The Thirteenth Workshop on Advanced Accelerator Concepts (AAC) was held from July 27 to August 2, 2008 at the Chaminade Conference Center in Santa Cruz, California, USA, organized by the Lawrence Berkeley National Laboratory and the University of California at Berkeley. There were unprecedented levels of interest in the 2008 AAC Workshop, and participation was by invitation, with 215 workshop attendees, including 58 students. Reflecting the world-wide growth of the advanced accelerator community, there was significant international participation, with participants from twelve countries attending.

Plant Metabolic Engineering is an emerging field that integrates a diverse range of disciplines including plant genetics, genomics, biochemistry, chemistry and cell biology. The Gordon-Kenan Graduate Research Seminar (GRS) in Plant Metabolic Engineering was initiated to provide a unique opportunity for future researcher leaders to present their work in this field. It also creates an environment allowing for peer-review and critical assessment of work without the intimidation usually associated with the presence of senior investigators. The GRS immediately precedes the Plant Metabolic Engineering Gordon Research Conference and will be for and by graduate students and post-docs, with the assistance of the organizers listed.

Uncertainty built into conceptual groundwater flow and transport models and associated parametric uncertainty should be appropriately included when such models are used to develop detection monitoring networks for contaminated sites. We compare alternative approaches of propagating such uncertainty from the flow and transport model into the network design. The focus is on detection monitoring networks where the primary objective is to intercept the contaminant before it reaches a boundary of interest (e.g., compliance boundary). Different uncertainty propagation approaches identify different well locations and different well combinations (networks) as having the highest detection efficiency. It is thus recommended that multiple uncertainty propagation approaches are considered. If several approaches yield consistent results in terms of identifying the best performing candidate wells and the best performing well network for detecting a contaminant plume, this would provide confidence in the suitability of the selected well locations.

Rainier Mesa (RM) is a tuffaceous, high-elevation plateau on the Nevada Test Site (NTS) that has been subjected to numerous nuclear tests between 1957 and 1992. Unlike other tests on the NTS located within or just above the saturated zone, tests at the RM T-tunnel complex were conducted within a variably saturated sequence of bedded and non-welded vitric and zeolitized tuff units, located approximately 500 m above the regional groundwater flow system. The low permeability and high porosity of the underlying zeolitized tuff units suggest the downward transport of radionuclides released from these tests are minimal through the tuff matrix. However, numerous faults observed to discharge water into tunnel drifts may serve as preferential pathways for radionuclide migration. Data collected from tunnel drifts indicate that faulting within the zeolitized tuff units is sparse with fractal clustering, and that connectivity between adjacent fault clusters is often weak to non-existent. The sparse fault density at RM, in conjunction with the extreme variability in the spatial distribution of faults, poses challenges not readily addressed by existing upscaling methods that upscale fracture properties as equivalent grid tensors. The unique fault statistics at RM has led to the development of a fracture continuum method designed …

Crosswell seismic acquisition provides an ideal geometry for monitoring travel time changes in the subsurface. Analysis of delay time in terms of a characteristic frequency allows us to estimate optimal acquisition parameters (frequency and distance). We have deployed standard data acquisition equipment for continuous monitoring of crosswell travel time in two separate field experiments, with well spacing of 3 and 30 m. The acquisition hardware used for the field experiments is described, along with environmental effects (such as temperature) that influence the measurements. Two field experiments are described that correlate changes in travel time (and therefore velocity) with changes in barometric pressure. The results from the two field sites show a pressure sensitivity for velocity of 10{sup -6}/Pa to 10{sup -8}/Pa.

The purpose of this report is to provide a concise but comprehensive overview of Atmospheric Radiation Measurement Climate Research Facility instrumentation status. The report is divided into the following five sections: (1) new instrumentation in the process of being acquired and deployed, (2) field campaigns, (3) existing instrumentation and progress on improvements or upgrades, (4) proposed future instrumentation, and (5) Small Business Innovation Research instrument development.

Community structures of active bacterial populations were investigated along a vertical redox profile in coastal Baltic Sea sediments by terminal-restriction fragment length polymorphism (T-RFLP) and clone library analysis. According to correspondence analysis of T-RFLP results and sequencing of cloned 16S rRNA genes, the microbial community structures at three redox depths (179 mV, -64 mV and -337 mV) differed significantly. The bacterial communities in the community DNA differed from those in bromodeoxyuridine (BrdU)-labeled DNA, indicating that the growing members of the community that incorporated BrdU were not necessarily the most dominant members. The structures of the actively growing bacterial communities were most strongly correlated to organic carbon followed by total nitrogen and redox potentials. Bacterial identification by sequencing of 16S rRNA genes from clones of BrdU-labeled DNA and DNA from reverse transcription PCR (rt-PCR) showed that bacterial taxa involved in nitrogen and sulfur cycling were metabolically active along the redox profiles. Several sequences had low similarities to previously detected sequences indicating that novel lineages of bacteria are present in Baltic Sea sediments. Also, a high number of different 16S rRNA gene sequences representing different phyla were detected at all sampling depths.

A linear scaling approach for general and accurate pseudopotential Density Functional Theory calculations is presented. It is based on a Finite Difference discretization. Effective O(N) scaling is achieved by confining the orbitals in spherical localization regions. To improve accuracy and flexibility while computing the smallest possible number of orbitals, we propose an algorithm to adapt localization regions during computation. Numerical results for a polyacethylene chain and a magnesium oxide ring are presented.

The recent Nevada Earthquake (M=6) produced an extraordinary set of crustal guided waves. In this study, we examine the three-component data at all the USArray stations in terms of how well existing models perform in predicting the various phases, Rayleigh waves, Love waves, and Pnl waves. To establish the source parameters, we applied the Cut and Paste Code up to distance of 5° for an average local crustal model which produced a normal mechanism (strike=35°,dip=41°,rake=-85°) at a depth of 9 km and Mw=5.9. Assuming this mechanism, we generated synthetics at all distances for a number of 1D and 3D models. The Pnl observations fit the synthetics for the simple models well both in timing (VPn=7.9km/s) and waveform fits out to a distance of about 5°. Beyond this distance a great deal of complexity can be seen to the northwest apparently caused by shallow subducted slab material. These paths require considerable crustal thinning and higher P-velocities. Small delays and advances outline the various tectonic province to the south, Colorado Plateau, etc. with velocities compatible with that reported on by Song et al.(1996). Five-second Rayleigh waves (Airy Phase) can be observed throughout the whole array and show a great deal of variation …

The objective of this program was to explore a combination of advanced injection control and urea-selective catalytic reduction (SCR) to reduce the emissions of oxides of nitrogen (NOx) and particulate matter (PM) from a Tier 2 off-highway diesel engine to Tier 3 emission targets while maintaining fuel efficiency. The engine used in this investigation was a 2004 4.5L John Deere PowerTechTM; this engine was not equipped with exhaust gas recirculation (EGR). Under the original CRADA, the principal objective was to assess whether Tier 3 PM emission targets could be met solely by increasing the rail pressure. Although high rail pressure will lower the total PM emissions, it has a contrary effect to raise NOx emissions. To address this effect, a urea-SCR system was used to determine whether the enhanced NOx levels, associated with high rail pressure, could be reduced to Tier 3 levels. A key attraction for this approach is that it eliminates the need for a Diesel particulate filter (DPF) to remove PM emissions. The original CRADA effort was also performed using No.2 Diesel fuel having a maximum sulfur level of 500 ppm. After a few years, the CRADA scope was expanded to include exploration of advanced injection strategies …

Remarkable advances have been made since rapid solidification was first introduced to the field of materials science and technology. New types of materials such as amorphous alloys and nanostructure materials have been developed as a result of rapid solidification techniques. While these advances are, in many respects, ground breaking, much remains to be discerned concerning the fundamental relationships that exist between a liquid and a rapidly solidified solid. The scope of the current dissertation involves an extensive set of experimental, analytical, and computational studies designed to increase the overall understanding of morphological selection, phase competition, and structural hierarchy that occurs under far-from equilibrium conditions. High pressure gas atomization and Cu-block melt-spinning are the two different rapid solidification techniques applied in this study. The research is mainly focused on Al-Si and Al-Sm alloy systems. Silicon and samarium produce different, yet favorable, systems for exploration when alloyed with aluminum under far-from equilibrium conditions. One of the main differences comes from the positions of their respective T{sub 0} curves, which makes Al-Si a good candidate for solubility extension while the plunging T{sub 0} line in Al-Sm promotes glass formation. The rapidly solidified gas-atomized Al-Si powders within a composition range of 15 to 50 …

In this study we analyze relative contributions to the cause and mechanism of injection-induced micro-earthquakes (MEQs) at The Geysers geothermal field, California. We estimated the potential for inducing seismicity by coupled thermal-hydrological-mechanical analysis of the geothermal steam production and cold water injection to calculate changes in stress (in time and space) and investigated if those changes could induce a rock mechanical failure and associated MEQs. An important aspect of the analysis is the concept of a rock mass that is critically stressed for shear failure. This means that shear stress in the region is near the rock-mass frictional strength, and therefore very small perturbations of the stress field can trigger an MEQ. Our analysis shows that the most important cause for injection-induced MEQs at The Geysers is cooling and associated thermal-elastic shrinkage of the rock around the injected fluid that changes the stress state in such a way that mechanical failure and seismicity can be induced. Specifically, the cooling shrinkage results in unloading and associated loss of shear strength in critically shear-stressed fractures, which are then reactivated. Thus, our analysis shows that cooling-induced shear slip along fractures is the dominant mechanism of injection-induced MEQs at The Geysers.

Non-enzymatic glycation of tissue proteins has important implications in the development of complications of diabetes mellitus. While electron transfer dissociation (ETD) has been shown to outperform collision-induced dissociation (CID) in sequencing glycated peptides by tandem mass spectrometry, ETD instrumentation is not yet available in all laboratories. In this study, we evaluated different advanced CID techniques (i.e., neutral-loss triggered MS3 and multi-stage activation) during LC-MSn analyses of Amadori-modified peptides enriched from human serum glycated in vitro. During neutral-loss triggered MS3 experiments, MS3 scans triggered by neutral-losses of 3 H2O or 3 H2O + HCHO produced similar results in terms of glycated peptide identifications. However, neutral losses of 3 H2O resulted in significantly more glycated peptide identifications during multi-stage activation experiments. Overall, the multi-stage activation approach produced more glycated peptide identifications, while the neutral-loss triggered MS3 approach resulted in much higher specificity. Both techniques offer a viable alternative to ETD for identifying glycated peptides when that method is unavailable.

Antisense oligodeoxynucleotide (ODN) inhibition emerges as an effective means for probing gene function in plant cells. Employing this method we have established the importance of the SUSIBA2 transcription factor for regulation of starch synthesis in barley endosperm, and arrived at a model for the role of the SUSIBAs in sugar signaling and source-sink commutation during cereal endosperm development. In this addendum we provide additional data demonstrating the suitability of the antisense ODN technology in studies on starch branching enzyme activities in barley leaves. We also comment on the mechanism for ODN uptake in plant cells. Antisense ODNs are short (12-25 nt-long) stretches of single-stranded ODNs that hybridize to the cognate mRNA in a sequence-specific manner, thereby inhibiting gene expression. They are naturally occurring in both prokaryotes and eukaryotes where they partake in gene regulation and defense against viral infection. The mechanisms for antisense ODN inhibition are not fully understood but it is generally considered that the ODN either sterically interferes with translation or promotes transcript degradation by RNase H activation. The earliest indication of the usefulness of antisense ODN technology for the purposes of molecular biology and medical therapy was the demonstration in 1978 that synthetic ODNs complementary to Raos …

Various single-molecule techniques were utilized for ultra-sensitive early diagnosis of viral DNA and antigen and basic mechanism study of enzymatic reactions. DNA of human papilloma virus (HPV) served as the screening target in a flow system. Alexa Fluor 532 (AF532) labeled single-stranded DNA probes were hybridized to the target HPV-16 DNA in solution. The individual hybridized molecules were imaged with an intensified charge-coupled device (ICCD) in two ways. In the single-color mode, target molecules were detected via fluorescence from hybridized probes only. This system could detect HPV-16 DNA in the presence of human genomic DNA down to 0.7 copy/cell and had a linear dynamic range of over 6 orders of magnitude. In the dual-color mode, fluorescence resonance energy transfer (FRET) was employed to achieve zero false-positive count. We also showed that DNA extracts from Pap test specimens did not interfere with the system. A surface-based method was used to improve the throughput of the flow system. HPV-16 DNA was hybridized to probes on a glass surface and detected with a total internal reflection fluorescence (TIRF) microscope. In the single-probe mode, the whole genome and target DNA were fluorescently labeled before hybridization, and the detection limit is similar to the flow …

Over the past half-century, the Applied Mathematics program in the U.S. Department of Energy's Office of Advanced Scientific Computing Research has made significant, enduring advances in applied mathematics that have been essential enablers of modern computational science. Motivated by the scientific needs of the Department of Energy and its predecessors, advances have been made in mathematical modeling, numerical analysis of differential equations, optimization theory, mesh generation for complex geometries, adaptive algorithms and other important mathematical areas. High-performance mathematical software libraries developed through this program have contributed as much or more to the performance of modern scientific computer codes as the high-performance computers on which these codes run. The combination of these mathematical advances and the resulting software has enabled high-performance computers to be used for scientific discovery in ways that could only be imagined at the program's inception. Our nation, and indeed our world, face great challenges that must be addressed in coming years, and many of these will be addressed through the development of scientific understanding and engineering advances yet to be discovered. The U.S. Department of Energy (DOE) will play an essential role in providing science-based solutions to many of these problems, particularly those that involve the energy, …

This paper describes a safety design basis documentation change control process. The process identifies elements that can be used to manage the project/facility configuration during design evolution through the Initiation, Definition, and Execution project phases. The project phases addressed by the process are defined in US Department of Energy (DOE) Order (O) 413.3A, Program and Project Management for the Acquisition of Capital Assets, in support of DOE project Critical Decisions (CD). This approach has been developed for application to two Hanford Site projects in their early CD phases and is considered to be a key element of safety and design integration. As described in the work that has been performed, the purpose of change control is to maintain consistency among design requirements, the physical configuration, related facility documentation, and the nuclear safety basis during the evolution of the design. The process developed (1) ensures an appropriate level of rigor is applied at each project phase and (2) is considered to implement the requirements and guidance provided in DOE-STD-1189-2008, Integration of Safety into the Design Process. Presentation of this work is expected to benefit others in the DOE Complex that may be implementing DOE-STD-1189-2008 or managing nuclear safety documentation in support …

Small animal SPECT imaging systems have multiple potential applications in biomedical research. Whereas SPECT data are commonly interpreted qualitatively in a clinical setting, the ability to accurately quantify measurements will increase the utility of the SPECT data for laboratory measurements involving small animals. In this work, we assess the effect of photon attenuation, scatter and partial volume errors on the quantitative accuracy of small animal SPECT measurements, first with Monte Carlo simulation and then confirmed with experimental measurements. The simulations modeled the imaging geometry of a commercially available small animal SPECT system. We simulated the imaging of a radioactive source within a cylinder of water, and reconstructed the projection data using iterative reconstruction algorithms. The size of the source and the size of the surrounding cylinder were varied to evaluate the effects of photon attenuation and scatter on quantitative accuracy. We found that photon attenuation can reduce the measured concentration of radioactivity in a volume of interest in the center of a rat-sized cylinder of water by up to 50percent when imaging with iodine-125, and up to 25percent when imaging with technetium-99m. When imaging with iodine-125, the scatter-to-primary ratio can reach up to approximately 30percent, and can cause overestimation of …

The interaction of metal ions and oxyanions with nanoscale mineral phases has not yet been extensively studied despite the increased recognition of their prevalence in natural systems as a significant component of geomedia. A combination of macroscopic uptake studies to investigate the adsorption behavior of As(V), Cu(II), Hg(II), and Zn(II) onto nanoparticulate goethite ({alpha}-FeOOH) as a function of aging time at elevated temperature (75 C) and synchrotron-based X-ray studies to track changes in both the sorption mode and the rate of nanoparticle growth reveal the effects that uptake has on particle growth. Metal(loid) species which sorb quickly to the iron oxyhydroxide particles (As(V), Cu(II)) appear to passivate the particle surface, impeding the growth of the nanoparticles with progressive aging; in contrast, species that sorb more slowly (Hg(II), Zn(II)) have considerably less impact on particle growth. Progressive changes in the speciation of these particular metals with time suggest shifts in the mode of metal uptake with time, possibly indicating structural incorporation of the metal(loid) into the nanoparticle; this is supported by the continued increase in uptake concomitant with particle growth, implying that metal species may transform from surface-sorbed species to more structurally incorporated forms. This type of incorporation would have implications …

Amorphous titania (TiO{sub 2}) is an important precursor for synthesis of single-phase nanocrystalline anatase. We synthesized x-ray amorphous titania by hydrolysis of titanium ethoxide at the ice point. Transmission electron microscopy examination and nitrogen gas adsorption indicated the particle size of the synthesized titania is {approx} 2 nm. Synchrotron wide-angle x-ray scattering (WAXS) was used to probe the atomic correlations in this amorphous sample. Atomic pair-distribution function (PDF) derived from Fourier transform of the WAXS data was used for reverse Monte Carlo (RMC) simulations of the atomic structure of the amorphous TiO{sub 2} nanoparticles. Molecular dynamics simulations were used to generate input structures for the RMC. X-ray absorption spectroscopy (XAS) simulations were used to screen candidate structures obtained from the RMC by comparing with experimental XAS data. The structure model that best describes both the WAXS and XAS data shows that an amorphous TiO{sub 2} particle consists of a highly distorted shell and a small strained anatase-like crystalline core. The average coordination number of Ti is 5.3 and most Ti-O bonds are populated around 1.940 {angstrom}. Relative to bulk TiO{sub 2}, the reduction of the coordination number is primarily due to the truncation of the Ti-O octahedra at the amorphous …

The measurement of flow obtained using continuous wave Doppler ultrasound is formulated as a directional projection of a flow vector field. When a continuous ultrasound wave bounces against a flowing particle, a signal is backscattered. This signal obtains a Doppler frequency shift proportional to the speed of the particle along the ultrasound beam. This occurs for each particle along the beam, giving rise to a Doppler velocity spectrum. The first moment of the spectrum provides the directional projection of the flow along theultrasound beam. Signals reflected from points further away from the detector will have lower amplitude than signals reflected from points closer to the detector. The effect is very much akin to that modeled by the attenuated Radon transform in emission computed tomography.A least-squares method was adopted to reconstruct a 2D vector field from directional projection measurements. Attenuated projections of only the longitudinal projections of the vector field were simulated. The components of the vector field were reconstructed using the gradient algorithm to minimize a least-squares criterion. This result was compared with the reconstruction of longitudinal projections of the vector field without attenuation. Ifattenuation is known, the algorithm was able to accurately reconstruct both components of the full vector …

Where Martian rocks have been exposed to liquid water, chemistry versus depth profiles could elucidate both Martian climate history and potential for life. The persistence of primary minerals in weathered profiles constrains the exposure time to liquid water: on Earth, mineral persistence times range from {approx}10 ka (olivine) to {approx}250 ka (glass) to {approx}1Ma (pyroxene) to {approx}5Ma (plagioclase). Such persistence times suggest mineral persistence minima on Mars. However, Martian solutions may have been more acidic than on Earth. Relative mineral weathering rates observed for basalt in Svalbard (Norway) and Costa Rica demonstrate that laboratory pH trends can be used to estimate exposure to liquid water both qualitatively (mineral absence or presence) and quantitatively (using reactive transport models). Qualitatively, if the Martian solution pH > {approx}2, glass should persist longer than olivine; therefore, persistence of glass may be a pH-indicator. With evidence for the pH of weathering, the reactive transport code CrunchFlow can quantitatively calculate the minimum duration of exposure to liquid water consistent with a chemical profile. For the profile measured on the surface of Humphrey in Gusev Crater, the minimum exposure time is 22 ka. If correct, this estimate is consistent with short-term, episodic alteration accompanied by ongoing surface …

The construction of a host of interesting patterns over one and two dimensions, as transformations of multifractal measures via fractal interpolating functions related to simple affine mappings, is reviewed. It is illustrated that, while space-filling fractal functions most commonly yield limiting Gaussian distribution measures (bells), there are also situations (depending on the affine mappings parameters) in which there is no limit. Specifically, the one-dimensional case may result in oscillations between two bells, whereas the two-dimensional case may give rise to unexpected circle map dynamics of an arbitrary number of two-dimensional circular bells. It is also shown that, despite the multitude of bells over two dimensions, whose means dance making regular polygons or stars inscribed on a circle, the iteration of affine maps yields exotic kaleidoscopes that decompose such an oscillatory pattern in a way that is similar to the many cases that converge to a single bell.

The U.S. Department of Energy (USDOE) is building a new long-range (to 2050) forecasting model for use in budgetary and management applications called the Stochastic Energy Deployment System (SEDS), which explicitly incorporates uncertainty through its development within the Analytica(R) platform of Lumina Decision Systems. SEDS is designed to be a fast running (a few minutes), user-friendly model that analysts can readily run and modify in its entirety through a visual programming interface. Lawrence Berkeley National Laboratory is responsible for implementing the SEDS Buildings Module. The initial Lite version of the module is complete and integrated with a shared code library for modeling demand-side technology choice developed by the National Renewable Energy Laboratory (NREL) and Lumina. The module covers both commercial and residential buildings at the U.S. national level using an econometric forecast of floorspace requirement and a model of building stock turnover as the basis for forecasting overall demand for building services. Although the module is fundamentally an engineering-economic model with technology adoption decisions based on cost and energy performance characteristics of competing technologies, it differs from standard energy forecasting models by including considerations of passive building systems, interactions between technologies (such as internal heat gains), and on-site power generation.