EPIcode (version 7.0) and ALOHA (version 5.2.3) are two of the designated toolbox codes identified in the Department of Energy's Implementation Plan for DNFSB Recommendation 2002-1 on Software Quality Assurance issues in the DOE Complex. Both have the capability to estimate evaporation rates from pools formed from chemical spills and to predict subsequent atmospheric transport and dispersion. This paper provides an overview of the algorithms used by EPIcode and ALOHA to calculate evaporation rates and downwind plume concentrations. The technical bases for these algorithms are briefly discussed, and differences in the EPIcode and ALOHA methodologies highlighted. In addition, sample calculations are performed using EPIcode and ALOHA for selected chemicals under various environmental conditions. Side-by-side comparisons of results from sample calculations are analyzed to illustrate the impact that the different methodologies used by EPIcode and ALOHA have on predicted evaporation rates and downwind concentrations.

Sqamate reptiles are traditionally divided into six groups: Iguania, Anguimorpha, Scincomorpha, Gekkota (these four are lizards), Serpentes (snakes), and Amphisbaenia (the so-called worm lizards). Currently there are complete mitochondrial genomes from two representatives of the Iguania (Janke et al., 2001; Kumazawa, 2004), three from the Anguimorpha (Kumazawa, 2004; Kumazawa and Endo, 2004), two from the Scincomorpha (Kumazawa and Nishida, 1999; Kumazawa, 2004), two from Serpentes (Kumazawa et al., 1998; Kumazawa, 2004) and 12 from Amphisbaenia (Macey et al., 2004). The only traditional group of Squamata from which a complete mitochondrial genome has not been sequenced is the Gekkota. Here we report the complete mitochondrial genome of Teratoscincus keyserlingii, a Middle Eastern representative of the Gekkota. The gekkonid lizard genus Teratoscincus is distributed throughout the deserts of central and southwest Asia as shown in figure 1, with five species currently recognized (Macey et al. 1997a, 1999b). Included in this figure are the positions of mountain ranges discussed in the text; see also figure 1 in Macey et al. (1999b). Two species, T. bedriagai and T. microlepis, are restricted to Southwest Asia south of the Kopet Dagh and Hindu Kush in Iran, Afghanistan, and Pakistan (Anderson, 1999). Two species are found in …

This report covers the final one-year period of work done by the Principal Investigator (S. T. Pantelides) and his group in collaboration with other team members. The focus of the work was to pursue understanding of core excitation spectra in doped manganites where experimental data obtained at Oak Ridge National Laboratory by S. J. Pennycook showed inequivalent Mn atoms. Calculations found that doping sets up a Peierls-like instability that drives the observed distortion. Further calculations of electron-energy-loss spectra to account for the observed L23 ratios in the Mn L2,3 spectra will be pursued in the future.

As a result of collaboration between the Berkeley Seismographic Station, Lawrence Livermore National Laboratory, and Caltrans, instrument packages have been placed in bedrock in six boreholes and two surface sites along the San Francisco/Oakland Bay Bridge. Since 1996 over 200 local earthquakes have been recorded. Prior to this study few seismic recording instruments existed in bed-rock in San Francisco Bay. We utilized the data to perform analysis of ground motion variability, wave passage, site response, and up-and down-hole wave propagation along the Bay Bridge. We also synthesized strong ground motion at nine locations along the Bay Bridge. Key to these studies is LLNL's effort to exploit the information available in weak ground motions (generally from earthquakes < M=4.0) to enhance predictions of seismic hazards. We found that Yerba Island has no apparent site response at the surface relative to a borehole site. The horizontal to vertical spectral ratio method best revealed no site response, while the complex signal spectral ratio method had the lowest variance for spectral ratios and best predicted surface recordings when the borehole recording was used as input. Both methods identified resonances at about the same frequencies. Regional attenuation results in a significant loss of high frequencies …

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Geothermal energy, defined as heat from the Earth, is a statute-recognized renewable resource. The first U.S. geothermal power plant, opened at The Geysers in California in 1960, continues to operate successfully. The United States, as the world's largest producer of geothermal electricity, generates an average of 15 billion kilowatt hours of power per year, comparable to burning close to 25 million barrels of oil or 6 million short tons of coal per year. Geothermal has a higher capacity factor (a measure of the amount of real time during which a facility is used) than many other power sources. Unlike wind and solar resources, which are more dependent upon weather fluctuations and climate changes, geothermal resources are available 24 hours a day, 7 days a week. While the carrier medium for geothermal electricity (water) must be properly managed, the source of geothermal energy, the Earth's heat, will be available indefinitely. A geothermal resource assessment shows that nine western states together have the potential to provide over 20 percent of national electricity needs. Although geothermal power plants, concentrated in the West, provide the third largest domestic source of renewable electricity after hydropower and biomass, they currently produce less than one percent of …

This paper describes a scheme for rapidly computing numerical values of definite integrals to very high accuracy, ranging from ordinary machine precision to hundreds or thousands of digits, even for functions with singularities or infinite derivatives at endpoints. Such a scheme is of interest not only in computational physics and computational chemistry, but also in experimental mathematics, where high-precision numerical values of definite integrals can be used to numerically discover new identities. This paper discusses techniques for a parallel implementation of this scheme, then presents performance results for 1-D and 2-D test suites. Results are also given for a certain problem from mathematical physics, which features a difficult singularity, confirming a conjecture to 20,000 digit accuracy. The performance rate for this latter calculation on 1024 CPUs is 690 Gflop/s. We believe that this and one other 20,000-digit integral evaluation that we report are the highest-precision non-trivial numerical integrations performed to date.

The analysis of interactions between lineages at varying levels of genetic divergence can provide insights into the process of speciation through the accumulation of incompatible mutations. Ring species, and especially the Ensatina eschscholtzii system exemplify this approach. The plethodontid salamanders Ensatina eschscholtzii xanthoptica and Ensatina eschscholtzii platensis hybridize in the Central Sierran foothills of California. We compared the genetic structure across two transects (southern and northern Calaveras Co.), one of which was re-sampled over 20 years, and examined diagnostic molecular markers (eight allozyme loci and mitochondrial DNA) and a diagnostic quantitative trait (color pattern). Key results across all studies were: (i) cline centers for all markers were coincident and the zones were narrow, with width estimates of 730m to 2000m; (ii) cline centers at the northern Calaveras transect were coincident between 1981 and 2001, demonstrating repeatability over 5 generations; (iii) there are very few if any putative F1's, but a relatively high number of backcrossed individuals (57-86 percent) in the central portion of transects; (iv) we found substantial linkage disequilibrium in all three studies and strong heterozygote deficit both in northern Calaveras, in 2001, and southern Calaveras. Both linkage disequilibrium and heterozygote deficit show maximum values near the center of …

The production of comprehensive cDNA clone collections is an important goal of the human and model organism genome projects. cDNA sequences are used to determine the structures of transcripts, including splice junctions, polyadenylation sites, and 5' and 3' untranslated regions (UTRs). cDNA collections are also valuable resources for functional studies of genes and proteins. Expressed Sequence Tag (EST)sequencing is the method of choice for recovering cDNAs representing a majority of the transcripts encoded in a eukaryotic genome. However, EST sequencing samples a library at random, so it realizes diminishing returns as the project progresses. To drive cDNA collections toward completion new methods are needed to recover cDNAs representing specific genes and alternative transcripts, including transcripts with low expression levels. We describe a simple and effective inverse-PCR-based method for screening plasmid libraries to recover intact cDNAs for specific transcripts. We tested the method by screening libraries used in our Drosophila EST projects for 153 transcription factor genes that were not yet represented by full-length cDNAs. We recovered target-specific clones for 104 of the genes: 46 exactly match, 30 improve and 28partially match current gene annotations. Successful application of the screening method depends on cDNA library complexity and quality of the gene …

The current operation strategy for using Saltstone Vault 4 to receive 0.2 Ci/gallon salt solution waste involves pouring a clean grout layer over the radioactive grout prior to initiating pour into another cell. This will minimize the radiating surface area and reduce the dose rate at the vault and surrounding area. The Clean Cap will be used to shield about four feet of Saltstone poured into a Z-Area vault cell prior to moving to another cell. The minimum thickness of the Clean Cap layer will be determined by the cesium concentration and resulting dose levels and it is expected to be about one foot thick based on current calculations for 0.1 Ci Saltstone that is produced in the Saltstone process by stabilization of 0.2 Ci salt solution. This report documents experiments performed to identify a formulation for the Clean Cap. Thermal transient calculations, adiabatic temperature rise measurements, pour height, time between pour calculations and shielding calculations were beyond the scope and time limitations of this study. However, data required for shielding calculations (composition and specific gravity) are provided for shielding calculations. The approach used to design a Clean Cap formulation was to produce a slurry from the reference premix (10/45/45 …

Seismoelectric phenomena in sediments arise from acoustic wave-induced fluid motion in the pore space, which perturbs the electrostatic equilibrium of the electric double layer on the grain surfaces. Experimental techniques and the apparatus built to study this electrokinetic (EK) effect are described and outcomes for studies of seismoelectric phenomena in loose glass microspheres and medium-grain sand are presented. By varying the NaCl concentration in the pore fluid, we measured the conductivity dependence of two kinds of EK behavior: (1) the electric fields generated within the samples by the passage of transmitted acoustic waves, and (2) the electromagnetic wave produced at the fluid-sediment interface by the incident acoustic wave. Both phenomena are caused by relative fluid motion in the sediment pores--this feature is characteristic of poroelastic (Biot) media, but not predicted by either viscoelastic fluid or solid models. A model of plane-wave reflection from a fluid-sediment interface using EK-Biot theory leads to theoretical predictions that compare well to the experimental data for both sand and glass microspheres.

Comparing complete animal mitochondrial genome sequences is becoming increasingly common for phylogenetic reconstruction and as a model for genome evolution. Not only are they much more informative than shorter sequences of individual genes for inferring evolutionary relatedness, but these data also provide sets of genome-level characters, such as the relative arrangements of genes, that can be especially powerful. We describe here the protocols commonly used for physically isolating mtDNA, for amplifying these by PCR or RCA, for cloning,sequencing, assembly, validation, and gene annotation, and for comparing both sequences and gene arrangements. On several topics, we offer general observations based on our experiences to date with determining and comparing complete mtDNA sequences.

There is interest in attempting to synthesize nearly pure uranium nitride (UN) kernels for high-temperature gas-cooled reactor (HTGR) fuel. Because the proposed process involves carbothermic conversion of a urania-carbon mixture in nitrogen and because there is a complete ideal solution of uranium carbide (UC) and UN, which is written as UC{sub 1-x}N{sub x}, the practical value of x for fuel irradiation needs to be determined. Insight is to be gained by relevant thermodynamic calculations of carbide-nitride equilibria for the fuel and fission product systems. The equilibria are readily compared on the nitrogen-based Ellingham diagram, which, in turn, provides guidance in interpreting past irradiations and in synthesis of the UC{sub 1-x}N{sub x} kernels.

[1] Douglass and Knox [2005], hereafter referred to as DK, present an analysis of the observed cooling following the 1991 Mt. Pinatubo eruption and claim that these data imply a very low value for the climate sensitivity (equivalent to 0.6 C equilibrium warming for a CO{sub 2} doubling). We show here that their analysis is flawed and their results are incorrect.