The goal of this Strategic Initiative LDRD project was to establish at LLNL a new core capability in computational biology, combining laboratory strengths in high performance computing, molecular biology, and computational chemistry and physics. As described in this report, this project has been very successful in achieving this goal. This success is demonstrated by the large number of referred publications, invited talks, and follow-on research grants that have resulted from this project. Additionally, this project has helped build connections to internal and external collaborators and funding agencies that will be critical to the long-term vitality of LLNL programs in computational biology. Most importantly, this project has helped establish on-going research groups in the Biology and Biotechnology Research Program, the Physics and Applied Technology Directorate, and the Computation Directorate. These groups include three laboratory staff members originally hired as post-doctoral researchers for this strategic initiative.

In this note, we describe the first of two updates to the uranium isotopes in Livermore's Evaluated Neutron Data Library, ENDL99. Here, we concentrate on improving the (n, f) and (n, {gamma}) evaluations for a limited set of uranium isotopes. The first improvement consisted of creating an evaluation for {sup 232}U using a combination of fission and capture cross sections from the JENDL-3.2 database and the outgoing particle distributions from the exiting ENDL99 {sup 234}U evaluation. The second improvement consisted of updating existing (n, f) and (n, {gamma}) evaluations for uranium isotopes with A=233-238. These improvements are particularly apparent in the neutron resonance region as ENDL99 often contains gross averages over the resonances. We have propagated these updates into various Livermore application libraries.

Homogeneous charge compression ignition (HCCI) engines are being considered as an alternative to diesel engines. The HCCI concept involves premixing fuel and air prior to induction into the cylinder (as is done in current spark-ignition engine) then igniting the fuel-air mixture through the compression process (as is done in current diesel engines). The combustion occurring in an HCCI engine is fundamentally different from a spark-ignition or Diesel engine in that the heat release occurs as a global autoignition process, as opposed to the turbulent flame propagation or mixing controlled combustion used in current engines. The advantage of this global autoignition is that the temperatures within the cylinder are uniformly low, yielding very low emissions of oxides of nitrogen (NO{sub x}, the chief precursors to photochemical smog). The inherent features of HCCI combustion allows for design of engines with efficiency comparable to, or potentially higher than, diesel engines. While HCCI engines have great potential, several technical barriers exist which currently prevent widespread commercialization of this technology. The most significant challenge is that the combustion timing cannot be controlled by typical in-cylinder means. Means of controlling combustion have been demonstrated, but a robust control methodology that is applicable to the entire range …

This ICN updates the assessment plan to reflect the addition of wells newly installed in FY2001. Project scientists will provide a schedule change request identifying the wells as new and providing a list of constituents and sample frequencies to the sample scheduler.

All planned National Ignition Facility (NIF) capsule targets except machined beryllium require a plastic mandrel upon which the ablator is applied. This mandrel must at least meet if not exceed the symmetry and surface finish requirements of the final capsule. The mandrels are produced by a two-step process. In the first step a thin-walled poly({alpha}-methylstyrene)(P{alpha}MS) shell is produced using microencapsulation techniques. This shell is overcoated with 10 to 15 {micro}m of glow discharge polymer (GDP) and then pyrolyzed at 300 C. This pyrolysis causes the P{alpha}MS to depolymerize to gas phase monomer that diffuses away through the more thermally stable plasma polymer shell, which retains all the symmetry of the original P{alpha}MS shell. Thus our challenge has been to produce 2-mm-diameter P{alpha}MS shells to serve as these initial ''decomposable'' mandrels that meet or exceed the current NIF design specifications. The basic microencapsulation process used in producing P{alpha}MS mandrels involves using a droplet generator to produce a water droplet (Wl) encapsulated by a fluorobenzene solution of P{alpha}MS (O), this compound droplet being suspended in a stirred aqueous bath (W2). Historically this bath has contained poly(vinyl alcohol) (PVA, 88% hydrolyzed, mol. wt. {approx}25,000 g/mol) to prevent agglomeration of the initially fluid compound …

A program to identify and eliminate the causes of UV laser-induced damage and growth in fused silica and DKDP has developed methods to extend optics lifetimes for large-aperture, high-peak-power, UV lasers such as the National Ignition Facility (NIF). Issues included polish-related surface damage initiation and growth on fused silica and DKDP, bulk inclusions in fused silica, pinpoint bulk damage in DKDP, and UV-induced surface degradation in fused silica and DKDP in a vacuum. Approaches included an understanding of the mechanism of the damage, incremental improvements to existing fabrication technology, and feasibility studies of non-traditional fabrication technologies. Status and success of these various approaches are reviewed. Improvements were made in reducing surface damage initiation and eliminating growth for fused silica by improved polishing and post-processing steps, and improved analytical techniques are providing insights into mechanisms of DKDP damage. The NIF final optics hardware has been designed to enable easy retrieval, surface-damage mitigation, and recycling of optics.

We present a novel chirped pulse amplification method which combines optical parametric amplification and laser amplification. We have demonstrated this hybrid CPA concept with a combination of beta-barium borate and Ti:sapphire. High-efficiency, multi-terawatt compatible amplification is achieved without gain narrowing and without electro-optic modulators using a simple commercial pump laser.

A new process is being developed to extract starch from millfeed, the low-value byproduct of wheat flour milling, and convert it to glucose through enzymatic processing. The millfeed-derived glucose will then be converted to value-added products, such as polyol, through a catalytic process, or lactic acid, through a fermentation process. The starch (glucose) recovery process has been tested through the pilot scale. Catalytic and fermentation processes have been tested in the laboratory. The process developed for glucose recovery from wheat millfeed includes hot water extraction of starch and filtration of a fibrous animal feed coproduct, followed by enzymatic liquefaction and saccharification of the extracted starch, with filtration of a high-protein coproduct. The bench-scale tests showed that a glucose yield of approximately 30% on a dry millfeed basis could be achieved, which corresponds to the recovery of essentially all the glucose value in the millfeed. Glucose yields with the pilot-scale system were comparable, although filtration was more difficult.

We report here results from power balance measurements for ohmically-heated plasmas in the Sustained Spheromak Physics Experiment (SSPX). The plasma is formed inside a close-fitting tungsten-coated copper shell; wall conditioning by baking, glow discharge cleaning (GDC), Ti gettering, and helium shot conditioning produces clean plasmas (Z{sub eff} < 2.5) and reduces impurity radiation to a small fraction of the input energy, except when the molybdenum divertor plate has been overheated. We find that most of the input energy is lost by conduction to the walls (the divertor plate and the inner electrode in the coaxial source region). Recently, carborane was added during GDC to boronize the plasma-facing surfaces, but little benefit was obtained.

The design, development, and performance testing of a prototype system known as the Remotely Operated Nondestructive Examination (RONDE)system to examine the knuckle region of a Hanford DST have been completed. The design and fabrication of a scanning bridge to support the Savannah River Site utilizing similar technology was also completed.

The goal of the Majorana Experiment is to determine the effective Majorana masss of the eletron neutrino. Detection of the neutrino mass implied by oscillation results in within our grasp. This exciting physics goal is best pursued using double-beta decay of germanium because of the historical and emerging advances in eliminating competing signals from radioactive backgrounds. The Majorana Experiment will consist of a large mass of 76Ge in the form of high-resolution detectors deep underground, searching for a sharp peak at the BB endpoint. We present here an overview of the entire project in order to help put in perspective the scope, the level and technial risk, and the readiness of the Collaboration to begin the undertaking.

The passive corrosion rate of Alloy 22 is exceptionally low in a wide range of aqueous solutions, temperatures and electrochemical potentials, Alloy 22 contains approximately 22% chromium (Cr) by weight; thus, it forms a Cr-rich passive film in most environments. Very little is known about the composition, thickness and other properties of this passive film. The aim of this research was to determine the general characteristics of the oxide film that forms on Alloy 22, as a function of solution pH, temperature and applied electrochemical potential.

None

The National Ignition Facility will be the highest energy laser in the world when completed. Many small optics ({le} 14 inches in diameter) have stringent transport efficiency and some have very high laser fluence requirements. For optics to sustain high spectral efficiencies and survive high fluences for a 30-year operation, these optics have cleanliness requirements to assure optimal laser system performance. These optical components have insufficient surface areas to validate the particulate and organic contamination requirements by methods used for mechanical parts. Also, the common validation techniques require some sort of surface contact which is not compatible with handling of laser optics. This presentation describes alternate cleanliness validation methods developed for the NIF small optical components. An organic validation procedure was devised based on the spectral transmission sensitivity to contamination layers on coated and uncoated fused silica windows. Optics were scanned in the near infrared before and after an application of a specific amount of organic contamination onto the surface. Changes in transmission correlated to organic contamination levels and used to determine non-volatile organic contamination optics. A validation method for particulate contamination was demonstrated on a large window, showing that acceptable cleanliness levels could be achieved after a wet-wipe and …

A photon collider interaction region has the possibility of expanding the physics reach of a future TeV scale electron-positron collider. A survey of ongoing efforts to design the required lasers and optics to create a photon collider is presented in this paper.

We describe our recent progress in the area of solid-state heat-capacity-lasers (SSHCL). In particular, we examine the physics of heat-capacity operation of a solid state laser and give the present technology status of our 10 kW flashlamp-pumped laser The current status of work leading to a diode-pumped Nd:GGG HCL is also described.

The approach of the Campus Earthquake Program (CEP) is to combine the substantial expertise that exists within the UC system in geology, seismology, and geotechnical engineering, to estimate the earthquake strong motion exposure of UC facilities. These estimates draw upon recent advances in hazard assessment, seismic wave propagation modeling in rocks and soils, and dynamic soil testing. The UC campuses currently chosen for application of our integrated methodology are Riverside, San Diego, and Santa Barbara. The procedure starts with the identification of possible earthquake sources in the region and the determination of the most critical fault(s) related to earthquake exposure of the campus. Combined geological, geophysical, and geotechnical studies are then conducted to characterize each campus with specific focus on the location of particular target buildings of special interest to the campus administrators. We drill, sample, and geophysically log deep boreholes next to the target structure, to provide direct in-situ measurements of subsurface material properties, and to install uphole and downhole 3-component seismic sensors capable of recording both weak and strong motions. The boreholes provide access below the soil layers, to deeper materials that have relatively high seismic shear-wave velocities. Analyses of conjugate downhole and uphole records provide a basis …

With laser-driven tabletop x-ray lasers now operating in the efficient saturation regime, the source characteristics of high photon flux, high monochromaticity, picosecond pulse duration, and coherence are well-matched to many applications involving the probing of matter undergoing rapid changes. We give an overview of recent experiments at the Lawrence Livermore National Laboratory (LLNL) Compact Multipulse Terawatt (COMET) laser using the picosecond 14.7 nm x-ray laser as a compact, ultrafast probe for surface analysis and for interferometry of laser-produced plasmas. The plasma density measurements for known laser conditions allow us to reliably and precisely benchmark hydrodynamics codes. In the former case, the x-ray laser ejects photo-electrons, from the valence band or shallow core-levels of the material, and are measured in a time-of-flight analyzer. Therefore, the electronic structure can be studied directly to determine the physical properties of materials undergoing rapid phase changes.

A key component in the National Ignition Facility (NIF) laser optic system is the amplifier frame assembly unit (FAU). The cast aluminum top plate that supports the FAU is required to withstand loads that would occur during an earthquake with a recurrence period of 1000 years. The stringent seismic requirements placed on the FAU top plate induced a study of the cast aluminum material used in the top plate. Ultrasonic testing was used to aid in characterizing the aluminum material used in the plates. This report documents the work performed using contact ultrasonic testing to characterize the FAU top plate material. The ultrasonic work reported here had 3 objectives: (1) inspect the plate material before cyclic testing conducted at the Pacific Earthquake Engineering Research Center (PEER); (2) determine the overall quality of individual plates; and (3) detect large defects in critical areas of individual plates. Section III, ''Pre-cyclic test inspection'', describes work performed in support of Objective 1. Section IV, ''Ultrasonic field measurements'', describes work performed in support of Objectives 2 and 3.

This note summarizes some of the work done on Vlasov simulation methods during the two-week visit of E. Sonnendrucker to LBNL in July-August, 2002. It describes a variety of algorithms which might be employed in solving the coupled Vlasov-Poisson system on a grid in phase space. In particular, it emphasizes a class of methods which do not employ the sort of operator splitting commonly used in Vlasov methods, whereby the distribution function information is alternately updated along planes of constant x and constant v. Instead, the distribution function information on the phase space nodes is given by either (a) multi-dimensional interpolation of the gridded f at an earlier time onto a set of phase space locations which are obtained by tracking the nodes back to that earlier time (''backward semi-Lagrangian''), or (b) weighted deposition or averaging of f values from orbits onto nodes (''forward semi-Lagrangian'' or ''fully Lagrangian'').

We report new results using the LLNL COMET laser to evaluate the effectiveness of different target architectures to improve the output and characteristics of the transient x-ray laser scheme. Surprising observations were found when the laser line focus irradiating a single slab Cr or Fe target was divided into two or three distinct plasma column sections with millimeter scale gaps between each plasma. The Ne-like 3p {sup 1}S{sub 0} {yields} 3s {sup 1}P{sub 1} 28.5 nm and 25.5 nm x-ray laser lines, for Cr and Fe, respectively, were improved in beam divergence, by 2-3 times, and peak intensity, by up to one order of magnitude, when compared with a single plasma column of the same length or longer. This was contrary to expectations since these large-scale inhomogeneities introduced along the plasma, as well as attenuation from the cold plasma at the end of each section, would be detrimental to the x-ray propagation and amplification. Instead an injector-amplifier (IA) type process appears to be at work where the plasma gaps may be beneficially modifying the ray propagation and coupling through the high Ne-like ion gain regions. We present results showing the output of the amplifier stage with increasing length for the …

This report describes the caustic leaching test conducted on Hanford Tank T-110 sludge during FY 2002 at the Pacific Northwest National Laboratory. The data presented here can be used to develop the baseline and alternative flowsheets for pretreating Hanford tank sludge. The U.S. Department of Energy funded the work through the Efficient Separations and Processing Crosscutting Program (ESP; EM-50).

Size and composition are key factors in determining the impact aerosols have on global climate change and human health. The DELTA group at UC Davis has developed sampling techniques that allow continuous collection of aerosols separated into 8 different size fractions with 1-hour time resolution. Total aerosol mass determination: Scanning Transmission Ion Microscopy (STIM) with a 3 MeV proton beam can produce profiles of aerosol mass with an error limit of less than 10%. The aerosol collection strip is scanned with a proton beam of 50 micrometer spatial resolution while recording the proton mean energy loss as a function of position (Bench et al., 1992). A differential beta attenuation mass monitor (beta-gauge) is also used for mass determination. The beta-gauge consists of a 63Ni source and a surface barrier detector. This technique allows quantitative mass measurement by recording attenuation of beta particles through the sample and substrate (Chueinta and Hopke, 2001). Mineral mass and elemental composition: Synchrotron X-ray Fluorescence (s-XRF) is performed at the Advanced Light Source (ALS) at LBNL. The s-XRF technique is quantitative for elements Na through U. The ALS synchrotron provides an extraordinarily intense white beam of X-rays (4-20 KeV) that are 100% polarized. These properties provide …

This form updates the groundwater monitoring plan for the B Pond system and documents revision agreed upon with the Washington State Department of Ecology concerning well network, constitutuent list, statistical analysis, and report procedures.