The goal of this project was the development of a family of wireless, single-chip, luminescence-sensing devices to solve a number of difficult distributed measurement problems in areas ranging from environmental monitoring and assessment to high-throughput screening of combinatorial chemistry libraries. These wireless luminescence integrated sensors (WLIS) consist of a microluminometer, wireless data transmitter, and RF power input circuit all realized in a standard integrated circuit (IC) process with genetically engineered, whole-cell, bioluminescent bioreporters encapsulated and deposited on the IC. The end product is a family of compact, low-power, rugged, low-cost sensors. As part of this program they developed an integrated photodiode/signal-processing scheme with an rms noise level of 175 electrons/second for a 13-minute integration time, and a quantum efficiency of 66% at the 490-nm bioluminescent wavelength. this performance provided a detection limit of < 1000 photons/second. Although sol-gel has previously been used to encapsulate yeast cells, the reaction conditions necessary for polymerization (primarily low pH) have beforehand proven too harsh for bacterial cell immobilizations. Utilizing sonication methods, they have were able to initiate polymerization under pH conditions conductive to cell survival. both a toluene bioreporter (Pseudomonas putida TVA8) and a naphthalene bioreporter (Pseudomonas fluorescens HK44) were successfully encapsulated in sol-gel …

This paper presents a series of modeling investigations to characterize percolation patterns in the unsaturated zone of Yucca Mountain, Nevada, a proposed underground repository site for storing high-level radioactive waste. The investigations are conducted using a modeling approach that integrates a wide variety of moisture, pneumatic, thermal, and isotopic geochemical field data into a comprehensive three-dimensional numerical model through model calibration. This integrated modeling approach, based on a dual-continuum formulation, takes into account the coupled processes of fluid and heat flow and chemical isotopic transport in Yucca Mountain's highly heterogeneous, unsaturated fractured tuffs. In particular, the model results are examined against different types of field-measured data and used to evaluate different hydrogeological conceptual models and their effects on flow patterns in the unsaturated zone. The objective of this work to provide understanding of percolation patterns and flow behavior through the unsaturated zone, which is a crucial issue in assessing repository performance.

This paper presents a methodology designed to measure synergy among energy-efficiency programs at the program participant level (e.g., households, firms). Three different definitions of synergy are provided: strong, moderate, and weak. Data to measure synergy can be collected through simple survey questions. Straightforward mathematical techniques can be used to estimate the three types of synergy and explore relative synergistic impacts of different subsets of programs. Empirical research is needed to test the concepts and methods and to establish quantitative expectations about synergistic relationships among programs. The market for new energy-efficient motors is the context used to illustrate all the concepts and methods in this paper.

This closure report documents the closure activities conducted for Corrective Action Unit 523: Housekeeping Waste, Nevada Test Site, Nevada.

Building designers and owners have always been fascinated with the extensive use of glass in building envelopes. Today the highly glazed facade has almost become an iconic element for a 'green building' that provides daylighting and a visual connection with the natural environment. Even before the current interest in green buildings there was no shortage of highly glazed building designs. But many of these buildings either rejected sunlight, and some associated daylight and view with highly reflective glazings or used highly transmissive glass and encountered serious internal comfort problems that could only be overcome with large HVAC systems, resulting in significant energy, cost and environmental penalties. From the 1960's to the 1990's innovation in glazing made heat absorbing glass, reflective glass and double glazing commonplace, with an associated set of aesthetic features. In the last decade there has been a subtle shift from trying to optimize an ideal, static design solution using these glazings to making the facade responsive, interactive and even intelligent. More sophisticated design approaches and technologies have emerged using new high-performance glazing, improved shading and solar control systems, greater use of automated controls, and integration with other building systems. One relatively new architectural development is the double …

Fast intermittent transport has been observed in the scrape-off layer (SOL) of major tokamaks including Alcator C-Mod, DIII-D, and NSTX. This kind of transport is not diffusive but rather convective. It strongly increases plasma flux to the chamber walls and enhances the recycling of neutral particles in the main chamber. We discuss anomalous cross-field convection (ACFC) model for impurity and main plasma ions and its relation to intermittent transport events, i.e. plasma density blobs and holes in the SOL. Along with plasma diffusivity coefficients, our transport model introduces time-independent anomalous cross-field convective velocity. In the discharge modelling, diffusivity coefficients and ACFC velocity profiles are adjusted to match a set of representative experimental data. We use this model in the edge plasma physics code UEDGE to simulate the multi-fluid two-dimensional transport for these three tokamaks. We present simulation results suggesting the dominance of anomalous convection in the far SOL transport. These results are consistent with the hypothesis that the chamber wall is an important source of impurities and that different impurity charge states have different directions of anomalous convective velocity.

The first three years of RHIC physics, with Au/Au collisions induced at 65, 130 and 200 GeV per nucleon pair, produced dramatic results, particularly with respect to collective observables such as transverse flow and anisotropies in transverse momentum spectra. It has become clear that the data show very strong rescattering at very early times of the reaction, strong enough in fact to be described by the hydrodynamic limit. Therefore, with today's experiments, we are able to investigate the equation of state of hot quark gluon matter, discuss its thermodynamic properties and relate them to experimental observables. At this workshop we came together to discuss our latest efforts both in the theoretical description of heavy ion collisions as well as most recent experimental results that ultimately allow us to extract information on the properties of RHIC matter. About 50 participants registered for the workshop, but many more dropped in from the offices at BNL. The workshop lasted for three days, of which each day was assigned a special topic on which the talks focused. On the first day we dealt with the more general question what the strong collective phenomena observed in RHIC collisions tell us about the properties and the …

The authors have used a study of the process e{sup +}e{sup -} {yields} {mu}{sup +}{mu}{sup -} {gamma} at a center-of-mass energy near the {Upsilon}(4S) resonance for a {mu}{sup +}{mu}{sup -} invariant mass range near the J/{psi} mass to extract the cross section {sigma}(e{sup +}e{sup -} {yields} J/{psi}{gamma} {yields} {mu}{sup +}{mu}{sup -}{gamma}). The data set, corresponding to an integrated luminosity of 88.4 fb{sup -1}, was collected using the BABAR detector at the PEP-II collider. They measure the product {Lambda}(J/{psi} {yields} e{sup +}e{sup -}) B(J/{psi} {yields} {mu}{sup +}{mu}{sup -}) to be 0.330 {+-} 0.008 {+-} 0.007 keV. Using the world averages for B(J/{psi} {yields} {mu}{sup +}{mu}{sup -}) and B(J/{psi} {yields} e{sup +}e{sup -}), they derive the J/{psi} electronic and total widths: {Lambda}(J/{psi} {yields} e{sup +}e{sup -}) = 5.61 {+-} 0.20 keV and {Lambda} = 94.7 {+-} 4.4 keV.

Based on annual tritium release rates from the five sources of tritium at Lawrence Livermore National Laboratory and the Tritium Research Laboratory at Sandia National Laboratory, the regulatory dispersion and dose model, CAP88-PC, was used to predict tritium concentrations in air at perimeter and offsite air surveillance monitoring locations for 1986 through 2001. These predictions were compared with mean annual measured concentrations, based on biweekly sampling. Deterministic predictions were compared with deterministic observations using predicted-to-observed ratios. In addition, the uncertainty on observations and predictions was assessed: when the uncertainty bounds of the observations overlapped with the uncertainty bounds of the predictions, the predictions were assumed to agree with the observations with high probability. Deterministically, 54% of all predictions were higher than the observations, and 96% fell within a factor of three. Accounting for uncertainty, 75% of all predictions agreed with the observations; 87% of the predictions either matched or exceeded the observations. Predictions equaled or exceeded observations at those sampling locations towards which the wind blows most frequently, except those in the hills. Under-predictions were seen at locations towards which the wind blows infrequently when released tritium was from elevated sources. When a high fraction of tritium was from area …

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The STK Bladestore is a disk subsystem consisting of ATA disks, fiber channel connectivity, and a RAID controller (LSI manufactured). There are essentially four host connections and four backend fiber connections. The host side ports are 2Gb/sec and with their advertised 400MB/sec bandwidth, the disk side ports are 1GB/sec. Our goal is to test this flavor of disk to see what the real world performance might be.

One of the major motivations driving recent interest in FFAGs is their use for the cost-effective acceleration of muons. This paper summarizes the progress in this area that was achieved leading up to and at the FFAG workshop at KEK from July 7-12, 2003. Much of the relevant background and references are also given here, to give a context to the progress we have made.

Thirty five years ago, while in the neutron cross section group led by Robert Howerton at LLNL, the concept of reconstructing a three dimensional spatial distribution from its projections onto two dimensional planes was tackled by some of us using three now well known methods: simple back projection, Fourier projection theorem methods and iterative least squares algebraic reconstruction. The method of iterative least squares reconstruction was implemented on patient data in the early 1970s using photons from radionuclides detected by the Anger Camera. The method useful for computed tomography was modified to include the attenuation of the photons from an unknown source through an unknown attenuation distribution (a problem thought to be intractable until 1974). These methods along with a multitude of other methods developed by my small group of Ronald Huesman, Grant Gullberg, William Greenberg and Stephen Derenzo were prepared as a library with examples in FORTRAN, RECLBL. Those codes were found useful for computed tomography, geophysical problems and plasma confinement research topics in addition to their use in Nuclear Medicine. The codes were used even in the early days of magnetic resonance imaging when back projection of filtered projection data were used before the incorporation of phase encoding …

Radiative corrections to the decay rate of n = 2 states of hydrogenic ions are calculated. The transitions considered are the M1 decay of the 2s state to the ground state and the E1(M2) decays of the 2p{sub 1/2} and 2p{sub 3/2} states to the ground state. The radiative corrections start in order {alpha}(Z{alpha}){sup 2}, but the method used sums all orders of Z{alpha}. The leading {alpha}(Z{alpha}){sup 2} correction for the E1 decays is calculated and compared with the exact result. The extension of the calculational method to parity nonconserving transitions in neutral atoms is discussed.

Complex networks appear in biology on many different levels: (1) All biochemical reactions taking place in a single cell constitute its metabolic network, where nodes are individual metabolites, and edges are metabolic reactions converting them to each other. (2) Virtually every one of these reactions is catalyzed by an enzyme and the specificity of this catalytic function is ensured by the key and lock principle of its physical interaction with the substrate. Often the functional enzyme is formed by several mutually interacting proteins. Thus the structure of the metabolic network is shaped by the network of physical interactions of cell's proteins with their substrates and each other. (3) The abundance and the level of activity of each of the proteins in the physical interaction network in turn is controlled by the regulatory network of the cell. Such regulatory network includes all of the multiple mechanisms in which proteins in the cell control each other including transcriptional and translational regulation, regulation of mRNA editing and its transport out of the nucleus, specific targeting of individual proteins for degradation, modification of their activity e.g. by phosphorylation/dephosphorylation or allosteric regulation, etc. To get some idea about the complexity and interconnectedness of protein-protein regulations …

The DOE tasked PNNL to investigate possible technological avenues for substantially advancing the state-of-the-art in gamma detection via large-area plastic scintillators. This report describes progress on this project as of the conclusion of FY 2003. The primary focus of the report is on experimental tests conducted with a single large-area plastic scintillator outfitted with a variety of photomultiplier tube configurations. Measurements performed to date incude scintillator response under broad-area exposure to various point-like gamma sources, and light-output uniformity mappings obtained by varying the position of a collimated beta-source over the surface of the scintillator. Development of a Monte Carlo program for modeling the response of a large-area scintillator sensor to ionizing radiation, explicitly including resolution-broadening effects of scintillation light generation, propagation, and collection is also described.

CDIC will provide state-of-the-art computational and computer science for the Laboratory and for the broader DOE and scientific community. We achieve this goal by performing advanced scientific computing research in the Laboratory's mission areas of High Energy and Nuclear Physics, Biological and Environmental Research, and Basic Energy Sciences. We also assist other groups at the Laboratory to reach new levels of achievement in computing. We are ''data intensive'' because the production and manipulation of large quantities of data are hallmarks of scientific research in the 21st century and are intrinsic features of major programs at Brookhaven. An integral part of our activity to accomplish this mission will be a close collaboration with the University at Stony Brook.

This ICN corrects a typing error that was identified for one of the wells listed in Tables 4.1 and 4.2 on page 4.3 of the original document.

This report documents research that was done during a ten week internship in the Sapphire research group at the Lawrence Livermore National Laboratory during the Summer of 2003. The goal of the study was to develop an algorithm that is capable of isolating (segmenting) moving objects in low resolution video sequences. This capability is currently being developed by the Sapphire research group as the first stage in a longer term video data mining project. This report gives a chronological account of what ideas were tried in developing the algorithm and what was learned from each attempt. The final version of the algorithm, which is described in detail, gives good results and is fast.

Paleorecords from Minnesota and adjacent areas have often been used to evaluate large-scale climatic processes in the mid-continent of North America. However, most of these records are compromised by chronological flaws, making problematic any comparisons with climatic interpretations based on other records (e.g., GISP2 in Greenland). We report here a high-resolution pollen record with a secure chronology constrained by 26 {sup 14}C dates on terrestrial macrofossils from Steel Lake, central Minnesota. About 11,200 years ago (calibrated yr BP) the late-glacial Picea forest near Steel Lake was succeeded abruptly by Pinus banksiana and/or resinosa. The Pinus forest began to open 9.4 ka cal BP with the expansion of prairie taxa, and a pine parkland or savanna prevailed until about 8 ka cal BP, when Quercus replaced Pinus to become the dominant tree in the prairie areas for 4500 years. The close chronological control permits the correlation of key vegetational changes with those at other reliably dated sites in the eastern Dakotas and in Minnesota, suggesting that the abrupt decline of the spruce forest was time-transgressive from southwest to northeast during 2000 years, and that the development of prairie was time-transgressive in the same direction over 2600 years. Correlation of key pollen …

Quarterly magazine with articles on recent additions to the Clean Cities Alternative Fuel Station Locator database, biodiesel buying co-ops, and developing the CNG infrastructure in Bangladesh. Also a memo from CIVITAS 2003.

A numerical study is undertaken comparing a fifth-order version of the weighted essentially non-oscillatory numerical (WENO5) method to a modern piecewise-linear, second-order, version of Godunov's (PLMDE) method for the compressible Euler Equations. A series of one-dimensional test problems are examined beginning with classical linear problems and ending with complex shock interactions. The problems considered are: (1) linear advection of a Gaussian pulse in density, (2) Sod's shock tube problem, (3) the ''peak'' shock tube problem, (4) a version of the Shu and Osher shock entropy wave interaction and (5) the Woodward and Colella interacting shock wave problem. For each problem and method, run times, density error norms and convergence rates are reported for each method as produced from a common code test-bed. The linear problem exhibits the advertised convergence rate for both methods as well as the expected large disparity in overall error levels; WENO5 has the smaller errors and an enormous advantage in overall efficiency (in accuracy per unit CPU time). For the nonlinear problems with discontinuities, however, we generally see both first-order self-convergence of error as compared to an exact solution, or when an analytic solution is not available, a converged solution generated on an extremely fine grid. …

Technology for a photon collider experiment at a future TeV-scale linear collider has been under development for many years. The laser and optics technology has reached the point where a GeV-scale photon collider experiment is now feasible. We report on the photon-photon luminosities that would be achievable at a photon collider experiment based on a refurbished Stanford Linear Collider.

Over 520 different amino acid substitution variants have been previously identified in the systematic screening of 91 human DNA repair genes for sequence variation. Two algorithms were employed to predict the impact of these amino acid substitutions on protein activity. Sorting Intolerant From Tolerant (SIFT) classified 226 of 508 variants (44%) as ''Intolerant''. Polymorphism Phenotyping (PolyPhen) classed 165 of 489 amino acid substitutions (34%) as ''Probably or Possibly Damaging''. Another 9-15% of the variants were classed as ''Potentially Intolerant or Damaging''. The results from the two algorithms are highly associated, with concordance in predicted impact observed for {approx}62% of the variants. Twenty one to thirty one percent of the variant proteins are predicted to exhibit reduced activity by both algorithms. These variants occur at slightly lower individual allele frequency than do the variants classified as ''Tolerant'' or ''Benign''. Both algorithms correctly predicted the impact of 26 functionally characterized amino acid substitutions in the APE1 protein on biochemical activity, with one exception. It is concluded that a substantial fraction of the missense variants observed in the general human population are functionally relevant. These variants are expected to be the molecular genetic and biochemical basis for the associations of reduced DNA repair …