This is the articles in this month's issue: (1) Close Collaborations Advance Progress in Genomic Research--Commentary by Elbert Branscomb; (2) Mining Genomes--Livermore computer programs help locate the stretches of DNA in gene deserts that regulate protein-making genes; (3) Shedding Light on Quantum Physics--Laboratory laser research builds from the foundation of Einstein's description of the quantization of light. (4) The Sharper Image for Surveillance--Speckle imaging-an image-processing technique used in astronomy is bringing long-distance surveillance into sharper focus. (5) Keeping Cool Close to the Sun--The specially coated gamma-ray spectrometer aboard the MESSENGER spacecraft will help scientists determine the abundance of elements in Mercury's crust.

The Center for Applied Scientific Computing (CASC) and the LLNL Atmospheric Science Division (ASD) are working together to improve predictions of future climate by applying the best available computational methods and computer resources to this problem. Over the last decade, researchers at the Lawrence Livermore National Laboratory (LLNL) have developed a number of climate models that provide state-of-the-art simulations on a wide variety of massively parallel computers. We are now developing and applying a second generation of high-performance climate models. As part of LLNL's participation in DOE's Scientific Discovery through Advanced Computing (SciDAC) program, members of CASC and ASD are collaborating with other DOE labs and NCAR in the development of a comprehensive, next-generation global climate model. This model incorporates the most current physics and numerics and capably exploits the latest massively parallel computers. One of LLNL's roles in this collaboration is the scalable parallelization of NASA's finite-volume atmospheric dynamical core. We have implemented multiple two-dimensional domain decompositions, where the different decompositions are connected by high-speed transposes. Additional performance is obtained through shared memory parallelization constructs and one-sided interprocess communication. The finite-volume dynamical core is particularly important to atmospheric chemistry simulations, where LLNL has a leading role.

This report details the research and findings generated over the course of a 3-year research project funded by Lawrence Livermore National Laboratory (LLNL) Laboratory Directed Research and Development (LDRD). Originally tasked with studying beryllium chemistry and chelation for the treatment of Chronic Beryllium Disease and environmental remediation of beryllium-contaminated environments, this work has yielded results in beryllium and uranium solubility and speciation associated with toxicology; specific and effective chelation agents for beryllium, capable of lowering beryllium tissue burden and increasing urinary excretion in mice, and dissolution of beryllium contamination at LLNL Site 300; {sup 9}Be NMR studies previously unstudied at LLNL; secondary ionization mass spec (SIMS) imaging of beryllium in spleen and lung tissue; beryllium interactions with aerogel/GAC material for environmental cleanup. The results show that chelator development using modern chemical techniques such as chemical thermodynamic modeling, was successful in identifying and utilizing tried and tested beryllium chelators for use in medical and environmental scenarios. Additionally, a study of uranium speciation in simulated biological fluids identified uranium species present in urine, gastric juice, pancreatic fluid, airway surface fluid, simulated lung fluid, bile, saliva, plasma, interstitial fluid and intracellular fluid.

We have recently completed a large-area, coded-aperture, gamma-ray imager for use in searching for radiation sources. The instrument was constructed to verify that weak point sources can be detected at considerable distances if one uses imaging to overcome fluctuations in the natural background. The instrument uses a rank-19, one-dimensional coded aperture to cast shadow patterns onto a 0.57 m{sup 2} NaI(Tl) detector composed of 57 individual cubes each 10 cm on a side. These are arranged in a 19 x 3 array. The mask is composed of four-centimeter thick, one-meter high, 10-cm wide lead blocks. The instrument is mounted in the back of a small truck from which images are obtained as one drives through a region.

We have demonstrated the feasibility of fabricating pure-metal foams via a novel four-step technique based upon ion beam lithography. In this report we discuss why and how such foams are useful as bright, high-photon-energy x-ray sources; the details of the fabrication technique we employed to make such foams; the results obtained; and what we plan to do in the future to improve the technique and turn the foams so fabricated into real laser targets for high-brightness, high-energy back lighting.

The Bulk Vitrification System is being pursued to assist in immobilizing the low-activity tank waste from the 53 million gallons of radioactive waste in the 177 underground storage tanks on the Hanford Site. To demonstrate the effectiveness of the bulk vitrification process, a research and development facility known as the Demonstration Bulk Vitrification System (DBVS) is being built to demonstrate the technology. Specific performance requirements for the final packaged bulk vitrification waste form have been identified. In addition to the specific product-performance requirements, performance targets/goals have been identified that are necessary to qualify the waste form but do not lend themselves to specifications that are easily verified through short-term testing. Collectively, these form the product requirements for the DBVS. This waste-form qualification (WFQ) strategy document outlines the general strategies for achieving and demonstrating compliance with the BVS product requirements. The specific objectives of the WFQ activities are discussed, the bulk vitrification process and product control strategy is outlined, and the test strategy to meet the WFQ objectives is described. The DBVS product performance targets/goals and strategies to address those targets/goals are described. The DBVS product-performance requirements are compared to the Waste Treatment and Immobilization Plant immobilized low-activity waste product specifications. …

CH2M HILL is producing risk/performance assessments to support the closure of single-shell tanks at the DOE's Hanford Site. As part of this effort, staff at PNNL were asked to develop release models for contaminants of concern that are present in residual sludge remaining in tank 241-C-106 (C-106) after final retrieval of waste from the tank. This report provides the information developed by PNNL.

In FY 2004, monitoring of the prototype Hanford barrier focused on barrier stability, vegetative cover, evidence of plant and animal intrusion, and the main components of the water balance. Monitored water-balance components included precipitation, runoff, storage, drainage, and deep percolation. Precipitation in FY 2004 was 26 percent less than in FY 2003 but was still higher than normal. The seasonal distribution in precipitation was also different from the previous year with a 43 percent reduction in spring precipitation and a 46 percent increase in summer precipitation. The cumulative amount of water received from October 1994, through September 2004, was 2,559.58 mm on the northern half of the barrier, which is the formerly irrigated treatment, and 1,886.71 mm on the southern non-irrigated treatments. Water storage continued to show a cyclic pattern, increasing in the winter and declining in the spring and summer to a lower limit of about 100 mm in response to evapotranspiration. The 600-mm design storage has never been exceeded. Total drainage from the soil-covered plots range from 2.9E-4 mm to 0.22 mm or 0.003 6 0.004 percent of precipitation. Side-slope drainage was much higher at 20.9 6 2.3 percent of precipitation from the gravel and 18.6 6 5.1 …

The purpose of this memo is to give an update on our work on ceramic laser materials--feasibility proposal 04-FS-006. Transparent ceramic materials have several major advantages over single crystals in laser applications including, ease and robustness of manufacturing, large apertures, design flexibility, fracture toughness, high activator concentrations, uniformity of composition, no residual stress, and others discussed in the proposal. After a decade of working on making transparent YAG:Nd in 1995 Japanese workers demonstrated samples for the first time that performed as well in lasers as their single crystal counterparts. Since then several laser materials have been made and evaluated. For these reasons, developing ceramic laser materials is the most exciting and futuristic materials topic in today's major solid-state laser conferences. The highlights and executive summary of our work to date are: (1) Ordered a slab of transparent YAG:Nd from Konoshima Chemical Co. for evaluation in the SSHCL. Konoshima is the only company in the world currently making ceramic laser materials for sale. Our slab, the largest one made to date, will arrive within a week and will be evaluated in the SSHCL. (2) Met with the inventor of the Konoshima laser ceramic, Dr. Takagimi Yanagitani, and discussed synthesis and performance …

The Performance Demonstration Program (PDP) for Nondestructive Assay (NDA) is a test program designed to yield data on measurement system capability to characterize drummed transuranic (TRU) waste generated throughout the Department of Energy (DOE) complex. The tests are conducted periodically and provide a mechanism for the independent and objective assessment of NDA system performance and capability relative to the radiological characterization objectives and criteria of the Office of Characterization and Transportation (OCT). The primary documents requiring an NDA PDP are the Waste Acceptance Criteria for the Waste Isolation Pilot Plant (WAC), which requires annual characterization facility participation in the PDP, and the Quality Assurance Program Document (QAPD). This NDA PDP implements the general requirements of the QAPD and applicable requirements of the WAC. Measurement facilities must demonstrate acceptable radiological characterization performance through measurement of test samples comprised of pre-specified PDP matrix drum/radioactive source configurations. Measurement facilities are required to analyze the NDA PDP drum samples using the same procedures approved and implemented for routine operational waste characterization activities. The test samples provide an independent means to assess NDA measurement system performance and compliance per criteria delineated in the NDA PDP Plan. General inter-comparison of NDA measurement system performance among DOE …

The purpose of this report is to provide information needed by the DOE to assess WIPP's environmental performance and to convey that performance to stakeholders and members of the public. This report has been prepared in accordance with DOE Order 231.1A and DOE guidance. This report documents WIPP's environmental monitoring programs and their results for 2003. The WIPP Project is authorized by the DOE National Security and Military Applications of Nuclear Energy Authorization Act of 1980 (Pub. L. 96-164). After more than 20 years of scientific study and public input, WIPP received its first shipment of waste on March 26, 1999. Located in southeastern New Mexico, WIPP is the nation's first underground repository permitted to safely and permanently dispose of TRU radioactive and mixed waste (as defined in the WIPP LWA) generated through the research and production of nuclear weapons and other activities related to the national defense of the United States. TRU waste is defined in the WIPP LWA as radioactive waste containing more than 100 nanocuries (3,700 becquerels [Bq]) of alpha-emitting transuranic isotopes per gram of waste, with half-lives greater than 20 years. Exceptions are noted as high-level waste, waste that has been determined not to require the …

A Joint Interagency Working Group (JIWG) under the auspices of the Department of Homeland Security Office of Research and Development conducted a technology assessment of emergency radiological dose assessment capabilities as part of the overall need for rapid emergency medical response in the event of a radiological terrorist event in the United States. The goal of the evaluation is to identify gaps and recommend general research and development needs to better prepare the Country for mitigating the effects of such an event. Given the capabilities and roles for responding to a radiological event extend across many agencies, a consensus of gaps and suggested development plans was a major goal of this evaluation and road-mapping effort. The working group consisted of experts representing the Departments of Homeland Security, Health and Human Services (Centers for Disease Control and the National Institutes of Health), Food and Drug Administration, Department of Defense and the Department of Energy's National Laboratories (see appendix A for participants). The specific goals of this Technology Assessment and Roadmap were to: (1) Describe the general context for deployment of emergency radiation dose assessment tools following terrorist use of a radiological or nuclear device; (2) Assess current and emerging dose assessment …

The purpose of this Workshop on ''Functional Requirements for the Modeling of Fate and Transport of Waterborne CBRN Materials'' was to solicit functional requirements for tools that help Incident Managers plan for and deal with the consequences of industrial or terrorist releases of materials into the nation's waterways and public water utilities. Twenty representatives attended and several made presentations. Several hours of discussions elicited a set of requirements. These requirements were summarized in a form for the attendees to vote on their highest priority requirements. These votes were used to determine the prioritized requirements that are reported in this paper and can be used to direct future developments.

Experimental measurements suggest that pentaerythritoltetranitrate (PETN) undergoes changes at the molecular level that cause macroscopic changes in the overall PETN powder characteristics over time. These changes have been attributed to the high molecular mobility of PETN, but the underlying mechanism(s) responsible for this redistribution are still uncertain. Two basic approaches have been implemented in the past year to provide insight into the nature of these underlying mechanisms. The first approach is of an experimental nature, utilizing both AFM and evaporation measurements, which address both surface mobility and evaporation. These data include AFM measurements performed at LLNL and evaporation rate measurements performed at Texas Tech. These results are compared to earlier vapor pressure measurements performed at SNL, and estimates of recrystallization time frames are given. The second approach utilizes first-principle calculations and simulations that will be used to compare directly to those experimental quantities measured. We are developing an accurate intermolecular potential for PETN, which via kinetic Monte Carlo (KMC) simulations would mimic real crystallite shapes. Once the basic theory is in place for the growth of single crystallites, we will be in a position to investigate realistic grain coarsening phenomena in multi-crystallite simulations. This will also enable us to study …

We have identified and developed new classes of quasi-axially symmetric configurations which have attractive properties from the standpoint of both near-term physics experiments and long-term power producing reactors. These new configurations were developed as a result of surveying the aspect ratio-rotational transform space to identify regions endowed with particularly interesting features. These include configurations with very small aspect ratios ({approx}2.5) having superior quasi-symmetry and energetic particle confinement characteristics, and configurations with strongly negative global magnetic shear from externally supplied rotational transforms so that the overall rotational transform, when combined with the transform from bootstrap currents at finite plasma pressures, will yield a small but positive shear, making the avoidance of low order rational surfaces at a given operating beta possible. Additionally, we have found configurations with NCSX-like characteristics but with the biased components in the magnetic spectrum that allow us to improve the confinement of energetic particles. For each new class of configurations, we have designed coils as well to ensure that the new configurations are realizable and engineering-wise feasible. The coil designs typically have coil aspect ratios R/{Delta}{sub min}(C-P) {le} 6 and coil separation ratios R/{Delta}{sub min}(C-C) {le} 10, where R is the plasma major radius, {Delta}{sub min}(C-P) and …

An approximate integral of the Manley-Rowe type is found for a particle moving in a high-frequency field, which may interact resonantly with natural particle oscillations. An effective ponderomotive potential is introduced accordingly and can capture nonadiabatic particle dynamics. We show that nonadiabatic ponderomotive barriers can trap classical particles, produce cooling effect, and generate one-way walls for resonant species. Possible atomic applications are also envisioned.

Gelled polymer treatments are applied to oil reservoirs to increase oil production and to reduce water production by altering the fluid movement within the reservoir. This report describes the results of the third year of a 42 month research program that is aimed at an understanding of gelation chemistry and the fundamental mechanisms that alter the flows of oil and water in reservoir rocks after a gel treatment. Work focused on a widely applied system in the field, the partially hydrolyzed polyacrylamide-chromium acetate gel. Gelation occurs by network formation through the crosslinking of polyacrylamide molecules as a result of reaction with chromium acetate. Pre-gel aggregates form and grow as reactions between chromium acetate and polyacrylamide proceed. A mathematical model that describes uptake and crosslinking reactions as a function of time was derived. The model was probability based and provides molecular-weight averages and molecular-weight distributions of the pre-gel aggregates as a function of time and initial system conditions. A liquid chromatography apparatus to experimentally measure the size and molecular weight distributions of polymer samples was developed. The method worked well for polymer samples without the chromium crosslinker. Sample retention observed during measurements of gelant samples during the gelation process compromised the …

The JWL is a standard equation of state used worldwide to describe the pressure-volume-energy behavior of a detonating explosive. Even so, not many people are very good at working with it. So I list all the various equations that describe how it works, then give one way that the solution can be obtained in an iterative manner. I have collaborated with Sedat Esen for several years. I am indebted to him for supplying almost all of our collection of dynamite data. He now works with ammonium nitrate/fuel oil, which is another area of interest to us.

This report describes Phase II of a project conducted for the Mechanical Utilities Division (UTel), Energy Management Program at Lawrence Livermore National Laboratory (LLNL) by Architectural Energy Corporation (AEC). The overall project covers energy efficiency and water conservation auditing services for 215 modular and prefabricated buildings at LLNL. The primary goal of this project is to demonstrate compliance with DOE Order 430.2A, Contractor Requirements Document section 2.d (2) Document, to demonstrate annual progress of at least 10 percent toward completing energy and water audits of all facilities. Although this project covers numerous buildings, they are all similar in design and use. The approach employed for completing audits for these facilities involves a ''model-similar building'' approach. In the model-similar building approach, similarities between groups of buildings are established and quantified. A model (or test case) building is selected and analyzed for each model-similar group using a detailed DOE-2 simulation. The results are extended to the group of similar buildings based on careful application of quantified similarities, or ''extension measures''. This approach leverages the relatively minor effort required to evaluate one building in some detail to a much larger population of similar buildings. The facility wide energy savings potential was calculated for …

During the RHIC run-4 polarized proton operation, the intensity and polarization profiles were measured by scanning the Coulomb-nuclear interference (CNI) polarimeter targets across the beam. The scans reported here were all performed on flattop at beam momenta {approx}100 GeV/c, and all but one was a vertical scan, since several of the vertical polarimeter targets had broken by the time of the measurements. This note summarizes some analyses of these profiles. Wall current monitor data are compared to these results for one beam and fill.

Large-scale scientific computation and all of the disciplines that support and help to validate it have been placed at the focus of Lawrence Livermore National Laboratory (LLNL) by the Advanced Simulation and Computing (ASC) program of the National Nuclear Security Administration (NNSA) and the Scientific Discovery through Advanced Computing (SciDAC) initiative of the Office of Science of the Department of Energy (DOE). The maturation of computational simulation as a tool of scientific and engineering research is underscored in the November 2004 statement of the Secretary of Energy that, ''high performance computing is the backbone of the nation's science and technology enterprise''. LLNL operates several of the world's most powerful computers--including today's single most powerful--and has undertaken some of the largest and most compute-intensive simulations ever performed. Ultrascale simulation has been identified as one of the highest priorities in DOE's facilities planning for the next two decades. However, computers at architectural extremes are notoriously difficult to use efficiently. Furthermore, each successful terascale simulation only points out the need for much better ways of interacting with the resulting avalanche of data. Advances in scientific computing research have, therefore, never been more vital to LLNL's core missions than at present. Computational science is …

This report documents the work performed during the first phase of the National Aeronautics and Space Administration (NASA), National Research Announcement (NRA) Technology Development Program for an Advanced Potassium Rankine Power Conversion System Compatible with Several Space Reactor Designs. The document includes an optimization of both 100-kW{sub e} and 250-kW{sub e} (at the propulsion unit) Rankine cycle power conversion systems. In order to perform the mass optimization of these systems, several parametric evaluations of different design options were investigated. These options included feed and reheat, vapor superheat levels entering the turbine, three different material types, and multiple heat rejection system designs. The overall masses of these Nb-1%Zr systems are approximately 3100 kg and 6300 kg for the 100- kW{sub e} and 250-kW{sub e} systems, respectively, each with two totally redundant power conversion units, including the mass of the single reactor and shield. Initial conceptual designs for each of the components were developed in order to estimate component masses. In addition, an overall system concept was presented that was designed to fit within the launch envelope of a heavy lift vehicle. A technology development plan is presented in the report that describes the major efforts that are required to reach a …

Photon-photon interactions have been an important probe into fundamental particle physics. Until recently, the only way to produce photon-photon collisions was parasitically in the collision of charged particles. Recent advances in short-pulse laser technology have made it possible to consider producing high intensity, tightly focused beams of real photons through Compton scattering. A linear e{sup +}e{sup -} collider could thus be transformed into a photon-photon collider with the addition of high power lasers. In this paper they show that it is possible to make a competitive photon-photon collider experiment using the currently mothballed Stanford Linear Collider. This would produce photon-photon collisions in the GeV energy range which would allow the discovery and study of exotic heavy mesons with spin states of zero and two.

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