Replication Protein A (RPA) is the primary eukaryotic ssDNA binding protein utilized in diverse DNA transactions in the cell. RPA is a heterotrimeric protein with seven globular domains connected by flexible linkers, which enable substantial inter-domain motion that is essential to its function. Small angle X-ray scattering (SAXS) experiments on two multi-domain constructs from the N-terminus of the large subunit (RPA70) were used to examine the structural dynamics of these domains and their response to the binding of ssDNA. The SAXS data combined with molecular dynamics simulations reveal substantial interdomain flexibility for both RPA70AB (the tandem high affinity ssDNA binding domains A and B connected by a 10-residue linker) and RPA70NAB (RPA70AB extended by a 70-residue linker to the RPA70N protein interaction domain). Binding of ssDNA to RPA70NAB reduces the interdomain flexibility between the A and B domains, but has no effect on RPA70N. These studies provide the first direct measurements of changes in orientation of these three RPA domains upon binding ssDNA. The results support a model in which RPA70N remains structurally independent of RPA70AB in the DNA bound state and therefore freely available to serve as a protein recruitment module.

California s major energy utilities and the California Energy Commission (CEC) are seeking to allocate capital that yields the greatest return on investment for energy infrastructure that meets any part of the need for reliable supplies of energy. The utilities are keenly interested in knowing the amount of electrical energy savings that would occur if cool roof color materials are adopted in the building market. To meet this need the Oak Ridge National Laboratory and the Lawrence Berkeley National Laboratory (LBNL) have been collaborating on a Public Interest Energy Research (PIER) project to develop an industry-consensus energy-savings calculator. The task was coordinated with an ongoing effort supported by the DOE to develop one calculator to achieve both the DOE and the EPA objectives for deployment of cool roof products. Recent emphasis on domestic building energy use has made the work a top priority by the Department of Energy s (DOE) Building Technologies Program. The Roof Savings Calculator (RSC) tool is designed to help building owners, manufacturers, distributors, contractors and practitioners easily run complex simulations. The latest web technologies and usability design were employed to provide an easy input interface to an annual simulation of hour-by-hour, whole-building performance using the world-class …

The MINOS experiment was designed to measure neutrino oscillation parameters with muon neutrinos. It achieves this by measuring the neutrino energy spectrum and flavor composition of the man-made NuMI neutrino beam 1km after the beam is formed and again after 735 km. By comparing the two spectra it is possible to measure the oscillation parameters. The NuMI beam is made up of 7.0%$\bar{v}$_μ, which can be separated from the v_μ because the MINOS detectors are magnetized. This makes it possible to study $\bar{v}$_μ oscillations separately from those of muon neutrinos, and thereby test CPT invariance in the neutrino sector by determining the $\bar{v}$_μ oscillation parameters and comparing them with those for v_μ, although any unknown physics of the antineutrino would appear as a difference in oscillation parameters. Such a test has not been performed with beam $\bar{v}$_μ before. It is also possible to produce an almost pure $\bar{v}$_μ beam by reversing the current through the magnetic focusing horns of the NuMI beamline, thereby focusing negatively, instead of positively charged particles. This thesis describes the analysis of the 7% $\bar{v}$_μ component of the forward horn current NuMI beam. The $\bar{v}$_μ of a data sample of 3.2 x 10{sup 20} protons on …

Young people these days are very concerned about the environment. There is also a great deal of interest in using technology to improve energy efficiency. Many physics students share these concerns and would like to find ways to use their scientific and quantitative skills to help overcome the environmental challenges that the world faces. This may be particularly true for female students. Showing physics students how they can contribute to environmental and energy solutions while doing scientific research which excites them is expected to attract more physicists to work on these very important problems and to retain more of the best and the brightest in physical science. This is a major thrust of the 'Gathering Storm' report, the 'American Competitiveness Initiative' report, and several other studies. With these concerns in mind, the American Physical Society (APS) and more specifically, the newly formed APS Topical Group on Energy Research and Applications (GERA), organized and conducted a one-day workshop for graduate students and post docs highlighting the contributions that physics-related research can make to meeting the nation's energy needs in environmentally friendly ways. A workshop program committee was formed and met four times by conference call to determine session topics and to …

Carbon dioxide (CO{sub 2}) sensors are often deployed in commercial buildings to obtain CO{sub 2} data that are used, in a process called demand-controlled ventilation, to automatically modulate rates of outdoor air ventilation. The objective is to keep ventilation rates at or above design specifications and code requirements and also to save energy by avoiding excessive ventilation rates. Demand controlled ventilation is most often used in spaces with highly variable and sometime dense occupancy. Reasonably accurate CO{sub 2} measurements are needed for successful demand controlled ventilation; however, prior research has suggested substantial measurement errors. Accordingly, this study evaluated: (a) the accuracy of 208 CO{sub 2} single-location sensors located in 34 commercial buildings, (b) the accuracy of four multi-location CO{sub 2} measurement systems that utilize tubing, valves, and pumps to measure at multiple locations with single CO{sub 2} sensors, and (c) the spatial variability of CO{sub 2} concentrations within meeting rooms. The field studies of the accuracy of single-location CO{sub 2} sensors included multi-concentration calibration checks of 90 sensors in which sensor accuracy was checked at multiple CO{sub 2} concentrations using primary standard calibration gases. From these evaluations, average errors were small, -26 ppm and -9 ppm at 760 and 1010 …

The deployment of the Scanning W-Band ARM Cloud Radar (SWACR) during the AMF campaign at Azores signals the first deployment of an ARM Facility-owned scanning cloud radar and offers a prelude for the type of 3D cloud observations that ARM will have the capability to provide at all the ARM Climate Research Facility sites by the end of 2010. The primary objective of the deployment of Scanning ARM Cloud Radars (SACRs) at the ARM Facility sites is to map continuously (operationally) the 3D structure of clouds and shallow precipitation and to provide 3D microphysical and dynamical retrievals for cloud life cycle and cloud-scale process studies. This is a challenging task, never attempted before, and requires significant research and development efforts in order to understand the radar's capabilities and limitations. At the same time, we need to look beyond the radar meteorology aspects of the challenge and ensure that the hardware and software capabilities of the new systems are utilized for the development of 3D data products that address the scientific needs of the new Atmospheric System Research (ASR) program. The SWACR observations at Azores provide a first look at such observations and the challenges associated with their analysis and interpretation. …

The problem of Network Traffic Classification (NTC) has attracted significant amount of interest in the research community, offering a wide range of solutions at various levels. The core challenge is in addressing high amounts of traffic diversity found in today's networks. The problem becomes more challenging if a quick detection is required as in the case of identifying malicious network behavior or new applications like peer-to-peer traffic that have potential to quickly throttle the network bandwidth or cause significant damage. Recently, Traffic Dispersion Graphs (TDGs) have been introduced as a viable candidate for NTC. The TDGs work by forming a network wide communication graphs that embed characteristic patterns of underlying network applications. However, these patterns need to be quickly evaluated for mounting real-time response against them. This paper addresses these concerns and presents a novel solution for real-time analysis of Traffic Dispersion Metrics (TDMs) in the TDGs. We evaluate the dispersion metrics of interest and present a dedicated solution on an FPGA for their analysis. We also present analytical measures and empirically evaluate operating effectiveness of our design. The mapped design on Virtex-5 device can process 7.4 million packets/second for a TDG comprising of 10k flows at very high accuracies …

Fluid particulate flows are common phenomena in nature and industry. Modeling of such flows at micro and macro levels as well establishing relationships between these approaches are needed to understand properties of the particulate matter. We propose a computational technique based on the direct numerical simulation of the particulate flows. The numerical method is based on the distributed Lagrange multiplier technique following the ideas of Glowinski et al. (1999). Each particle is explicitly resolved on an Eulerian grid as a separate domain, using solid volume fractions. The fluid equations are solved through the entire computational domain, however, Lagrange multiplier constrains are applied inside the particle domain such that the fluid within any volume associated with a solid particle moves as an incompressible rigid body. Mutual forces for the fluid-particle interactions are internal to the system. Particles interact with the fluid via fluid dynamic equations, resulting in implicit fluid-rigid-body coupling relations that produce realistic fluid flow around the particles (i.e., no-slip boundary conditions). The particle-particle interactions are implemented using explicit force-displacement interactions for frictional inelastic particles similar to the DEM method of Cundall et al. (1979) with some modifications using a volume of an overlapping region as an input to the …

3s{sub 1/2} - 3p{sub 3/2} and 3p{sub 1/2} - 3d{sub 3/2} transitions have been studied in potassium-like W{sup 55+} through neon-like W{sup 64}+ ions at the electron-beam ion trap facility in Livermore. The wavelengths of the lines have been measured in high resolution relative to well known reference lines from oxygen and nitrogen ions. Using the high-energy SuperEBIT electron-beam ion trap and an R = 44.3 m grazing-incidence soft x-ray spectrometer, the lines were observed with a cryogenic charge-coupled device camera. The wavelength data for the sodium-like and magnesium-like tungsten lines are compared with theoretical predictions for ions along the isoelectronic sequences.

The speciation and distribution of Cr(VI) in the solid phase was investigated for two types of chromite ore processing residue (COPR) found at two deposition sites in the United States: gray-black (GB) granular and hard brown (HB) cemented COPR. COPR chemistry and mineralogy were investigated using micro-X-ray absorption spectroscopy and micro-X-ray diffraction, complemented by laboratory analyses. GB COPR contained 30percent of its total Cr(VI) (6000 mg/kg) as large crystals(>20 ?m diameter) of a previously unreported Na-rich analog of calcium aluminum chromate hydrates. These Cr(VI)-rich phases are thought to be vulnerable to reductive and pH treatments. More than 50percent of the Cr(VI) was located within nodules, not easily accessible to dissolved reductants, and bound to Fe-rich hydrogarnet, hydrotalcite, and possibly brucite. These phases are stable over a large pH range, thus harder to dissolve. Brownmilleritewasalso likely associated with physical entrapment of Cr(VI) in the interior of nodules. HB COPR contained no Cr(VI)-rich phases; all Cr(VI) was diffuse within the nodules and absent from the cementing matrix, with hydrogarnet and hydrotalcite being the main Cr(VI) binding phases. Treatment ofHBCOPRis challenging in terms of dissolving the acidity-resistant, inaccessible Cr(VI) compounds; the same applies to ~;;50percent of Cr(VI) in GB COPR.

Using X-ray microprobe analysis of samples from comet Wild 2 returned by the Stardust mission, we determine that the crystalline Fe-bearing silicate fraction in this Jupiter-family comet is greater than 0.5. Assuming this mixture is a composite of crystalline inner solar system material and amorphous cold molecular cloud material, we deduce that more than half of Wild 2 has been processed in the inner solar system. Several models exist that explain the presence of crystalline materials in comets. We explore some of these models in light of our results.

The effect of pressure on the crystal structure of white phosphorus has been studied up to 22.4 GPa. The ?alpha phase was found to transform into the alpha' phase at 0.87 +- 0.04 GPa with a volume change of 0.1 +- 0.3 cc/mol. A fit of a second order Birch- Murnaghan equation to the data gave Vo = 16.94 ? 0.08 cc/mol and Ko = 6.7 +- 0.5 GPa for the alpha phase and Vo = 16.4 +- 0.1 cc/mol and Ko = 9.1 +- 0.3 GPa for the alpha' phase. The alpha' phase was found to transform to the A17 phase of black phosphorus at 2.68 +- 0.34 GPa and then with increasing pressure to the A7 and then simple cubic phase of black phosphorus. A fit of a second order Birch-Murnaghan equation to our data combined with previous measurements gave Vo = 11.43 +- 0.05 cc/mol and Ko = 34.7 +- 0.5 GPa for the A17 phase, Vo = 9.62 +- 0.01 cc/mol and Ko = 65.0 +- 0.6 GPa for the A7 phase and , Vo = 9.23 +- 0.01 cc/mol and Ko = 72.5 +- 0.3 GPa for the simple cubic phase.

This report describes the use of thermo luminescent dosimeters for environmental surveillance of external radiation on and around the Hanford Site for the period of 1970 to 2005. It addresses changes in the technology and associated quality control and assurance used in this work and summarizes the results of the 35 year period of external radiation surveillance. The appendices to this report provide trend plots for each location that comprised the shoreline, onsite, perimeter, and offsite sample design.

A recent study concluded that serum prostate specific antigen (PSA)-based screening is beneficial for reducing the lethality of PCa, but was also associated with a high risk of 'overdiagnosis'. Nevertheless, also PCa patients who suffered from organ confined tumors and had negative bone scans succumb to distant metastases after complete tumor resection. It is reasonable to assume that those tumors spread to other organs long before the overt manifestation of metastases. Our current results confirm that prostate tumors are highly heterogeneous. Even a small subpopulation of cells bearing BRCA1 losses can initiate PCa cell regional and distant dissemination indicating those patients which might be at high risk of metastasis. A preliminary study performed on a small cohort of multifocal prostate cancer (PCa) detected BRCA1 allelic imbalances (AI) among circulating tumor cells (CTCs). The present analysis was aimed to elucidate the biological and clinical role of BRCA1 losses on metastatic spread and tumor progression in prostate cancer patients. Experimental Design: To map molecular progression in PCa outgrowth we used FISH analysis of tissue microarrays (TMA), lymph node sections and CTC from peripheral blood. We found that 14% of 133 tested patients carried monoallelic BRCA1 loss in at least one tumor focus. …

The impact of carbon contamination on extreme ultraviolet (EUV) masks is significant due to throughput loss and potential effects on imaging performance. Current carbon contamination research primarily focuses on the lifetime of the multilayer surfaces, determined by reflectivity loss and reduced throughput in EUV exposure tools. However, contamination on patterned EUV masks can cause additional effects on absorbing features and the printed images, as well as impacting the efficiency of cleaning process. In this work, several different techniques were used to determine possible contamination topography. Lithographic simulations were also performed and the results compared with the experimental data.

Final report covering the development, deployment and lessons learning while making the Sophia proof of concept.

The need for renewable fiber reinforced composites has never been as prevalent as it currently is. Natural fibers offer both cost savings and a reduction in density when compared to glass fibers. Though the strength of natural fibers is not as great as glass, the specific properties are comparable. Currently natural fiber composites have two issues that need to be addressed: resin compatibility and water absorption. The following preliminary research has investigated the use of Kenaf, Hibiscus cannabinus, as a possible glass replacement in fiber reinforced composites.

This presentation describes the fuel cell power model for CHP and CHHP economics and performance analysis.

We present Poblano v1.0, a Matlab toolbox for solving gradient-based unconstrained optimization problems. Poblano implements three optimization methods (nonlinear conjugate gradients, limited-memory BFGS, and truncated Newton) that require only first order derivative information. In this paper, we describe the Poblano methods, provide numerous examples on how to use Poblano, and present results of Poblano used in solving problems from a standard test collection of unconstrained optimization problems.

Scientists at the Chemical Dynamics Beamline of the Advanced Light Source in Berkeley are continuously reinventing synchrotron investigations of physical chemistry and chemical physics with vacuum ultraviolet light. One of the unique aspects of a synchrotron for chemical physics research is the widely tunable vacuum ultraviolet light that permits threshold ionization of large molecules with minimal fragmentation. This provides novel opportunities to assess molecular energetics and reaction mechanisms, even beyond simple gas phase molecules. In this perspective, significant new directions utilizing the capabilities at the Chemical Dynamics Beamline are presented, along with an outlook for future synchrotron and free electron laser science in chemical dynamics. Among the established and emerging fields of investigations are cluster and biological molecule spectroscopy and structure, combustion flame chemistry mechanisms, radical kinetics and product isomer dynamics, aerosol heterogeneous chemistry, planetary and interstellar chemistry, and secondary neutral ion-beam desorption imaging of biological matter and materials chemistry.

This report provides a baseline assessment of the current state of energy efficiency-related education and training programs and analyzes training and education needs to support expected growth in the energy efficiency services workforce. In the last year, there has been a significant increase in funding for 'green job' training and workforce development (including energy efficiency), through the American Recovery and Reinvestment Act (ARRA). Key segments of the energy efficiency services sector (EESS) have experienced significant growth during the past several years, and this growth is projected to continue and accelerate over the next decade. In a companion study (Goldman et al. 2009), our research team estimated that the EESS will increase two- to four-fold by 2020, to 220,000 person-years of employment (PYE) (low-growth scenario) or up to 380,000 PYE (high-growth scenario), which may represent as many as 1.3 million individuals. In assessing energy efficiency workforce education and training needs, we focus on energy-efficiency services-related jobs that are required to improve the efficiency of residential and nonresidential buildings. Figure ES-1 shows the market value chain for the EESS, sub-sectors included in this study, as well as the types of market players and specific occupations. Our assessment does not include the manufacturing, …

This project evaluated the air leakage and electric power consumption of Residential HVAC components, with a particular focus on air leakage of furnace cabinets. Laboratory testing of HVAC components indicated that air leakage can be significant and highly variable from unit to unit ? indicating the need for a standard test method and specifying maximum allowable air leakage in California State energy codes. To further this effort, this project provided technical assistance for the development of a national standard for Residential HVAC equipment air leakage. This standard is being developed by ASHRAE and is called"ASHRAE Standard 193P - Method of test for Determining the Air Leakage Rate of HVAC Equipment". The final part of this project evaluated techniques for measurement of furnace blower power consumption. A draft test procedure for power consumption was developed in collaboration with the Canadian General Standards Board: CSA 823"Performance Standard for air handlers in residential space conditioning systems".

Recent experiments on the National Spherical Torus eXperiment (NSTX) have shown the benefits of solid lithium coatings on carbon PFC's to diverted plasma performance, in both Land H- mode confinement regimes. Better particle control, with decreased inductive flux consumption, and increased electron temperature, ion temperature, energy confinement time, and DD neutron rate were observed. Successive increases in lithium coverage resulted in the complete suppression of ELM activity in H-mode discharges. A liquid lithium divertor (LLD), which will employ the porous molybdenum surface developed for the LTX shell, is being installed on NSTX for the 2010 run period, and will provide comparisons between liquid walls in the Lithium Tokamak eXperiment (LTX) and liquid divertor targets in NSTX. LTX, which recently began operations at the Princeton Plasma Physics Laboratory, is the world's first confinement experiment with full liquid metal plasma-facing components (PFCs). All materials and construction techniques in LTX are compatible with liquid lithium. LTX employs an inner, heated, stainless steel-faced liner or shell, which will be lithium-coated. In order to ensure that lithium adheres to the shell, it is designed to operate at up to 500 - 600 oC to promote wetting of the stainless by the lithium, providing the first …

Most interesting materials in nature are heterogeneous, so it is useful to have analytical techniques with spatial resolution sufficient to resolve these heterogeneities.This article presents the basics of X-ray photon-in/photon-out chemical imaging. This family of methods allows one to derive images reflectingthe chemical state of a given element in a complex sample, at micron or deep sub-micron scale. X-ray chemical imaging is relatively non-destructiveand element-selective, and requires minimal sample preparation. The article presents the basic concepts and some considerations of data takingand data analysis, along with some examples.