineralogically similar to that of the pristine sediment. Batch experiments showed that Fe(III) reduction occurred at a similar rate although the time required for Fe(II) accumulation to begin was longer in the pristine sediment than the re-oxidized sediment under identical seeding conditions. This rate change was attributed to oxidized Mn that acted as a temporary redox buffer in the pristine sediment. The oxidized Mn was transformed to Mn(II) during bio-reduction but, unlike silicate Fe(II), the Mn(II) was not re-oxidized when exposed to oxygen. A paper describing the results of this research was published in the July 2007 edition of the journal Water Research (Komlos et al. 2007).

Citation

Komlos J, RK Kukkadapu, JM Zachara, and PR Jaffé. 2007. "Biostimulation of Iron Reduction and Subsequent Oxidation of Sediment Containing Fe-Silicates and Fe-Oxides: Effect of Redox Cycling of Fe(III) Bioreduction." Water Research 41(13):2996-3004.

Probing Oxidative Stress Using Intact-Protein, High-Field LC-FTICR Mass Spectrometry

NM Lourette,^(a) HS Smallwood,^(a) CB Boschek,^(a) S Wu,^(a) RD Smith,^(a) and L Paša-Tolic^(a)

(a) Pacific Northwest National Laboratory, Richland, Washington

Figure 1. The time vs. mass two-dimensional display (left) highlights our ability to resolve intact protein masses of individual oxidized CaM species that are indicators of denitrase activity. CaM species detected prior to (red symbols) and following (black symbols) incubation with cell lysate from activated macrophages: a) CaM & CaMox; b) nYCaMox & 2nYCaMox; c) CaM-Lysine and CaMox-Lysine; d) nYCaM, and e) 2nYCaM. The panel at the right displays the relative abundance of CaM within each of these five areas. Definitions of the abbreviations follow: CaM, calmodulin; CaMox (nYCaMox), oxidized CaM containing methionine sulfoxides or (and) nTyrs.
Full Image [png 142kb]

Mechanisms that regulate the removal of nitrated and oxidized proteins in cells are critical for preventing a number of diseases (such as diabetes, cardiovascular disease, cancer, and neurological disorders), as well as for reducing the effects of aging. In this work, we used high-resolution liquid chromatography (LC) separations in conjunction with high-mass-measurement accuracy and high-resolution measurements afforded by 12 tesla Fourier transform ion cyclotron resonance (FTICR) mass spectrometer in the EMSL High-Performance Mass Spectrometry Facility to probe oxidative stress in calmodulin, which is a signaling protein in macrophages. Importantly, we identified a novel oxidation-dependent lysine cleavage that potentially acts as a biomarker of oxidative stress.

Oxidative species not only mediate static and cidal effects on a variety of pathogens, but also nitrate and oxidize host proteins during the immune response. These post-translational modifications (PTMs) to intracellular proteins in various inflammatory states also are implicated in many age-related diseases. In this context, the accumulation of nitrotyrosines in proteins may result from an aberrant repair pathway. Previous works have postulated denitrase activity in various tissues based on the loss of immunoreactivity involving antibodies against nitrotyrosine. However, attributing the loss in immunoreactivity to denitration is equivocal, as this effect may be caused by degradation of the nitrated protein, alterations in protein structure that cover the epitope, chemical alteration of the nitrotyrosine, and/or enzymatic denitration.

Characterization of the product following denitration and corresponding loss of immunoreactivity requires the use of an analytical tool that can confirm the involvement of specific proteins, thereby ruling out the ambiguous interpretations based on antibody recognition.

We used intact protein reversed phase LC-FTICR mass spectrometry to monitor the time dependent changes in the nitration of calmodulin (nYCaM) in macrophages following macrophage activation with lipopoly-saccharide endotoxin (Figure 1). Tentative identifications of PTMs were assigned by combining tryptic peptide information generated from bottom-up analyses with online collision-induced dissociation tandem mass spectrometry at the intact protein level, which confirmed localization of the nitrated sites. Our results indicate that macrophage activation associated with an oxidative burst stimulates a dramatic reduction in the abundance and diversity of oxidatively modified proteins. More specifically, we established that macrophage repair pathways can repair nitrated tyrosines and oxidized methionines within a signaling protein (i.e., calmodulin) to their original unmodified states to retain optimal protein function.

Oriented ZnO Films Deposited by MOCVD with Low Carbon Concentrations

LV Saraf,^(a) MH Engelhard,^(a) CM Wang,^(a) AS Lea,^(a) DE McCready,^(a) V Shutthanandan,^(a) DR Baer,^(a) and SA Chambers, ^(a)

(a) W.R. Wiley Environmental Molecular Sciences Laboratory, Richland, Washington
(b) Pacific Northwest National Laboratory, Richland, Washington

Figure 1. High-resolution C 1s spectra of ZnO films before and after sputtering.
Full Image (png 6kb)

Figure 2. Low- and high-resolution TEM images of ZnO films.

Growth of high-purity and carbon-free, wide-band-gap semiconductors is very important for researchers in the optical and semiconductor industries. Carbon contamination is one of the major problems in metal organic chemical vapor deposition (MOCVD) semiconductor growths because the majority of the precursors are carbon dominated. In this report, we show that successful decomposition of Zn(TMHD)2 precursor resulted in low-carbon ZnO films.

The use of environmentally friendly precursors in the MOCVD process is essential because of safety hazards present in commonly used precursors. Because of the popularity and usefulness of ZnO material in transparent conducting oxide coating, spintronics, catalysis, and sensors, literature on ZnO growth by MOCVD is plentiful. Most of the work is based on use of hazardous di-methyl zinc (DMZ), di-ethyl zinc (DEZ), zinc acetate, zinc acetylacetonate-based precursors. In this report, we discuss the relatively uninvestigated Zn(TMHD) precursor for the growth of oriented ZnO films on silicon. The cleanliness of the Zn(TMHD) precursor decomposition was determined by measuring the amount of carbon in the deposited films. We show by x-ray photoelectron spectroscopy (XPS) that despite the high carbon content in the precursor (i.e., C22 in a single Zn(TMHD)2 precursor molecule), much less than 1 atomic (at.) % carbon was present in ZnO films grown with this precursor.

Figure 1 shows high resolution C 1s spectra before and after sputtering. The overall C concentration at the surface was 21 at. %, and was reduced after sputtering to below 1 at. %. Excess oxygen, revealed by an increase in the O to Zn ratio, is attributed to the presence of C-O and C=O functionalities on the surface. Removal of surface C layer appeared to restore the Zn/O ratio to 1:1. The inset in Figure 1 represents the reproducibility of our results. These spectra indicate high-resolution XPS scans of C 1s for ZnO films grown on single crystal silicon and Al₂O₃. The two sets of spectra represent carbon content on as-grown ZnO surfaces before and after 5 nm sputtering of the same position. Sample numbers 1, 3, and 4 are grown on single-crystal silicon, samples 2 and 6 on single-crystal c-plane Al₂O₃, and sample number 5 on r-plane Al₂O₃ under similar conditions.

As expected, we have not detected any substrate relationship to carbon content. The surface carbon concentration in the as-grown films was observed to be in the range of 11 to 34 at. %. However, the carbon was reduced to much less than 1 at. % on all samples after 5 nm of sputtering. Figure 2 indicates low- and high-resolution transmission electron microscope (TEM) micrographs of a typical ZnO film grown on silicon. A columnar structure in low-resolution TEM and the c-axis oriented atomic planar arrangement of ZnO are clearly visible in the images. A paper describing this research was published in the May issue of the Journal of Materials Research (Saraf et al. 2007).

Citation

Saraf LV, MH Engelhard, CM Wang, AS Lea, DE McCready, V Shutthanandan, DR Baer, and SA Chambers. 2007. "Metalorganic Chemical Vapor Deposition of Carbon-Free ZnO Using the Bis(2,2,6,6-tetramethyl-3,5-heptanedionato) Zinc Precursor." Journal of Materials Research 22(5):1230-1234.

Nucleation and Growth of MOCVD Grown (Cr, Zn)O Films: Uniform Doping vs. Secondary Phase Formation

LV Saraf,^(a) ) MH Engelhard,^(a) P Nachimuthu,^(a) V Shutthanandan, ^(a) CM Wang,^(a) SM Heald,^(a) DE McCready,^(a) AS Lea,^(a) DR Baer,^(a) and SA Chambers^(b)

(a) W.R. Environmental Molecular Sciences Laboratory, Richland, Washington
(b) Pacific Northwest National Laboratory, Richland, Washington

Figure 1. PIXE spectra of (a) pure ZnO and (b) (Cr, Zn)O films.
Full Image (png 11kb)

Figure 2. Rutherford backscattering and x-ray photoelectron spectroscopy depth profiles for (Cr, Zn)O films.
Full Image (png 19kb)

Understanding of doping limitations in wide-band-gap semiconductors is crucial before using them for various studies. Zinc oxide (ZnO) is a popular wide-band-gap semiconductor (oxide) studied for its usefulness in light emission, transparency, and doping-assisted, band-gap tuning ability. In this report, we focus on major limitations for chromium as a dopant in ZnO resulting secondary phase formations.

ZnO is a II-VI semiconducting oxide with the bandgap of 3.3 eV. It stabilizes in the hexagonal structure with lattice constants 0.32 nm (a) and 0.52 nm (c). ZnO is a well-known, multi-functional oxide that is useful in thermoelectric, optical, magnetic, dielectric, and sensing applications. Chromium (Cr) is of potential interest as a magnetic and electronic dopant in ZnO. Thus, the aim of this study was to determine the extent to which Cr can be incorporated into the ZnO lattice as a subsitutional cation. From our results, we concluded that little, if any, Cr occupies tetrahedral sites in the ZnO lattice. Instead, the secondary phases and ZnCr₂O₄, in which Cr is in octahedral sites, preferentially nucleate. Cr₂O₃ is present predominantly as a disordered phase at the interface. ZnCr₂O₄ also is largely segregated at the interface, although some nanocrystalline ZnCr₂O₄ may be present in the ZnO matrix.

Figure 1 indicates particle induced x-ray emission (PIXE) results for ZnO and (Cr, Zn)O films. The experimental PIXE data are shown as solid circles and the solid curve represents K-fitted spectra for pure and (Cr, Zn)O films. The initial peak at 0.7 is from Kß lines. Peaks representing Cr lines are clearly seen in Figure 1b. The total Cr atomic percentage (at. %) in the film is 5.5 at. %. However, from an x-ray photoelectron spectroscopy depth profile and Rütherford backscattering measurements as shown in Figure 2, very little chromium is observed at the surface. As seen in Figures 1 and 2, a good correlation is observed between the two profiles (i.e., evidence of Cr-rich interface is visible). We have also confirmed from extended x-ray absorption fine structure measurements that Cr indeed occupies octahedral position. X-ray diffraction analysis also was performed to confirm the identity of the secondary spinel phases. The data discussed in this study clearly show that the solid solubility of Cr is significantly less in ZnO.

Citation

Saraf LV, MH Engelhard, P Nachimuthu, V Shutthanandan, CM Wang, SM Heald, DE McCready, AS Lea, DR Baer, and SA Chambers. 2007. "Nucleation and Growth of MOCVD Grown (Cr, Zn)O Films." Journal of the Electrochemical Society 154(3):D134-D138.

Atomistic Simulations of Hydrated Nafion and Temperature Effects on Hydronium Ion Mobility

A Venkatnathan,^(a) R Devanathan,^(b) and M Dupuis^(a)

(a) Pacific Northwest National Laboratory, Richland, Washington

Figure 1. Left: Snapshot of hydrated Nafion membrane at low hydration. Right: Radial distribution functions of sulfur atoms in hydrated Nafion.
Full Image [png 31kb]

Figure 2. Snapshot of local structure of hydrated Nafion membrane at various level of membrane hydration (λ).
Full Image [png 76kb]

Polymer electrolyte membrane fuel cells (PEMFCs) can generate power with high efficiency and minimal greenhouse gas emissions. They have the potential to revolutionize power generation for the transportation, residential, and aerospace sectors. The polymer membrane is the heart of the fuel cell. Desired membrane properties are high proton conductivity; thermal, mechanical, and chemical stability; and low cost. None of the existing membranes meet all these requirements. There is a pressing need to design and optimize fuel cell membranes based on a molecular-level understanding of proton transport in polymer membranes.

In this study, molecular simulations are employed to study nanostructure and molecular transport in the widely used polymer membrane, NafionTM (Dupont). The results reveal that the extent of membrane hydration specifically affects the sulfonate groups on the polymer chains where protons tend to reside. Figure 1 shows a snapshot of a Nafion membrane at low hydration and radial distribution functions at various hydration levels.

At low hydration levels of a Nafion membrane, the sulfonate groups aggregate, which diminishes proton transport through the membrane. At higher membrane hydration levels, the distance between the sulfonate groups increases, thereby enhancing proton transport. The dynamical properties of proton and water transport, such as diffusion at fuel cell operating temperatures, also have been examined. This work was recently published as a cover article in the Journal of Physical Chemistry B (Venkatnathan et al. 2007). More recently, a detailed examination of the nanostructure of Nafion and the dynamics of proton and water using a different force-field model was performed. The local structure of Nafion membrane around the acidic sulfonate groups that are critical for proton transport is shown in Figure 2. Details of this work appeared in the Journal of Physical Chemistry B (Devanathan et al. 2007). The results, which are in good agreement with experimental measurements of the water diffusion coefficient in hydrated Nafion, help in the interpretation of results obtained from recent neutron scattering experiments.

Citations

Devanathan R, A Venkatnathan and M Dupuis. 2007. "Atomistic Simulation of Nafion Membrane: I. Effect of Hydration on Membrane Nanostructure." Journal of Physical Chemistry B 111(28):8069-8079.

Venkatnathan A, R Devanathan, and M Dupuis. 2007. "Nanostructure of Proton Exchange Membrane Under Low Hydration and Hydronium Mobility: Atomistic Simulation and Characterization." Journal of Physical Chemistry B 111(25):7234-7244.

Scientific Grand Challenge Highlights

Systems Approach to Understanding the Molecular Mechanism of the Light-Dark Cycles of Cyanothece sp. 51142

CS Oehmen,^(a) J McDermott,^(a) J Stockel,^(b) E Welsh, ^(b) J Jacobs,^(a) T Metz,^(a) A Dohnalkova,^(c) GW Buchko,^(a) and HB Pakrasi^(b)

(a) Pacific Northwest National Laboratory, Richland, Washington
(b) Washington University, St. LouisSt. Louis, Missouri
(c) W.R. Wiley Environmental Molecular Sciences Laboratory, Richland, Washington

Studying complex biological phenomena at multi-levels of detail requires analyzing different types of data from many sources, including imaging technologies, bio-informatics, transcriptomics, and proteomics. As a wider variety of high throughput methods enter mainstream scientific analyses, handling the complexity and volume of data from these disparate sources requires new algorithms for processing, visualization, and analysis.

We present integrative, multi-level analysis of circadian cycling in Cyanothece sp. 51142 under the auspices of the EMSL Grand Challenge in Membrane Biology project, which is a multi-institutional collaboration among Washington University in St. Louis, Purdue University, Saint Louis University, the Danforth Center in St. Louis, and PNNL. The focus of the Grand Challenge consortium is to understand how cycling of metabolites, gene expression, and proteins leads to physiological changes in Cyanothece during light and dark cycles. Integration of correlations across transcriptomic, proteomic, and metabolomic datasets is being accomplished with a novel suite of computational tools developed at PNNL. These integrated tools include Similarity Box (Sofia and Nakamura 2007), an interactive dendogram/clustering tool, PQuad (Harve et al. 2004), a proteomics dataset viewer, SEBINI (Taylor et al. 2006), a network inference environment and ScalaBLAST (Oehmen and Nieplocha 2006), and a high-performance BLAST accelerator (Altschul et al. 1990). Analyzing this large and complex collection of datasets using novel tools and hardware has made it possible to identify vital molecular components in the circadian cycles. Once identified, the goal is to experimentally verify the importance of these components in vivo.

Citation

Sofia HJ and GC Nakamura. 2007. "Similarity Box: Visual Analytics for Large Genomic Sets." (submitted to Bioinformatics).

Havre SL, M Singhal, DA Payne, and BM Webb-Robertson. 2004. "PQuad: Visualization of Predicted Peptides and Proteins." Visualization,2004, IEEE 473-480.

Taylor RC, A Shah, CC Treatman, and ML Blevins. 2006. "SEBINI Software Environment for Biological Network Inference." Bioinformatics 22(21):2706-2708.

Oehmen CS and J Nieplocha. 2006. "ScalaBLAST: A Scalable implementation of BLAST for high-performance data-intensive bioinformatics analysis." IEEE Transactions on Parallel and Distributed Systems 17(8):740-749.

Altschul SF, W Gish, W Miller, EW Myers, and DJ Lipman. 1990. "Basic Local Alignment Search Tool." Journal of Molecular Biology 215(3):403-410.

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