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In recent years there has been a revival of interest in Fixed Field Alternating Gradient (FFAG) accelerators. In Japan a number have been built, or are under construction. A new non-scaling approach to the FFAG reduces the required orbit offsets during acceleration and the size of the required aperture, while maintaining the advantage of the low cost magnets associated with fixed fields. An advantage of the non-scaling FFAG accelerator, with respect to synchrotrons, is the fixed field and hence the possibility of high current and high repetition rate for spot scanning. There are possible advantages of the nonscaling design with respect to fixed-field cyclotrons. The non-scaling FFAG allows strong focusing and hence smaller aperture requirements compared to scaling designs, thus leading to very low losses and better control over the beam. We present, here, a non-scaling FFAG designed to be used for proton therapy.

Dose and risk assessments are an integral part of decommissioning activities. Most human health risk assessments are performed for a reasonable maximum exposure to an individual with assumed intake and exposure parameters that depend on the end state of the decommissioning activities and the likely future use of the site. Regardless of how the potentially exposed individual is defined, the subsequent calculated human health risk is not a measurable quantity. To demonstrate compliance with risk-based acceptance or cleanliness criteria, facility-specific risk assessments usually are performed after final-verification sampling and analysis. Alternatively, conservative, a priori, guideline concentrations for residual contaminants can be calculated and rapidly compared to the subsequently measured contaminant concentrations to demonstrate compliance. In response to the request for accelerated cleanup at U.S. Department of Energy facilities, the Savannah River Site (SRS) is decommissioning its excess facilities through removal of the facility structures leaving only the concrete-slab foundations in place. Site-specific, risk-based derived concentration guideline levels (DCGLs) for radionuclides have been determined for a future industrial worker potentially exposed to residual contamination on these concrete slabs. When appropriate, these conservative DCGLs will be used at SRS in lieu of facility-specific risk assessments to further accelerate the decommissioning process. This …

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Despite the information content of genomic DNA, ancient DNA studies to date have largely been limited to amplification of mitochondrial DNA due to technical hurdles such as contamination and degradation of ancient DNAs. In this study, we describe two metagenomic libraries constructed using unamplified DNA extracted from the bones of two 40,000-year-old extinct cave bears. Analysis of {approx}1 Mb of sequence from each library showed that, despite significant microbial contamination, 5.8 percent and 1.1 percent of clones in the libraries contain cave bear inserts, yielding 26,861 bp of cave bear genome sequence. Alignment of this sequence to the dog genome, the closest sequenced genome to cave bear in terms of evolutionary distance, revealed roughly the expected ratio of cave bear exons, repeats and conserved noncoding sequences. Only 0.04 percent of all clones sequenced were derived from contamination with modern human DNA. Comparison of cave bear with orthologous sequences from several modern bear species revealed the evolutionary relationship of these lineages. Using the metagenomic approach described here, we have recovered substantial quantities of mammalian genomic sequence more than twice as old as any previously reported, establishing the feasibility of ancient DNA genomic sequencing programs.

We describe the performance of the block-structured Adaptive Mesh Refinement (AMR) code Raptor on the 32k node IBM BlueGene/L computer. This machine represents a significant step forward towards petascale computing. As such, it presents Raptor with many challenges for utilizing the hardware efficiently. In terms of performance, Raptor shows excellent weak and strong scaling when running in single level mode (no adaptivity). Hardware performance monitors show Raptor achieves an aggregate performance of 3:0 Tflops in the main integration kernel on the 32k system. Results from preliminary AMR runs on a prototype astrophysical problem demonstrate the efficiency of the current software when running at large scale. The BG/L system is enabling a physics problem to be considered that represents a factor of 64 increase in overall size compared to the largest ones of this type computed to date. Finally, we provide a description of the development work currently underway to address our inefficiencies.

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 …

Contaminating clouds of electrons are a concern for most accelerators of positive-charged particles, but there are some unique aspects of heavy-ion accelerators for fusion and high-energy density physics which make modeling such clouds especially challenging. In particular, self-consistent electron and ion simulation is required, including a particle advance scheme which can follow electrons in regions where electrons are strongly-, weakly-, and un-magnetized. They describe their approach to such self-consistency, and in particular a scheme for interpolating between full-orbit (Boris) and drift-kinetic particle pushes that enables electron time steps long compared to the typical gyro period in the magnets. They present tests and applications: simulation of electron clouds produced by three different kinds of sources indicates the sensitivity of the cloud shape to the nature of the source; first-of-a-kind self-consistent simulation of electron-cloud experiments on the High-Current Experiment (HCX) at Lawrence Berkeley National Laboratory, in which the machine can be flooded with electrons released by impact of the ion beam and an end plate, demonstrate the ability to reproduce key features of the ion-beam phase space; and simulation of a two-stream instability of thin beams in a magnetic field demonstrates the ability of the large-timestep mover to accurately calculate the instability.

The effects of harvest-created canopy gaps in bottomland hardwood forests on arthropod abundance and, hence, the foraging ecology of birds are poorly understood. I predicted that arthropod abundance would be high near edges of group-selection harvest gaps and lower in the surrounding forest, and that male Hooded Warblers (Wilsonia citrina) foraging near gaps would find more prey per unit time than those foraging in the surrounding forest. In fact, arthropod abundance was greater >100 m from a gap edge than at 0-30 m or 30-100 m from an edge, due to their abundance on switchcane (Arundinaria gigantea); arthropods did not differ in abundance among distances from gaps on oaks (Quercus spp.) or red maple (Acer rubrum). Similarly, Hooded Warbler foraging attack rates were not higher near gap edges: when foraging for fledglings, attack rate did not differ among distances from gaps, but when foraging for themselves, attack rates actually were lower 0-30 m from gap edges than 30-100 m or >100 m from a gap edge. Foraging attack rate was positively associated with arthropod abundance. Hooded Warblers apparently encountered fewer prey and presumably foraged less efficiently where arthropods were least abundant, i.e., near gaps. That attack rates among birds foraging …

ABSTRACT Malaise and pitfall traps were used to sample herbivorous insects in canopy gaps created by group-selection cutting in a bottomland hardwood forest in South Carolina. The traps were placed at the centers, edges, and in the forest adjacent to gaps of different sizes (0.13, 0.26, and 0.50 ha) and ages (1 and 7 yr old) during four sampling periods in 2001. Overall, the abundance and species richness of insect herbivores were greater at the centers of young gaps than at the edge of young gaps or in the forest surrounding young gaps. There were no differences in abundance or species richness among old gap locations (i.e., centers, edges, and forest), and we collected significantly more insects in young gaps than old gaps. The insect communities in old gaps were more similar to the forests surrounding them than young gap communities were to their respective forest locations, but the insect communities in the two forests locations (surrounding young and old gaps) had the highest percent similarity of all. Although both abundance and richness increased in the centers of young gaps with increasing gap size, these differences were not significant.Weattribute the increased numbers of herbivorous insects to the greater abundance of …

Although operons are often subject to horizontal gene transfer (HGT), non-HGT genes are particularly likely to be in operons. To resolve this apparent discrepancy and to determine whether HGT is involved in operon formation, we examined the evolutionary history of the genes and operons in Escherichia coli K12. We show that genes that have homologs in distantly related bacteria but not in close relatives of E. coli (indicating HGTi) form new operons at about the same rates as native genes. Furthermore, genes in new operons are no more likely than other genes to have phylogenetic trees that are inconsistent with the species tree. In contrast, essential genes and ubiquitous genes without paralogs (genes believed to undergo HGT rarely) often form new operons. We conclude that HGT is not associated with operon formation, but instead promotes the prevalence of pre-existing operons. To explain operon formation, we propose that new operons reduce the amount of regulatory information required to specify optimal expression patterns. Consistent with this hypothesis, operons have greater amounts of conserved regulatory sequences than do individually transcribed genes.

In spent nuclear fuel (SNF), the metal epsilon phase consists of an alloy of Mo-Ru-Pd-Tc-Rh, occurring at a micron to sub-micron scale. {sup 99}Tc has a long half life (2.13 x 10{sup 5} years) and can be an important contributor to dose in safety assessments of nuclear waste repositories. Under oxidizing conditions, TcO{sub 4}{sup -} is the predominant species of Tc. In this form, Tc is highly soluble and weakly adsorbed onto mineral surfaces. Because the Oklo reactors are 2.0 billion years old, a majority of the {sup 99}Tc formed by natural fission reactions has decayed to {sup 99}Ru. Thus, this study is focused on Ru and the other constituents of the epsilon phase in order to investigate the occurrence and the fate of epsilon phase elements during the corrosion of this natural SNF. Samples from reactor zone (RZ)-10 (836, 819, 687); from RZ-13 (864, 910); from Okklobondo (943) were studied. High resolution transmission electron microscopy (HRTEM) and high-angle annular dark-field scanning TEM (HAADF-STEM) with energy dispersive X-ray analysis (EDX) were completed on thin foil specimens of uraninite from each reactor zone. Among these samples, no Ru-bearing phase is observed in 910 and 943. A Bi-Pd particle (40-60 nm), froodite, …

One way to reduce the computational cost of electronic structure calculations is to employ auxiliary basis expansions to approximate 4 center integrals in terms of 2 and 3-center integrals, usually using the variationally optimum Coulomb metric to determine the expansion coefficients. However the long-range decay behavior of the auxiliary basis expansion coefficients has not been characterized. We find that this decay can be surprisingly slow. Numerical experiments on linear alkanes and a toy model both show that the decay can be as slow as 1/r in the distance between the auxiliary function and the fitted charge distribution. The Coulomb metric fitting equations also involve divergent matrix elements for extended systems treated with periodic boundary conditions. An attenuated Coulomb metric that is short-range can eliminate these oddities without substantially degrading calculated relative energies. The sparsity of the fit coefficients is assessed on simple hydrocarbon molecules, and shows quite early onset of linear growth in the number of significant coefficients with system size using the attenuated Coulomb metric. This means it is possible to design linear scaling auxiliary basis methods without additional approximations to treat large systems.

Resistance upset welding is used to attach small diameter machined tubes to small gas vessels. Recently there has been interest in determining the level of residual stresses caused by this attachment method and its influence on environmental interactions. A test program was initiated to determine the residual stresses present due to welding using the nominal weld parameters and varying the interference between the foot and the counter bore. In this paper, the residual stress measurement technique is described, the welding conditions are provided, and the residual stress due to welding at the nominal conditions are presented.

Recent progresses in the study of jet modification in hotmedium and their consequences in high-energy heavy-ion collisions are reviewed. In particular, I will discuss energy loss for propagating heavy quarks and the resulting modified fragmentation function. Medium modification of the parton fragmentation function due to quark recombination are formulated within finite temperature field theory and their implication on the search for deconfined quark-gluon plasma is also discussed.

We present a novel technique for fitting rest frame I-bandlight curves on a data set of 42 type Ia supernovae (SNe Ia). Using the result of the fit, we construct a Hubble diagram with 26 SNe from the subset at 0.01 < z < 0.1. Adding two SNe at z {approx} 0.5 yields results consistent with a flat Lambda-dominated ''concordance universe'' (OmegaM,Omega Lambda) = (0.25, 0.75). For one of these, SN 2000fr, new near infrared data are presented. The high redshift supernova NIR data are also used to test for systematic effects in the use of SNe Ia as distance estimators. A flat, Lambda = 0, universe where the faintness of supernovae at z {approx} 0.5 is due to grey dust homogeneously distributed in the intergalactic medium is disfavored based on the high-z Hubble diagram using this small data-set. However, the uncertainties are large and no firm conclusion may be drawn. We explore the possibility of setting limits on intergalactic dust based on B - I and B - V color measurements, and conclude that about 20 well measured SNe are needed to give statistically significant results. We also show that the high redshift restframe I-band data points are better …

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.

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 caustic precipitation of plutonium (Pu) and uranium (U) from Pu and U containing waste solutions has been investigated to determine whether gadolinium (Gd) could be used as a neutron poison for precipitation with greater than a fissile mass containing both Pu and enriched U. Precipitation experiments were performed using both actual samples and simulant solutions with a range of 2.6-5.16 g/L U and 0-4.3 to 1 U to Pu. Analyses were performed on solutions at intermediate pH to determine the partitioning of elements for accident scenarios. When both Pu and U were present in the solution, precipitation began at pH 4.5 and by pH 7, 99 percent of Pu and U had precipitated. When complete neutralization was achieved at pH greater than 14 with 1.2 M excess OH-, greater than 99 percent of Pu, U, and Gd had precipitated. At pH greater than 14, the particles sizes were larger and the distribution was a single mode. The ratio of hydrogen to fissile atoms in the precipitate was determined after both settling and centrifuging and indicates that sufficient water was associated with the precipitates to provide the needed neutron moderation for Gd to prevent a criticality in solutions containing up …

ABSTRACT In the southeastern United States, coarse woody debris (CWD) typically harbors high densities of invertebrates. However, its importance as a foraging substrate for southeastern amphibians is relatively unknown. We examined effects of CWD manipulations on diet composition of southern toads (Bufo terrestris) in upland loblolly pine (Pinus taeda) stands in the Coastal Plain of South Carolina. Twelve 9.3-ha plots were assigned one of the following treatments: removal- all CWD _10 cm in diameter and _60 cm long removed; downed- five-fold increase in volume of down CWD; and unmanipulated control stands. We collected southern toads _4 cm snout-vent length (SVL) during 14 d sampling periods in June and October 2002, June 2003 and during a 28 d sampling period in April 2003. We collected 80, 36 and 35 southern toads in control, downed and removal treatments, respectively. We found no difference in relative abundance or frequency of invertebrate groups consumed among treatments (P.0.05). Average body weight (g), SVL (cm) and stomach content weight (g wet) of individuals also were similar among treatments (P . 0.05). The role of CWD as a foraging substrate for southern toads in loblolly pine stands of the southeastern Coastal Plain may be negligible, at least …

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The objective of the analysis is to examine the potential for lid ejection from a vented transuranic (TRU) waste drum due to pressure buildup caused by the deflagration of hydrogen and volatile organic compounds (VOCs) inside the drum. In this analysis, the AICC pressure for a stoichiometric mixture of VOCs is calculated and then compared against the experimental peak pressure of stoichiometric combustion of propane and hexane in a combustion chamber. The experimental peak pressures of propane and hexane are about 12 percent lower than the calculated AICC pressure. Additional losses in the drum are calculated due to venting of the gases, drum bulging, waste compaction, and heat losses from the presence of waste in the drum. After accounting for these losses, the final pressures are compared to the minimum observed pressure that ejects the lid from a TRU drum. The ejection pressure of 105 psig is derived from data that was recorded for a series of tests where hydrogen-air mixtures were ignited inside sealed TRU drums. Since the calculated pressures are below the minimum lid ejection pressure, none of the VOCs and the hydrogen (up to 4 percent) mixtures present in the TRU waste drum is expected to cause …

One of the problems in the high-power lasers design is in outcoupling of a powerful laser beam out of a vacuum volume into atmosphere. Usually the laser device is located inside a vacuum tank. The laser radiation is transported to the outside world through the transparent vacuum window. While considered transparent, some of the light passing through the glass is absorbed and converted to heat. For most applications, these properties are academic curiosities; however, in multi-kilowatt lasers, the heat becomes significant and can lead to a failure. The absorbed power can result in thermal stress, reduction of light transmission and, consequently, window damage. Modern optical technology has developed different types of glass (Silica, BK7, diamond, etc.) that have high thermal conductivity and damage threshold. However, for kilo- and megawatt lasers the issue still remains open. In this paper we present a solution that may relieve the heat load on the output window. We discuss advantages and issues of this particular window design.