This is the final report for the DOE Project 10749-4.2.2.1 for the FY2007 - FY2009 period. This report is non-proprietary, and will be submitted to DOE as a final project report. The report covers activities under the DOE Project inside CRADA 269 (Project 53231) as well as project activites outside of that CRADA (Project 56662). This is the final report that is summarized from the non-proprietary quarterlies submitted to DOE over the past 2.5 years, which in turn are summaries from the proprietary technical reporting to UOP.

The three human LIG genes encode polypeptides that catalyze phosphodiester bond formation during DNA replication, recombination and repair. While numerous studies have identified protein partners of the human DNA ligases (hLigs), there has been little characterization of the catalytic properties of these enzymes. In this study, we developed and optimized a fluorescence-based DNA ligation assay to characterize the activities of purified hLigs. Although hLigI joins DNA nicks, it has no detectable activity on linear duplex DNA substrates with short, cohesive single-strand ends. By contrast, hLigIII{beta} and the hLigIII{alpha}/XRCC1 and hLigIV/XRCC4 complexes are active on both nicked and linear duplex DNA substrates. Surprisingly, hLigIV/XRCC4, which is a key component of the major non-homologous end joining (NHEJ) pathway, is significantly less active than hLigIII on a linear duplex DNA substrate. Notably, hLigIV/XRCC4 molecules only catalyze a single ligation event in the absence or presence of ATP. The failure to catalyze subsequent ligation events reflects a defect in the enzyme-adenylation step of the next ligation reaction and suggests that, unless there is an in vivo mechanism to reactivate DNA ligase IV/XRCC4 following phosphodiester bond formation, the cellular NHEJ capacity will be determined by the number of adenylated DNA ligaseIV/XRCC4 molecules.

This report summarizes results from pulse jet mixing (PJM) tests with noncohesive solids in Newtonian liquid conducted during FY 2007 and 2008 to support the design of mixing systems for the Hanford Waste Treatment and Immobilization Plant (WTP). Tests were conducted at three geometric scales using noncohesive simulants. The test data were used to independently develop mixing models that can be used to predict full-scale WTP vessel performance and to rate current WTP mixing system designs against two specific performance requirements. One requirement is to ensure that all solids have been disturbed during the mixing action, which is important to release gas from the solids. The second requirement is to maintain a suspended solids concentration below 20 weight percent at the pump inlet. The models predict the height to which solids will be lifted by the PJM action, and the minimum velocity needed to ensure all solids have been lifted from the floor. From the cloud height estimate we can calculate the concentration of solids at the pump inlet. The velocity needed to lift the solids is slightly more demanding than "disturbing" the solids, and is used as a surrogate for this metric. We applied the models to assess WTP …

Recent results obtained with high harmonic fast wave (HHFW) heating and current drive (CD) on NSTX strongly support the hypothesis that the onset of perpendicular fast wave propagation right at or very near the launcher is a primary cause for a reduction in core heating efficiency at long wavelengths that is also observed in ICRF heating experiments in numerous tokamaks. A dramatic increase in core heating efficiency was first achieved in NSTX L-mode helium majority plasmas when the onset for perpendicular wave propagation was moved away from the antenna and nearby vessel structures. Efficient core heating in deuterium majority L mode and H mode discharges, in which the edge density is typically higher than in comparable helium majority plasmas, was then accomplished by reducing the edge density in front of the launcher with lithium conditioning and avoiding operational points prone to instabilities. These results indicate that careful tailoring of the edge density profiles in ITER should be considered to limit rf power losses to the antenna and plasma facing materials. Finally, in plasmas with reduced rf power losses in the edge regions, the first direct measurements of high harmonic fast wave current drive were obtained with the motional Stark effect …

The Duck Valley Reservoirs Fish Stocking and Operations and Maintenance (DV Fisheries) project is an ongoing resident fish program designed to enhance both subsistence fishing, educational opportunities for Tribal members of the Shoshone-Paiute Tribes, and recreational fishing facilities for non-Tribal members. In addition to stocking rainbow trout (Oncorhynchus mykiss) in Mountain View, Lake Billy Shaw, and Sheep Creek Reservoirs, the program also intends to afford and maintain healthy aquatic conditions for fish growth and survival, to provide superior facilities with wilderness qualities to attract non-Tribal angler use, and to offer clear, consistent communication with the Tribal community about this project as well as outreach and education within the region and the local community. Tasks for this performance period are divided into operations and maintenance plus monitoring and evaluation. Operation and maintenance of the three reservoirs include fences, roads, dams and all reservoir structures, feeder canals, water troughs and stock ponds, educational signs, vehicles and equipment, and outhouses. Monitoring and evaluation activities included creel, gillnet, wildlife, and bird surveys, water quality and reservoir structures monitoring, native vegetation planting, photo point documentation, control of encroaching exotic vegetation, and community outreach and education. The three reservoirs are monitored in terms of water quality …

The Duck Valley Reservoirs Fish Stocking and Operations and Maintenance (DV Fisheries) project is an ongoing resident fish program that serves to partially mitigate the loss of anadromous fish that resulted from downstream construction of the hydropower system. The project's goals are to enhance subsistence fishing and educational opportunities for Tribal members of the Shoshone-Paiute Tribes and provide resident fishing opportunities for non-Tribal members. In addition to stocking rainbow trout (Oncorhynchus mykiss) in Mountain View, Lake Billy Shaw, and Sheep Creek Reservoirs, the program is also designed to maintain healthy aquatic conditions for fish growth and survival, to provide superior facilities with wilderness qualities to attract non-Tribal angler use, and to offer clear, consistent communication with the Tribal community about this project as well as outreach and education within the region and the local community. Tasks for this performance period are divided into operations and maintenance plus monitoring and evaluation. Operation and maintenance of the three reservoirs include fences, roads, dams and all reservoir structures, feeder canals, water troughs and stock ponds, educational signs, vehicles and equipment, and outhouses. Monitoring and evaluation activities included creel, gillnet, wildlife, and bird surveys, water quality and reservoir structures monitoring, native vegetation planting, photo …

GenOpt is an optimization program for the minimization of a cost function that is evaluated by an external simulation program. It has been developed for optimization problems where the cost function is computationally expensive and its derivatives are not available or may not even exist. GenOpt can be coupled to any simulation program that reads its input from text files and writes its output to text files. The independent variables can be continuous variables (possibly with lower and upper bounds), discrete variables, or both, continuous and discrete variables. Constraints on dependent variables can be implemented using penalty or barrier functions. GenOpt uses parallel computing to evaluate the simulations. GenOpt has a library with local and global multi-dimensional and one-dimensional optimization algorithms, and algorithms for doing parametric runs. An algorithm interface allows adding new minimization algorithms without knowing the details of the program structure. GenOpt is written in Java so that it is platform independent. The platform independence and the general interface make GenOpt applicable to a wide range of optimization problems. GenOpt has not been designed for linear programming problems, quadratic programming problems, and problems where the gradient of the cost function is available. For such problems, as well as …

This report summarizes the Lawrence Berkeley National Laboratory's research to date in characterizing energy efficiency and open automated demand response opportunities for industrial refrigerated warehouses in California. The report describes refrigerated warehouses characteristics, energy use and demand, and control systems. It also discusses energy efficiency and open automated demand response opportunities and provides analysis results from three demand response studies. In addition, several energy efficiency, load management, and demand response case studies are provided for refrigerated warehouses. This study shows that refrigerated warehouses can be excellent candidates for open automated demand response and that facilities which have implemented energy efficiency measures and have centralized control systems are well-suited to shift or shed electrical loads in response to financial incentives, utility bill savings, and/or opportunities to enhance reliability of service. Control technologies installed for energy efficiency and load management purposes can often be adapted for open automated demand response (OpenADR) at little additional cost. These improved controls may prepare facilities to be more receptive to OpenADR due to both increased confidence in the opportunities for controlling energy cost/use and access to the real-time data.

The External Flowsheet Review Team (EFRT) has identified the issues relating to the Waste Treatment and Immobilization Plant (WTP) pipe plugging. Per the review’s executive summary, “Piping that transports slurries will plug unless it is properly designed to minimize this risk. This design approach has not been followed consistently, which will lead to frequent shutdowns due to line plugging.” To evaluate the potential for plugging, testing was performed to determine critical velocities for the complex WTP piping layout. Critical velocity is defined as the point at which a moving bed of particles begins to form on the pipe bottom during slurry-transport operations. Pressure drops across the fittings of the test pipeline were measured with differential pressure transducers, from which the critical velocities were determined. A WTP prototype flush system was installed and tested upon the completion of the pressure-drop measurements. We also provide the data for the overflow relief system represented by a WTP complex piping geometry with a non-Newtonian slurry. A waste simulant composed of alumina (nominally 50 μm in diameter) suspended in a kaolin clay slurry was used for this testing. The target composition of the simulant was 10 vol% alumina in a suspending medium with a yield …

Expression of the A and B forms of progesterone receptor (PR) in an appropriate ratio is critical for mammary development. Mammary glands of PR-A transgenic mice, carrying an additional A form of PR as a transgene, exhibit morphological features associated with the development of mammary tumors. Our objective was to determine the roles of estrogen (E) and progesterone (P) in the genesis of mammary hyperplasias/preneoplasias in PR-A transgenics. We subjected PR-A mice to hormonal treatments and analyzed mammary glands for the presence of hyperplasias and used BrdU incorporation to measure proliferation. Quantitative image analysis was carried out to compare levels of latency-associated peptide and transforming growth factor beta 1 (TGF{beta}1) between PR-A and PR-B transgenics. Basement membrane disruption was examined by immunofluorescence and proteolytic activity by zymography. The hyperplastic phenotype of PR-A transgenics is inhibited by ovariectomy, and is reversed by treatment with E + P. Studies using the antiestrogen ICI 182,780 or antiprogestins RU486 or ZK 98,299 show that the increase in proliferation requires signaling through E/estrogen receptor alpha but is not sufficient to give rise to hyperplasias, whereas signaling through P/PR has little impact on proliferation but is essential for the manifestation of hyperplasias. Increased proliferation is correlated …

This paper highlights some of the current basic nuclear physics research at Lawrence Livermore National Laboratory (LLNL). The work at LLNL concentrates on investigating nuclei at the extremes. The Experimental Nuclear Physics Group performs research to improve our understanding of nuclei, nuclear reactions, nuclear decay processes and nuclear astrophysics; an expertise utilized for important laboratory national security programs and for world-class peer-reviewed basic research.

We present an x-ray absorption spectroscopy results for fully broken to a complete H-bond network of water molecules on Ru(0001) by varying the morphology from isolated water molecules via two-dimensional clusters to a fully covered monolayer as probed by scanning tunneling microscopy. The sensitivity of x-ray absorption to the symmetry of H-bonding is further elucidated for the amino (-NH{sub 2}) group in glycine adsorbed on Cu(110) where the E-vector is parallel either to the NH donating an H-bond or to the non-H-bonded NH. The results give further evidence for the interpretation of the various spectral features of liquid water and for the general applicability of x-ray absorption spectroscopy to analyze H-bonded systems.