The research funded by this NEER grant establishes the framework for a detailed understanding of the challenges in beta dosimetry, especially in the presence of a mixed radiation field. The work also stimulated the thinking of the research group which will lead to new concepts in digital signal processing to allow collection of detection signals and real-time analysis such that simultaneous beta and gamma spectroscopy can take place. The work described herein (with detail in the many publications that came out of this research) was conducted in a manner that provided dissertation and thesis topics for three students, one of whom was completely funded by this grant. The overall benefit of the work came in the form of a dramatic shift in signal processing that is normally conducted in analog pulse shape analysis. Analog signal processing was shown not to be feasible for this type of work; digital signal processing was a must. This, in turn, led the research team to a new understanding of pulse analysis, one in which expands the state-of-the-art in simultaneous beta and gamma spectroscopy with a single detector.

The objectives of this project were (1) to alter a metalloregulatory protein (MerR) so that it would bind other toxic metals or radionuclides with similar affinity so that the engineered protein itself and/or bacteria expressing it could be deployed in the environment to specifically sequester such metals and (2) to alter the mercuric reductase, MerA, to reduce radionuclides and render them less mobile. Both projects had a basic science component. In the first case, such information about MerR illuminates how proteins discriminate very similar metals/elements. In the second case, information about MerA reveals the criteria for transmission of reducing equivalents from NADPH to redox-active metals. The work involved genetic engineering of all or parts of both proteins and examination of their resultant properties both in vivo and in vitro, the latter with biochemical and biophysical tools including equilibrium and non-equilibrium dialysis, XAFS, NMR, x-ray crystallography, and titration calorimetry. We defined the basis for metal specificity in MerR, devised a bacterial strain that sequesters Hg while growing, characterized gold reduction by MerA and the role of the metallochaperone domain of MerA, and determined the 3-D structure of MerB, the organomercurial lyase.

The Site Environmental Report is an integrated report on Berkeley Lab's environmental programs to satisfy the requirements of DOE Order 231.1A, Environment, Safety, and Health Reporting. It summarizes Berkeley Lab's environmental management performance, presents environmental monitoring results, and describes significant programs for calendar year 2007. Volume I is organized into an executive summary followed by six chapters that contain an overview of the Laboratory, a discussion of the Laboratory's environmental management system, the status of environmental programs, and summarized results from surveillance and monitoring activities.

The Center for Extended Magnetohydrodynamic Modeling (CEMM) is developing computer simulation models for predicting the behavior of magnetically confined plasmas. Over the first phase of support from the Department of Energy’s Scientific Discovery through Advanced Computing (SciDAC) initiative, the focus has been on macroscopic dynamics that alter the confinement properties of magnetic field configurations. The ultimate objective is to provide computational capabilities to predict plasma behavior—not unlike computational weather prediction—to optimize performance and to increase the reliability of magnetic confinement for fusion energy. Numerical modeling aids theoretical research by solving complicated mathematical models of plasma behavior including strong nonlinear effects and the influences of geometrical shaping of actual experiments. The numerical modeling itself remains an area of active research, due to challenges associated with simulating multiple temporal and spatial scales. The research summarized in this report spans computational and physical topics associated with state of the art simulation of magnetized plasmas. The tasks performed for this grant are categorized according to whether they are primarily computational, algorithmic, or application-oriented in nature. All involve the development and use of the Non-Ideal Magnetohydrodynamics with Rotation, Open Discussion (NIMROD) code, which is described at http://nimrodteam.org. With respect to computation, we have tested and …

Among the olivine-structured metal phosphate family, LiMnPO{sub 4} exhibits a high discharge potential (4V), which is still compatible with common electrolytes, making it interesting for use in the next generation of Li ion batteries. The extremely low electronic conductivity of this material severely limits its electrochemical performance, however. One strategy to overcome this limitation is to make LiMnPO{sub 4} nanoparticulate to decrease the diffusion distance. Another is to add a carbon or other conductive coating in intimate contact with the nanoparticles of the main phase, as is commonly done with LiFePO{sub 4}. The electrochemical performance of LiFePO{sub 4} is highly dependent on the quality of the carbon coatings on the particles [1-2], among other variables. Combustion synthesis allows the co-synthesis of nanoparticles coated with carbon in one step. Hydrothermal synthesis is used industrially to make LiFePO{sub 4} cathode materials [3] and affords a good deal of control over purity, crystallinity, and particle size. A wide range of olivine-structured materials has been successfully prepared by this technique [4], including LiMnPO{sub 4} in this study. In this paper, we report on the new synthesis of nano-LiMnPO{sub 4} by a combustion method. The purity is dependent upon the conditions used for synthesis, including …

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.

The attached report contains the final technical report for the above-mentioned project.

In order to efficiently perform particle simulations in systems with widely varying magnetization, we developed a drift-Lorentz mover, which interpolates between full particle dynamics and drift kinetics in such a way as to preserve a physically correct gyroradius and particle drifts for both large and small ratios of the timestep to the cyclotron period. In order to extend applicability of the mover to systems with plasma frequency exceeding the cyclotron frequency such as one may have with fully neutralized drift compression of a heavy-ion beam we have developed an implicit version of the mover. A first step in this direction, in which the polarization charge was added to the field solver, was described previously. Here we describe a fully implicit algorithm (which is analogous to the direct-implicit method for conventionalparticle-in-cell simulation), summarize a stability analysis of it, and describe several tests of the resultant code.

Fenton's reagent, a solution of hydrogen peroxide and ferrous iron catalyst, is used for an in-situ chemical oxidation of organic contaminants. Sulfuric acid is commonly used to create an acidic condition needed for catalytic oxidation. Fenton's reaction often involves pressure buildup and precipitation of reaction products, which can cause safety hazards and diminish efficiency. We selected citric acid, a food-grade substance, as an acidifying agent to evaluate its efficiencies for organic contaminant removal in Fenton's reaction, and examined the impacts of using citric acid on the unwanted reaction products. A series of batch and column experiments were performed with varying H{sub 2}O{sub 2} concentrations to decompose selected chlorinated ethylenes. Either dissolved iron from soil or iron sulfate salt was added to provide the iron catalyst in the batch tests. Batch experiments revealed that both citric and sulfuric acid systems achieved over 90% contaminant removal rates, and the presence of iron catalyst was essential for effective decontamination. Batch tests with citric acid showed no signs of pressure accumulation and solid precipitations, however the results suggested that an excessive usage of H{sub 2}O{sub 2} relative to iron catalysts (Fe{sup 2+}/H{sub 2}O{sub 2} < 1/330) would result in lowering the efficiency of contaminant …

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.

Finite element method was used to analyze the three-point bend experimental data of A533B-1 pressure vessel steel obtained by Sherry, Lidbury, and Beardsmore [1] from -160 to -45 C within the ductile-brittle transition regime. As many researchers have shown, the failure stress ({sigma}{sub f}) of the material could be approximated as a constant. The characteristic length, or the critical distance (r{sub c}) from the crack tip, at which {sigma}{sub f} is reached, is shown to be temperature dependent based on the crack tip stress field calculated by the finite element method. With the J-A{sub 2} two-parameter constraint theory in fracture mechanics, the fracture toughness (J{sub C} or K{sub JC}) can be expressed as a function of the constraint level (A{sub 2}) and the critical distance r{sub c}. This relationship is used to predict the fracture toughness of A533B-1 in the ductile-brittle transition regime with a constant {sigma}{sub f} and a set of temperature-dependent r{sub c}. It can be shown that the prediction agrees well with the test data for wide range of constraint levels from shallow cracks (a/W= 0.075) to deep cracks (a/W= 0.5), where a is the crack length and W is the specimen width.

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 …

TMVOC-MP is a massively parallel version of the TMVOC code (Pruess and Battistelli, 2002), a numerical simulator for three-phase non-isothermal flow of water, gas, and a multicomponent mixture of volatile organic chemicals (VOCs) in multidimensional heterogeneous porous/fractured media. TMVOC-MP was developed by introducing massively parallel computing techniques into TMVOC. It retains the physical process model of TMVOC, designed for applications to contamination problems that involve hydrocarbon fuels or organic solvents in saturated and unsaturated zones. TMVOC-MP can model contaminant behavior under 'natural' environmental conditions, as well as for engineered systems, such as soil vapor extraction, groundwater pumping, or steam-assisted source remediation. With its sophisticated parallel computing techniques, TMVOC-MP can handle much larger problems than TMVOC, and can be much more computationally efficient. TMVOC-MP models multiphase fluid systems containing variable proportions of water, non-condensible gases (NCGs), and water-soluble volatile organic chemicals (VOCs). The user can specify the number and nature of NCGs and VOCs. There are no intrinsic limitations to the number of NCGs or VOCs, although the arrays for fluid components are currently dimensioned as 20, accommodating water plus 19 components that may be either NCGs or VOCs. Among them, NCG arrays are dimensioned as 10. The user may select …

Starch branching enzyme (SBE) activity in the cassava storage root exhibited a diurnal fluctuation, dictated by a transcriptional oscillation of the corresponding SBE genes. The peak of SBE activity coincided with the onset of sucrose accumulation in the storage, and we conclude that the oscillatory mechanism keeps the starch synthetic apparatus in the storage root sink in tune with the flux of sucrose from the photosynthetic source. When storage roots were uncoupled from the source, SBE expression could be effectively induced by exogenous sucrose. Turanose, a sucrose isomer that cannot be metabolized by plants, mimicked the effect of sucrose, demonstrating that downstream metabolism of sucrose was not necessary for signal transmission. Also glucose and glucose-1-P induced SBE expression. Interestingly, induction by sucrose, turanose and glucose but not glucose-1-P sustained an overt semidian (12-h) oscillation in SBE expression and was sensitive to the hexokinase (HXK) inhibitor glucosamine. These results suggest a pivotal regulatory role for HXK during starch synthesis. Abscisic acid (ABA) was another potent inducer of SBE expression. Induction by ABA was similar to that of glucose-1-P in that it bypassed the semidian oscillator. Both the sugar and ABA signaling cascades were disrupted by okadaic acid, a protein phosphatase inhibitor. …

To meet the needs of a growing population and to provide us with a higher quality of life, increasing pressures are being placed on our environment through the development of agriculture, industry, and infrastructures. Soil erosion, groundwater depletion, salinization, and pollution have been recognized for decades as major threats to ecosystems and human health. More recently, the progressive substitution of fossil fuels by biofuels for energy production and climate change have been recognized as potential threats to our water resources and sustained agricultural productivity. The vadose zone mediates many of the processes that govern water resources and quality, such as the partition of precipitation into infiltration and runoff , groundwater recharge, contaminant transport, plant growth, evaporation, and energy exchanges between the Earth's surface and its atmosphere. It also determines soil organic carbon sequestration and carbon-cycle feedbacks, which could substantially impact climate change. The vadose zone's inherent spatial variability and inaccessibility precludes direct observation of the important subsurface processes. In a societal context where the development of sustainable and optimal environmental management strategies has become a priority, there is a strong prerequisite for the development of noninvasive characterization and monitoring techniques of the vadose zone. In particular, hydrogeophysical approaches applied at …

Here we show that labile particulate iron and manganese concentrations in the upper 500m of the Western Subarctic Pacific, an iron-limited High Nutrient Low Chlorophyll (HNLC) region, have prominent subsurface maxima between 100-200 m, reaching 3 nM and 600 pM, respectively. The subsurface concentration maxima in particulate Fe are characterized by a more reduced oxidation state, suggesting a source from primary volcagenic minerals such as from the Kuril/Kamchatka margin. The systematics of these profiles suggest a consistently strong lateral advection of labile Mn and Fe from redox-mobilized labile sources at the continental shelf supplemented by a more variable source of Fe from the upper continental slope. This subsurface supply of iron from the continental margin is shallow enough to be accessible to the surface through winter upwelling and vertical mixing, and is likely a key source of bioavailable Fe to the HNLC North Pacific.

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.

The goal of this research program was to develop improved methods for chemical peptide and protein synthesis, and to apply these methods to the total synthesis of small proteins (<80 amino acids) & integral membrane proteins.

Although electrokinetic effects are not new, only recently have they been investigated for possible use in energy conversion devices. We have recently reported the electrokinetic generation of molecular hydrogen from rapidly flowing liquid water microjets [Duffin et al. JPCC 2007, 111, 12031]. Here, we describe the use of liquid water microjets for direct conversion of electrokinetic energy to electrical power. Previous studies of electrokinetic power production have reported low efficiencies ({approx}3%), limited by back conduction of ions at the surface and in the bulk liquid. Liquid microjets eliminate energy dissipation due to back conduction and, measuring only at the jet target, yield conversion efficiencies exceeding 10%.

Using 226 million B{bar B} events recorded on the {Upsilon}(4S) resonance with the BABAR detector at the SLAC e{sup +}e{sup -} PEP-II storage rings, they reconstruct B{sup -} {yields} D*{sup 0}e{sup -}{bar {nu}}{sub e} decays using the decay chain D*{sup 0} {yields} D{sup 0}{pi}{sup 0} and D{sup 0} {yields} K{sup -} {pi}{sup +}. From the dependence of their differential rate on the w, the dot product of the four-velocities of B{sup -} and D*{sup 0}, and using the form factor description by Caprini et al. with the parameters F(1) and {rho}{sub 1{sub 1}}{sup 2}, they obtain the results {rho}{sub A{sub 1}}{sup 2} = 1.16 {+-} 0.06 {+-} 0.08, F(1) {center_dot} |V{sub cb}| = (35.9 {+-} 0.6 {+-} 1.4) {center_dot} 10{sup -3}, and {beta}(B{sup -} {yields} D*{sup 0} e{sup -}{bar {nu}}{sub e}) = (5.56 {+-} 0.08 {+-} 0.41)%.

Sparse parallel factorization is among the most complicated and irregular algorithms to analyze and optimize. Performance depends both on system characteristics such as the floating point rate, the memory hierarchy, and the interconnect performance, as well as input matrix characteristics such as such as the number and location of nonzeros. We present LUsim, a simulation framework for modeling the performance of sparse LU factorization. Our framework uses micro-benchmarks to calibrate the parameters of machine characteristics and additional tools to facilitate real-time performance modeling. We are using LUsim to analyze an existing parallel sparse LU factorization code, and to explore a latency tolerant variant. We developed and validated a model of the factorization in SuperLU_DIST, then we modeled and implemented a new variant of slud, replacing a blocking collective communication phase with a non-blocking asynchronous point-to-point one. Our strategy realized a mean improvement of 11percent over a suite of test matrices.

We examine the relative merits of gravity measurements as a monitoring tool for geological CO{sub 2} sequestration in three different modeling scenarios. The first is a combined CO{sub 2} enhanced oil recovery (EOR) and sequestration in a producing oil field, the second is sequestration in a brine formation, and the third is for a coalbed methane formation. EOR/sequestration petroleum reservoirs have relatively thin injection intervals with multiple fluid components (oil, hydrocarbon gas, brine, and CO{sub 2}), whereas brine formations usually have much thicker injection intervals and only two components (brine and CO{sub 2}). Coal formations undergoing methane extraction tend to be thin (3-10 m), but shallow compared to either EOR or brine formations. The injection of CO{sub 2} into the oil reservoir produced a bulk density decrease in the reservoir. The spatial pattern of the change in the vertical component of gravity (G{sub z}) is directly correlated with the net change in reservoir density. Furthermore, time-lapse changes in the borehole G{sub z} clearly identified the vertical section of the reservoir where fluid saturations are changing. The CO{sub 2}-brine front, on the order of 1 km within a 20 m thick brine formation at 1900 m depth, with 30% CO{sub 2} …

An automatic data-smoothing algorithm for data from digital oscilloscopes is described. The algorithm adjusts the bandwidth of the filtering as a function of time to provide minimum mean squared error at each time. It produces an estimate of the root-mean-square error as a function of time and does so without any statistical assumptions about the unknown signal. The algorithm is based on least-squares fitting to the data of cubic spline functions.

Angle- and time-resolved two-photon photoemission (2PPE) was used to study systems of organic semiconductors on Ag(111). The 2PPE studies focused on electronic behavior specific to interfaces and ultrathin films. Electron time dynamics and band dispersions were characterized for ultrathin films of a prototypical n-type planar aromatic hydrocarbon, PTCDA, and representatives from a family of p-type oligothiophenes.In PTCDA, electronic behavior was correlated with film morphology and growth modes. Within a fewmonolayers of the interface, image potential states and a LUMO+1 state were detected. The degree to which the LUMO+1 state exhibited a band mass less than a free electron mass depended on the crystallinity of the layer. Similarly, image potential states were measured to have free electron-like effective masses on ordered surfaces, and the effective masses increased with disorder within the thin film. Electron lifetimes were correlated with film growth modes, such that the lifetimes of electrons excited into systems created by layer-by-layer, amorphous film growth increased by orders of magnitude by only a few monolayers from the surface. Conversely, the decay dynamics of electrons in Stranski-Krastanov systems were limited by interaction with the exposed wetting layer, which limited the barrier to decay back into the metal.Oligothiophenes including monothiophene, quaterthiophene, and …