We present a summary of recent progress on the development and application of adaptive mesh refinement algorithms for low Mach number reacting flows. Our approach uses a form of the low Mach number equations based on a general equation of state that discretely conserves both mass and energy. The discretization methodology is based on a robust projection formulation that accommodates large density contrasts. The algorithm supports modeling of multicomponent systems and incorporates an operator-split treatment of stiff reaction terms. The basic computational approach is embedded in an adaptive projection framework that uses structured hierarchical grids with subcycling in time that preserves the discrete conservation properties of the underlying single-grid algorithm. We present numerical examples illustrating the application of the methodology to turbulent premixed combustion and nuclear flames in type Ia supernovae.

The problem of imaging of targets in random media or cluttered environments is found in a wide variety of different applications, including ocean acoustics, medical ultrasound, geophysics, and radar. The solution often requires separating targets of interest from other scatterers, and compensating for wave speed variations in the medium. The problem is not usually the lack of data, but too much data, specifically the lack of a useful organizing principle for the data. The difficult part is separating the meaningful data from the remainder. It would therefore be most helpful if there were some means for skipping over those parts of the data that we do not really want to image very much, and looking at those parts (targets) that do interest us. This sounds challenging (maybe even impossible), but recent developments in acoustics make it clear that certain very limited imaging goals are achievable with much smaller data sets than are traditionally needed in, for example, seismic array processing. Early versions of this new method have been given the names of ''time-reversal acoustics'' or ''time-reversal mirrors,'' and have been developed most extensively by the French ultrasonics group led by Fink.

Networks have recently emerged as a unifying theme in complex systems research [1]. It is in fact no coincidence that networks and complexity are so heavily intertwined. Any future definition of a complex system should reflect the fact that such systems consist of many mutually interacting components. These components are far from being identical as say electrons in systems studied by condensed matter physics. In a truly complex system each of them has a unique identity allowing one to separate it from the others. The very first question one may ask about such a system is which other components a given component interacts with? This information system wide can be visualized as a graph, whose nodes correspond to individual components of the complex system in question and edges to their mutual interactions. Such a network can be thought of as a backbone of the complex system. Of course, system's dynamics depends not only on the topology of an underlying network but also on the exact form of interaction of components with each other, which can be very different in various complex systems. However, the underlying network may contain clues about the basic design principles and/or evolutionary history of the complex …

The goal of this project was to make a first assessment of the major carbon stocks and fluxes and their climatic determinants in a lowland neotropical rain forest, the La Selva Biological Station, Costa Rica. Our research design was based on the concurrent use of several of the best available approaches, so that data could be cross-validated. A major focus of our effort was to combine meteorological studies of whole-forest carbon exchange (eddy flux), with parallel independent measurements of key components of the forest carbon budget. The eddy flux system operated from February 1998 to February 2001. To obtain field data that could be scaled up to the landscape level, we monitored carbon stocks, net primary productivity components including tree growth and mortality, litterfall, woody debris production, root biomass, and soil respiration in a series of replicated plots stratified across the major environmental gradients of the forest. A second major focus of this project was on the stocks and changes of carbon in the soil. We used isotope studies and intensive monitoring to investigate soil organic stocks and the climate-driven variation of soil respiration down the soil profile, in a set of six 4m deep soil shafts stratified across the …

Neutron-induced fission cross sections on targets of {sup 236,236m,237,238}Np, {sup 237,237m}Pu, and {sup 240,241,242,242m,243,244,244m}Am have been estimated for incident neutron energies of up to 6 MeV, using the ''surrogate'' technique and the ({sup 3}He,df) and ({sup 3}He,tf) reactions on stable targets to measure fission probabilities. In isotopes where low-lying isomeric states are known to exist, the (n,f) cross section on the corresponding isomeric targets has been estimated, using the surrogate technique. For targets of {sup 237}Np, {sup 241}Am, {sup 242m}Am, {sup 243}Am, measurements of the (n,f) cross section exist, and comparison with the surrogate-method results suggests that the (n,f) cross sections estimated by the surrogate technique are reliable to within 10% for incident neutron energies E{sub n}{approx}>2 MeV. Tabulated values of the estimated (n,f) cross sections are given in an appendix.

Resonant magnetic x-ray scattering from dense self-assemblies of 9-nm diameter epsilon-Co and hcp-Co particles is reported. For lower anisotropy epsilon-Co we find remanent magnetic scattering that is significantly enhanced, indicating preferred inter-particle moment orientations of both antiferromagnetic and ferromagnetic character. This interaction-mediated collective behavior is consistent with dipolar fields and exists well above the isolated particles blocking temperature where thermal activation is operative, suggesting that magnetostatic super-spin waves exist in such systems.

Despite the rapid combustion typically experienced in Homogeneous Charge Compression Ignition (HCCI), components in fuel mixtures do not ignite in unison or burn equally. In our experiments and modeling of blends of diethyl ether (DEE) and ethanol (EtOH), the DEE led combustion and proceeded further toward completion, as indicated by {sup 14}C isotope tracing. A numerical model of HCCI combustion of DEE and EtOH mixtures supports the isotopic findings. Although both approaches lacked information on incompletely combusted intermediates plentiful in HCCI emissions, the numerical model and {sup 14}C tracing data agreed within the limitations of the single zone model. Despite the fact that DEE is more reactive than EtOH in HCCI engines, they are sufficiently similar that we did not observe a large elongation of energy release or significant reduction in inlet temperature required for light-off, both desired effects for the combustion event. This finding suggests that, in general, HCCI combustion of fuel blends may have preferential combustion of some of the blend components.

The microstructural evolution of high purity steel under irradiation is modeled including a dislocation density that evolves simultaneously with void nucleation and growth. The predicted void swelling trends versus temperature, flux, and time are compared to experiment and to earlier calculations with a fixed dislocation density. The behavior is further analyzed within a simplified picture of segregation of irradiation defects to microstructural sinks. Agreement with experimental swelling behavior improves when dislocations co-evolve with the void content versus simulations with a fixed dislocation density. The time-dependent dislocation content dictates the rate of void nucleation and shapes the overall void size distribution so as to give steady swelling behavior over long times.

This report describes how Learning-by-Doing (LBD) is implemented endogenously in the National Energy Modeling System (NEMS) for generating plants. LBD is experiential learning that correlates to a generating technology's capacity growth. The annual amount of Learning-by-Doing affects the annual overnight cost reduction. Currently, there is no straightforward way to integrate and make sense of all the diffuse information related to the endogenous learning calculation in NEMS. This paper organizes the relevant information from the NEMS documentation, source code, input files, and output files, in order to make the model's logic more accessible. The end results are shown in three ways: in a simple spreadsheet containing all the parameters related to endogenous learning; by an algorithm that traces how the parameters lead to cost reductions; and by examples showing how AEO 2004 forecasts the reduction of overnight costs for generating technologies over time.

Nitrate is the number one drinking water contaminant in the United States. It is pervasive in surface and groundwater systems, and its principal anthropogenic sources have increased dramatically in the last 50 years. In California alone, one third of the public drinking-water wells has been lost since 1988 and nitrate contamination is the most common reason for abandonment. Effective nitrate management in groundwater is complicated by uncertainties related to multiple point and non-point sources, hydrogeologic complexity, geochemical reactivity, and quantification of dentrification processes. In this paper, we review an integrated experimental and simulation-based framework being developed to study the fate of nitrate in a 25 km-long groundwater subbasin south of San Jose, California, a historically agricultural area now undergoing rapid urbanization with increasing demands for groundwater. The modeling approach is driven by a need to integrate new and archival data that support the hypothesis that nitrate fate and transport at the basin scale is intricately related to hydrostratigraphic complexity, variability of flow paths and groundwater residence times, microbial activity, and multiple geochemical reaction mechanisms. This study synthesizes these disparate and multi-scale data into a three-dimensional and highly resolved reactive transport modeling framework.

Two-dimensional full-wave time-dependent simulations in full plasma geometry are presented which show that conventional reflectometry (without a lens) can be used to synthetically image density fluctuations in fusion plasmas under conditions where the parallel correlation length greatly exceeds the poloidal correlation length of the turbulence. The advantage of synthetic imaging is that the image can be produced without the need for a large lens of high optical quality, and each frequency that is launched can be independently imaged. A particularly simple arrangement, consisting of a single receiver located at the midpoint of a microwave beam propagating along the plasma midplane is shown to suffice for imaging purposes. However, as the ratio of the parallel to poloidal correlation length decreases, a poloidal array of receivers needs to be used to synthesize the image with high accuracy. Simulations using DIII-D relevant parameters show the similarity of synthetic and optical imaging in present-day experiments.

(B204)The fundamental motivation for our work is that supernovae are not well understood. Recent observations have clarified the depth of our ignorance, by producing observed phenomena that current theory and computer simulations cannot reproduce. Such theories and simulations involve, however, a number of physical mechanisms that have never been studied in isolation. We perform experiments, in compressible hydrodynamics and radiation hydrodynamics, relevant to supernovae and supernova remnants. These experiments produce phenomena in the laboratory that are believed, based on simulations, to be important to astrophysics but that have not been directly observed in either the laboratory or in an astrophysical system. During the period of this grant, we have focused on the scaling of an astrophysically relevant, radiative-precursor shock, on preliminary studies of collapsing radiative shocks, and on the multimode behavior and the three-dimensional, deeply nonlinear evolution of the Rayleigh-Taylor (RT) instability at a decelerating, embedded interface. These experiments required strong compression and decompression, strong shocks (Mach {approx}10 or greater), flexible geometries, and very smooth laser beams, which means that the 60-beam Omega laser is the only facility capable of carrying out this program.

We describe the design and implementation of a vacuum compatible laser-based absolute distance measurement gauge with sub-nm resolution. The present system is compatible with operation in the 10{sup -8} Torr range and with some minor modifications could be used in the 10{sup -9} Torr range. The system is based on glancing incidence reflection and dual segmented diode detection. The system has been implemented as a focus sensor for extreme ultraviolet interferometry and microlithography experiments at Lawrence Berkeley National Laboratory's Advanced Light Source synchrotron radiation facility and 1{sigma} operational measurement noise floor of 0.26 nm has been demonstrated.

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This project explored a new concept for high-pressure xenon ionization chambers by replacing the Frisch grid with coplanar grid electrodes similar to those used in wide bandgap semiconductor gamma-ray spectrometers. This work is the first attempt to apply the coplanar grid anode design in a gas ionization chamber in order to achieve to improved energy resolution. Three prototype detectors, two cylindrical and one parallel plate configurations, were built and tested. While the detectors did not demonstrate energy resolutions as good as other high pressure xenon gamma-ray spectrometers, the results demonstrated that the concept of single polarity charge sending using coplanar grid electrodes will work in a gas detector.

This goal of this project was to perform feasibility experiments and measurements of the fundamental interactions between hydrogen and single wall carbon nanotubes (SWNT) at high pressures. High-pressure is an adjustable experimental parameter for tuning interaction strengths, thereby elucidating and providing insights into the fundamental nature of the H{sub 2}/SWNT system. We have developed and utilized systems and methodologies to make x-ray scattering, optical spectroscopic and electrical transport measurements. These activities have been productive in demonstrating capabilities and measuring properties of SWNTs under high-pressure conditions. We have also developed strong cooperative and complementary relationships with academic research colleagues at Stanford University. Building on these results and relationships, we hope to continue and expand our research as co-investigators in a joint Harvard-LLNL-Stanford proposal to the DOE ''Grand Challenge'' for Basic and Applied Research in Hydrogen Storage (Solicitation No. DE-PS36-03GO93013). Hydrogen storage is an active research topic with important basic science implications and a crucial enabling technology for advanced energy systems. Measurements of the H{sub 2} storage capacity indicate that it may achieve or exceed the storage capacity level (6.5 wt-%) mandated by the DOE hydrogen plan for fielding a hydrogen-fueled vehicle. The H{sub 2}/SWNT system has been the subject of intensive …

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We are currently investigating the use of magnetic particles--polymeric-based spheres containing dispersed magnetic nanocrystalline phases--for the precise delivery of drugs via the human vasculature. According to this review, meticulously prepared magnetic drug targeting holds promise as a safe and effective method of delivering drugs to specific organ, tissue or cellular targets. We have critically examined the wide range of approaches in the design and implementation of magnetic-particle-based drug delivery systems to date, including magnetic particle preparation, drug encapsulation, biostability, biocompatibility, toxicity, magnetic field designs, and clinical trials. However, we strongly believe that there are several limitations with past developments that need to be addressed to enable significant strides in the field. First, particle size has to be carefully chosen. Micrometer-sized magnetic particles are better attracted over a distance than nanometer sized magnetic particles by a constant magnetic field gradient, and particle sizes up to 1 {micro}m show a much better accumulation with no apparent side effects in small animal models, since the smallest blood vessels have an inner diameter of 5-7 {micro}m. Nanometer-sized particles <70 nm will accumulate in organ fenestrations despite an effective surface stabilizer. To be suitable for future human applications, our experimental approach synthesizes the magnetic drug …

The goal of this Strategic Initiative in Applied Computational Biology has been to apply LLNL's expertise in computational simulation to forge a new laboratory core competency in biological simulation. By every measure, this SI has been very successful in this goal. Based on a strong publication record and large number of conference presentations and invited talks, we have built a recognized niche for LLNL in the burgeoning field of computational biology. Further, many of the projects that were previously part of this LDRD are now externally funded based on the research results and expertise developed under this SI. We have created successful collaborations with a number of outside research groups including several joint projects with the new UC Davis/LLNL Comprehensive Cancer Center. In addition to these scientific collaborations, the staff developed on this SI is involved in computational biology program development and advisory roles with other DOE laboratories and DOE Headquarters. Moreover, a number of capabilities and expertise created by this SI are finding use in LLNL programmatic applications. Finally, and most importantly, this SI project has brought to LLNL the human talent on who will be the ensuring the further success of computational biology at this laboratory.

One of the key missions of the U.S. Department of Energy (DOE) is to ensure an abundant and affordable energy supply for the nation. As part of the process of producing oil and natural gas, operators also must manage large quantities of water that are found in the same underground formations. The quantity of this water, known as produced water, generated each year is so large that it represents a significant component in the cost of producing oil and gas. Produced water is water trapped in underground formations that is brought to the surface along with oil or gas. It is by far the largest volume byproduct or waste stream associated with oil and gas production. Management of produced water presents challenges and costs to operators. This white paper is intended to provide basic information on many aspects of produced water, including its constituents, how much of it is generated, how it is managed and regulated in different settings, and the cost of its management.

It is important to have experimental methods to estimate the maximum beam intensity for the Fermilab Booster as objective input into long term program commitments. An important existing limit is set by the available rf power. This limit is difficult to set a priori, because the real longitudinal impedance is not well known. The synchrotron phase at transition crossing was measured using both the mountain range plot and the direct phase measurement of the RF accelerating voltage relative to the beam, and results were consistent. They were applied to predict 6 x 10{sup 12} maximum Booster beam intensity with present running conditions.

Natural convection heat and mass transfer under post-closure conditions has been calculated for Yucca Mountain drifts using the computational fluid dynamics (CFD) code FLUENT. Calculations have been performed for 300, 1000, 3000, and 10,000 years after repository closure. Effective dispersion coefficients that can be used to calculate mass transfer in the drift have been evaluated as a function of time and boundary temperature tilt.

Two methods of up-scaling coupled equations at the microscale to equations valid at the mesoscale and/or macroscale for fluid-saturated and partially saturated porous media are discussed, compared, and contrasted. The two methods are: (1) two-scale and multiscale homogenization, and (2) volume averaging. Both these methods have advantages for some applications and disadvantages for others. For example, homogenization methods can give formulas for coefficients in the up-scaled equations, whereas volume averaging methods give the form of the up-scaled equations but generally must be supplemented with physical arguments and/or data in order to determine the coefficients. Homogenization theory requires a great deal of mathematical insight from the user in order to choose appropriate scalings for use in the resulting power-law expansions, while volume averaging requires more physical insight to motivate the steps needed to find coefficients. Homogenization often is performed on periodic models, while volume averaging does not require any assumption of periodicity and can therefore be related very directly to laboratory and/or field measurements. Validity of the homogenization process is often limited to specific ranges of frequency - in order to justify the scaling hypotheses that must be made - and therefore cannot be used easily over wide ranges of frequency. …

Yucca Mountain, Nevada, was approved as the site for development of the geologic repository for high-level radioactive waste and spent nuclear fuel in the United States. The U.S. Department of Energy has been conducting studies to characterize the site and assess its future performance as a geologic repository. As part of these studies, a program of deep seismic profiling, to depths of 200 m, was conducted along the top of Yucca Mountain to evaluate the shear-wave velocity (V{sub s}) structure of the repository block. The resulting V{sub s} data were used as input into the development of ground motions for the preclosure seismic design of the repository and for postclosure performance assessment. The noninvasive spectral-analysis-of-surface-waves (SASW) method was employed in the deep profiling. Field measurements involved the use of a modified Vibroseis as the seismic source. The modifications allowed the Vibroseis to be controlled by a signal analyzer so that slow frequency sweeps could be performed while simultaneous narrow-band filtering was performed on the receiver outputs. This process optimized input energy from the source and signal analysis of the receiver outputs. Six deep V{sub s} profiles and five intermediate-depth (about 100 m) profiles were performed along the top of Yucca …