We investigate the evolution of structures that result when spherical Cd nanoparticles of a few hundred nanometers in diameter react with dissolved molecular sulfur species in solution to form hollow CdS. Over a wide range of temperatures and concentrations, we find that rapid Cd diffusion through the growing CdS shell localizes the reaction front at the outermost CdS/S interface, leading to hollow particles when all the Cd is consumed. When we examine partially reacted particles, we find that this system differs significantly from others in which the nanoscale Kirkendall effect has been used to create hollow particles. In previously reported systems, partial reaction creates a hollow particle with a spherically symmetric metal core connected to the outer shell by filaments. In contrast, here we obtain a lower symmetry structure, in which the unreacted metal core and the coalesced vacancies separate into two distinct spherical caps, minimizing the metal/void interface. This pattern of void coalescence is likely to occur in situations where the metal/vacancy self-diffusivities in the core are greater than the diffusivity of the cations through the shell.

Paired-end library sequencing has been proven useful in scaffold construction during de novo assembly of genomic sequences. The ability of generating mate pairs with 8 Kb or greater insert sizes is especially important for genomes containing long repeats. While the current 454 GS LT Paired-end library preparation protocol can successfully construct libraries with 3 Kb insert size, it fails to generate longer insert sizes because the protocol is optimized to purify shorter fragments. We have made several changes in the protocol in order to increase the fragment length. These changes include the use of Promega column to increase the yield of large size DNA fragments, two gel purification steps to remove contaminated short fragments, and a large reaction volume in the circularization step to decrease the formation of chimeras. We have also made additional changes in the protocol to increase the overall quality of the libraries. The quality of the libraries are measured by a set of metrics, which include levels of redundant reads, linker positive, linker negative, half linker reads, and driver DNA contamination, and read length distribution, were used to measure the primary quality of these libraries. We have also assessed the quality of the resulted mate pairs …

One of the biggest challenges in Chemical Dynamics is describing the behavior of complex systems accurately. Classical MD simulations have evolved to a point where calculations involving thousands of atoms are routinely carried out. Capturing coherence, tunneling and other such quantum effects for these systems, however, has proven considerably harder. Semiclassical methods such as the Initial Value Representation (SC-IVR) provide a practical way to include quantum effects while still utilizing only classical trajectory information. For smaller systems, this method has been proven to be most effective, encouraging the hope that it can be extended to deal with a large number of degrees of freedom. Several variations upon the original idea of the SCIVR have been developed to help make these larger calculations more tractable; these range from the simplest, classical limit form, the Linearized IVR (LSC-IVR) to the quantum limit form, the Exact Forward-Backward version (EFB-IVR). In this thesis a method to tune between these limits is described which allows us to choose exactly which degrees of freedom we wish to treat in a more quantum mechanical fashion and to what extent. This formulation is called the Tuning IVR (TIVR). We further describe methodology being developed to evaluate the prefactor …

This report was prepared by PNNL for the US Department of Energy Building Technologies Program, Solid-State Lighting Program. The report will be provided to teams of university students who are building houses for the 2009 Solar Decathlon, a home design competition sponsored in part by DOE, to encourage teams to build totally solar powered homes. One aspect of the competition is lighting. This report provides the teams with information about LED lighting that can help them determine how they incorporate LED lighting into their homes. The report provides an overview of LED technology, a status of where LED technology is today, questions and answers about lighting quality, efficiency, lifetime etc.; numerous examples of LED products; and several weblinks for further research.

The goal is to quantify and explain the carbon (C) budget for Oregon and N. California. The research compares "bottom -up" and "top-down" methods, and develops prototype analytical systems for regional analysis of the carbon balance that are potentially applicable to other continental regions, and that can be used to explore climate, disturbance and land-use effects on the carbon cycle. Objectives are: 1) Improve, test and apply a bottom up approach that synthesizes a spatially nested hierarchy of observations (multispectral remote sensing, inventories, flux and extensive sites), and the Biome-BGC model to quantify the C balance across the region; 2) Improve, test and apply a top down approach for regional and global C flux modeling that uses a model-data fusion scheme (MODIS products, AmeriFlux, atmospheric CO2 concentration network), and a boundary layer model to estimate net ecosystem production (NEP) across the region and partition it among GPP, R(a) and R(h). 3) Provide critical understanding of the controls on regional C balance (how NEP and carbon stocks are influenced by disturbance from fire and management, land use, and interannual climate variation). The key science questions are, "What are the magnitudes and distributions of C sources and sinks on seasonal to decadal …

In support of the closure of Tank 16H, the remaining waste material in the tank annulus must be removed. Samples of the waste material from Tank 16H annulus were obtained and sent to Savannah River National Laboratory (SRNL) to determine the chemical and radiochemical composition prior to further waste removal. The three samples obtained from the Tank 16H annulus show some similarity as to the types of mineral phases present in the materials but differ in the relative amounts of each phase present. The samples from outside the dehumidification duct at two locations in the annulus show very different compositions and estimated solubility in water. This indicates the waste material in Tank 16H annulus may have a wide range of compositions at different locations. The table below provides a simplified description of the composition of each sample. The limited characterization techniques conducted and the complex mixture of materials in each sample makes assigning a definitive composition for each sample difficult. Given the variability in composition with just the three small samples characterized, a more detailed description of any single sample may be of limited value.

Highly enantioselective catalytic intramolecular ortho-alkylation of aromatic imines containing alkenyl groups tethered at the meta position relative to the imine directing group has been achieved using [RhCl(coe){sub 2}]{sub 2} and chiral phosphoramidite ligands. Cyclization of substrates containing 1,1- and 1,2-disubstituted as well as trisubstituted alkenes were achieved with enantioselectivities >90% ee for each substrate class. Cyclization of substrates with Z-alkene isomers proceeded much more efficiently than substrates with E-alkene isomers. This further enabled the highly stereoselective intramolecular alkylation of certain substrates containing Z/E-alkene mixtures via a Rh-catalyzed alkene isomerization with preferential cyclization of the Z-isomer.

Here we examine Fe speciation within Fe-encrusted biofilms formed during 2-month seafloor incubations of sulfide mineral assemblages at the Main Endeavor Segment of the Juan de Fuca Ridge. The biofilms were distributed heterogeneously across the surface of the incubated sulfide and composed primarily of particles with a twisted stalk morphology resembling those produced by some aerobic Fe-oxidizing microorganisms. Our objectives were to determine the form of biofilm-associated Fe, and identify the sulfide minerals associated with microbial growth. We used micro-focused synchrotron-radiation X-ray fluorescence mapping (mu XRF), X-ray absorption spectroscopy (mu EXAFS), and X-ray diffraction (mu XRD) in conjunction with focused ion beam (FIB) sectioning, and highresolution transmission electron microscopy (HRTEM). The chemical and mineralogical composition of an Fe-encrusted biofilm was queried at different spatial scales, and the spatial relationship between primary sulfide and secondary oxyhydroxide minerals was resolved. The Fe-encrusted biofilms formed preferentially at pyrrhotite-rich (Fe1-xS, 0<_ x<_ 0.2) regions of the incubated chimney sulfide. At the nanometer spatial scale, particles within the biofilm exhibiting lattice fringing and diffraction patterns consistent with 2-line ferrihydrite were identified infrequently. At the micron spatial scale, Fe mu EXAFS spectroscopy and mu XRD measurements indicate that the dominant form of biofilm Fe is a …

A new method for correcting magnetic field errors in the ITER tokamak is developed using the Ideal Perturbed Equilibrium Code (IPEC). The dominant external magnetic field for driving islands is shown to be localized to the outboard midplane for three ITER equilibria that represent the projected range of operational scenarios. The coupling matrices between the poloidal harmonics of the external magnetic perturbations and the resonant fields on the rational surfaces that drive islands are combined for different equilibria and used to determine an ordered list of the dominant errors in the external magnetic field. It is found that efficient and robust error field correction is possible with a fixed setting of the correction currents relative to the currents in the main coils across the range of ITER operating scenarios that was considered.

We show that the eigenvalue equations describing a cylindrical ideal magnetophydrodynamicsw (MHD) plasma interacting with a thin resistive wall can be put into the standard mathematical form: Α⋅χ = λΒ⋅ χ. This is accomplished by using a finite element basis for the plasma, and by adding an extra degree of freedom corresponding to the electrical current in the thin wall. The standard form allows the use of linear eigenvalue solvers, without additional interations, to compute the complete spectrum of plasma modes in the presence of a surrounding restrictive wall at arbitrary separation. We show that our method recovers standard results in the limits of (1) an infinitely resistive wall (no wall), and (2) a zero resistance wall (ideal wall).

Ultra low frequency (ULF) waves, which are assumed to be standing waves on the field, are observed by the Mariner 10 spacecraft at Mercury. These waves are oscillating at 38% of the proton gyrofrequency. It is well known that the heavy ions, such as Na+, are abundant in Mercury's magnetosphere. Because the presence of different ion species has an influence on the plasma dispersion characteristics near the ion gyro-frequencies, such relatively high frequencies of magnetospheric eigenoscillations at Mercury require a multi-fluid treatment for the plasma. Thus ULF waves at Mercury may have a distinct difference from typical ULF oscillations at Earth, which are often described in terms of magnetohydrodynamics (MHD). By adopting a multi-fluid numerical wave model, we examine how magnetic eigenoscillations occur in Mercury's magnetosphere. Because protons and sodium ions are the main constituents at Mercury, we assume an electron-proton- sodium plasma in our model. The frequency spectra and time histories of the electromagnetic fields at the ion-ion hybrid (IIH) and cavity resonances are presented. Our results show: (1) The observed ULF waves are likely compressional waves rather than FLR. (2) Resonant absorption occurs at the IIH resonance, thus incoming compressional waves are converted into the IIH resonance. (3) …

Individual raw data streams from instrumentation at the Atmospheric Radiation Measurement (ARM) Program Climate Research Facility (ACRF) fixed and mobile sites are collected and sent to the Data Management Facility (DMF) at Pacific Northwest National Laboratory (PNNL) for processing in near real time. Raw and processed data are then sent daily to the ACRF Archive, where they are made available to users. For each instrument, we calculate the ratio of the actual number of data records received daily at the Archive to the expected number of data records. The results are tabulated by (1) individual data stream, site, and month for the current year and (2) site and fiscal year (FY) dating back to 1998. Table 1 shows the accumulated maximum operation time (planned uptime), actual hours of operation, and variance (unplanned downtime) for the period January 1 - March 31, 2008, for the fixed sites. The AMF is being deployed to China and is not in operation this quarter. The second quarter comprises a total of 2,184 hours. The average as well as the individual site values exceeded our goal this quarter. The Site Access Request System is a web-based database used to track visitors to the fixed and …