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 …

Bioenergy crops, which displace fossil fuels when used to produce ethanol, biobased products, and/or electricity, have the potential to further reduce atmospheric carbon levels by building up soil carbon levels, especially when planted on lands where these levels have been reduced by intensive tillage. The purpose of this study is to improve the characterization of the soil carbon (C) sequestration for bioenergy crops (switchgrass, poplars, and willows) in the Greenhouse gases, Regulated Emissions, and Energy Use in Transportation (GREET) model (Wang 1999) by using the latest results reported in the literature and by Oak Ridge National Laboratory (ORNL). Because soil carbon sequestration for bioenergy crops can play a significant role in reducing greenhouse gas (GHG) emissions for cellulosic ethanol, it is important to periodically update the estimates of soil carbon sequestration from bioenergy crops as new and better data become available. We used the three-step process described below to conduct our study.

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.

We report on an improved measurement of the Cabibbo-Kobayashi-Maskawa CP-violating phase {gamma} through a Dalitz plot analysis of neutral D meson decays to K{sub s}{sup 0}{pi}{sup +}{pi}{sup -} and K{sub s}{sup 0}K{sup +}K{sup -} produced in the processes B{sup {-+}} {yields} DK{sup {-+}}, B{sup {-+}} {yields} D* K{sup {-+}} with D* {yields} D{pi}{sup 0}, D{gamma}, and B{sup {-+}} {yields} DK*{sup {-+}} with K8{sup {-+}} {yields} K{sub S}{sup 0}{pi}{sup {-+}}. Using a sample of 383 million B{bar B} pairs collected by the BABAR detector, we measure {gamma} = (76 {+-} 22 {+-} 5{+-} 5){sup o} (mod 180{sup o}), where the first error is statistical, the second is the experimental systematic uncertainty and the third reflects the uncertainty on the description of the Dalitz plot distributions. The corresponding two standard deviation region is 29{sup o} < {gamma} < 122{sup o}. This result has a significance of direct CP violation ({gamma} {ne} 0) of 3.0 standard deviations.

We report an analysis of {tau}{sup -} decaying into {omega}{pi}{sup -} {nu}{sub {tau}} with {omega} {yields} {pi}{sup +}{pi}{sup -}{pi}{sup 0} using a data sample containing nearly 320 million {tau} pairs collected with the BABAR detector at the PEP-II B-Factory. We find no evidence for second-class currents and we set an upper limit of 0.69% at 90% confidence level for the fraction of second-class currents in this decay mode.

The authors present measurements of branching fractions for five B-meson decays to two-body charmless final states. The data, collected with the BABAR detector at the Stanford Linear Accelerator Center, represent 459 million B{bar B} pairs. The results for branching fractions are, in units of 10{sup -6} (upper limits at 90% C.L.): {Beta}(B{sup +} {yields} {eta}{rho}{sup +}) = 9.9 {+-} 1.2 {+-} 0.8, {Beta}(B{sup 0} {yields} {eta}{prime}{eta}) = 0.5 {+-} 0.4 {+-} 0.1 (< 1.2), {Beta}(B{sup 0} {yields} {eta}{pi}{sup 0}) = 0.9 {+-} 0.4 {+-} 0.1 (< 1.5), {Beta}(B{sup 0} {yields} {eta}{prime}{pi}{sup 0}) = 0.9 {+-} 0.4 {+-} 0.1 (< 1.5), and {Beta}(B{sup 0}{sup 0} {yields} {omega}{pi}{sup 0}) = {eta}{rho}{sup +} mode, they measure the charge asymmetry {Alpha}{sub ch} (B{sup +} {yields} {eta}{rho}{sup +}) = 0.13 {+-} 0.11 {+-} 0.02.

Petascale systems are in existence today and will become common in the next few years. Such systems are inevitably very complex, highly distributed and heterogeneous. Monitoring a petascale system in real-time and understanding its status at any given moment without impacting its performance is a highly intricate task. Common approaches and off-the-shelf tools are either unusable, do not scale, or severely impact the performance of the monitored servers. This paper describes unobtrusive monitoring software developed at Stanford Linear Accelerator Center (SLAC) for a highly distributed petascale production data set. The paper describes the employed solutions, the lessons learned, the problems still to be addressed, and explains how the system can be reused elsewhere.

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.

Recovery and comparison of toolmarks, footprint impressions, and fractured surfaces connected to a crime scene are of great importance in forensic science. The purpose of this project is to provide statistical tools for the validation of the proposition that particular manufacturing processes produce marks on the work-product (or tool) that are substantially different from tool to tool. The approach to validation involves the collection of digital images of toolmarks produced by various tool manufacturing methods on produced work-products and the development of statistical methods for data reduction and analysis of the images. The developed statistical methods provide a means to objectively calculate a ''degree of association'' between matches of similarly produced toolmarks. The basis for statistical method development relies on ''discriminating criteria'' that examiners use to identify features and spatial relationships in their analysis of forensic samples. The developed data reduction algorithms utilize the same rules used by examiners for classification and association of toolmarks.

The purpose of the Financial Analysis for Phase 1 Privatization for the Tank Farm Contractor is to provide a third-party quantitative and qualitative cost and schedule risk analysis of HNF-1946. The purpose of this Financial Analysis for Phase 1 Privatization for the Tank Farm Contractor (TFC) is to document the results of the risk-based financial analysis of HNF-1946, Programmatic Baseline Summary for Phase 1 Privatization f o r the Tank Farm Contractor (Diediker 2000). This analysis was performed to evaluate how well the proposed baseline meets the U. S. Department of Energy, Office of River Protection (ORP) Letter OO-MSO-009, ''Contract NO. DE-AC06-99RL14047--The US Department of Energy, Office of River Protection (ORP) Mission Planning Guidance for Fiscal Year (FY) 2002--Revision 1'' (Short 2000). The letter requires a confidence level in the baseline schedule that is consistent with the Phase 1A readiness-to-proceed (RTP) assessment conducted in fiscal year (FY) 1998. Because the success of the project depends not only on the budget but also on the schedule, this risk analysis addresses both components of the baseline.

The primary goal of this program is to develop a commercially viable enthalpy exchangers that exhibits performance comparable to state-of-the-art exchangers, meets flammability test standards, supports no biological growth, maintains mechanical integrity for a 10 year life (typical of competitive warrantees) and exhibits a total media raw material cost of approximately 1/5 of that of the competition. The first three program tasks were devoted to: (1) gathering background information on competitors and their methods of manufacturing; (2) establishing experimental and evaluation procedures for the program; (3) identifying potential desiccants, supports and binders to be tested; (4) preparing matrix combinations on a laboratory scale; (5) testing component combinations for equilibrium moisture uptakes at different relative humidities (isotherms) and dynamic moisture adsorption rates; (6) using media adsorption properties to models to predict exchanger performance; (7) estimating ease of manufacture and finished wheel costs; and (8) calculating raw material, wheel and cassette costs based on the best media formulations. Since the rotary enthalpy exchangers have high rotational speeds, uptake rate is at least as important as equilibrium moisture uptake. Therefore, a procedure and apparatus were developed to determine adsorption rate so that the Lewis number (the ratio of mass transfer resistance to heat …

In this paper we use numerical simulation to investigate shock-induced ignition and combustion of a hydrocarbon gas. The focus of this paper is on quantifying the effect of fidelity in the chemical kinetics on the overall solution. We model the system using the compressible Navier Stokes equations for a reacting mixture. These equations express conservation of species mass, momentum, total energy.

Thiobacillus denitrificans is one of the few known obligate chemolithoautotrophic bacteria capable of energetically coupling thiosulfate oxidation to denitrification as well as aerobic respiration. As very little is known about the differential expression of genes associated with ke chemolithoautotrophic functions (such as sulfur-compound oxidation and CO2 fixation) under aerobic versus denitrifying conditions, we conducted whole-genome, cDNA microarray studies to explore this topic systematically. The microarrays identified 277 genes (approximately ten percent of the genome) as differentially expressed using Robust Multi-array Average statistical analysis and a 2-fold cutoff. Genes upregulated (ca. 6- to 150-fold) under aerobic conditions included a cluster of genes associated with iron acquisition (e.g., siderophore-related genes), a cluster of cytochrome cbb3 oxidase genes, cbbL and cbbS (encoding the large and small subunits of form I ribulose 1,5-bisphosphate carboxylase/oxygenase, or RubisCO), and multiple molecular chaperone genes. Genes upregulated (ca. 4- to 95-fold) under denitrifying conditions included nar, nir, and nor genes (associated respectively with nitrate reductase, nitrite reductase, and nitric oxide reductase, which catalyze successive steps of denitrification), cbbM (encoding form II RubisCO), and genes involved with sulfur-compound oxidation (including two physically separated but highly similar copies of sulfide:quinone oxidoreductase and of dsrC, associated with dissimilatory sulfite reductase). Among …

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The growth of nanocrystalline MoO{sub 3} islands on Au(111) using physical vapor deposition of Mo has been studied by scanning tunneling microscopy (STM) and low energy electron diffraction (LEED). The growth conditions affect the shape and distribution of the MoO{sub 3} nanostructures, providing a means of preparing materials with different percentages of edge sites that may have different chemical and physical properties than atoms in the interior of the nanostructures. MoO{sub 3} islands were prepared by physical vapor deposition of Mo and subsequent oxidation by NO{sub 2}exposure at temperatures between 450 K and 600 K. They exhibit a crystalline structure with a c(4x2) periodicity relative to unreconstructed Au(111). While the atomic-scale structure is identical to that of MoO{sub 3} islands prepared by chemical vapor deposition, we demonstrate that the distribution of MoO{sub 3} islands on the Au(111) surface reflects the distribution of Mo clusters prior to oxidation although the growth of MoO{sub 3} involves long-range mass transport via volatile MoO{sub 3} precursor species. The island morphology is kinetically controlled at 450 K, whereas an equilibrium shape is approached at higher preparation temperatures or after prolonged annealing at the elevated temperature. Mo deposition at or above 525 K leads to the …

A dosage analysis of gene expression was conducted using aneuploids of maize. The findings of this project led to the concept that regulatory genes in higher eukaryotes has mostly dosage dependent and are the underlying basis of quantitative traits and aneuploid syndromes.

The current experimental lower bound on the Higgs mass significantly restricts the allowed parameter space in most realistic supersymmetric models, with the consequence that these models exhibit significant fine-tuning. We propose a solution to this `supersymmetric little hierarchy problem'. We consider scenarios where the stop masses are relatively heavy - in the 500 GeV to a TeV range. Radiative stability of the Higgs soft mass against quantum corrections from the top quark Yukawa coupling is achieved by imposing a global SU(3) symmetry on this interaction. This global symmetry is only approximate - it is not respected by the gauge interactions. A subgroup of the global symmetry is gauged by the familiar SU(2) of the Standard Model. The physical Higgs is significantly lighter than the other scalars because it is the pseudo-Goldstone boson associated with the breaking of this symmetry. Radiative corrections to the Higgs potential naturally lead to the right pattern of gauge and global symmetry breaking. We show that both the gauge and global symmetries can be embedded into a single SU(6) grand unifying group, thereby maintaining the prediction of gauge coupling unification. Among the firm predictions of this class of models are new states with the quantum numbers …

This report describes the groundwater monitoring and corrective-action program at the M-Area Hazardous Waste Management Facility (HWMF) and the Metallurgical Laboratory (Met Lab) HWMF at the Savannah River Site (SRS) during the third and fourth quarters of 2001. The report also provides a summary of the corrective-action program for the entire year. This program is required by South Carolina Resource Conservation and Recovery Act (RCRA) Hazardous Waste Permit SC1 890 008 989 and Section 264.100(g) of the South Carolina Hazardous Waste Management Regulations.

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.

The authors designed, implemented and tested cryogenic RF filters with zero DC resistance, based on wires with a superconducting core inside a resistive sheath. The superconducting core allows low frequency currents to pass with negligible dissipation. Signals above the cutoff frequency are dissipated in the resistive part due to their small skin depth. The filters consist of twisted wire pairs shielded with copper tape. Above approximately 1 GHz, the attenuation is exponential in {radical}{omega}, as typical for skin depth based RF filters. By using additional capacitors of 10 nF per line, an attenuation of at least 45 dB above 10 MHz can be obtained. Thus, one single filter stage kept at mixing chamber temperature in a dilution refrigerator is sufficient to attenuate room temperature black body radiation to levels corresponding to 10 mK above about 10 MHz.

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.

The CeTIn_5 superconductors (T=Co, Rh, or Ir) have generated great interest due to their relatively high transition temperatures, non-Fermi liquid behavior, and their proximity to antiferromagnetic order and quantum critical points. In contrast to small changes with the T-species, electron doping in CeT(In_1-x M_x)_5 with $M$=Sn and hole doping with Cd or Hg have a dramatic effect on the electronic properties at very low concentrations. The present work reports local structure measurements usingthe extended x-ray absorption fine-structure (EXAFS) technique that address the substituent atom distribution as a function of T, M, and x, in the vicinity of the superconducting phase. Together with previous measurements for M=Sn, the proportion of the $M$ atom residing on the In(1) site, f_\textrm In(1), increases in the order M=Cd, Sn, and Hg, ranging from about 40\percent to 70percent, showing a strong preference for each of these substituents to occupy the In(1) site (random occupation = 20percent). In addition, f_In(1) ranges from 70percent to 100percent for M=Hg in the order T=Co,Rh, and Ir. These fractions track the changes in the atomic radii of the various species, and help explain the sharp dependence of $T_c$ on substituting into the In site. However, it is difficult to reconcile …

Partial ytterbium f-orbital occupancy (i.e., intermediate valence) and open-shell singlet formation are established for a variety of bipyridine and diazabutadiene adducts with decamethylytterbocene, (C5Me5)2Yb, abbreviated as Cp*2Yb. Data used to support this claim include ytterbium valence measurements using Yb LIII-edge X-ray absorption near-edge structure spectroscopy, magnetic susceptibility, and complete active space self-consistent field (CASSCF) multiconfigurational calculations, as well as structural measurements compared to density functional theory calculations. The CASSCF calculations indicate that the intermediate valence is the result of a multiconfigurational ground-state wave function that has both an open-shell singlet f13(?*)1, where pi* is the lowest unoccupied molecular orbital of the bipyridine or dpiazabutadiene ligands, and a closed-shell singlet f14 component. A number of other competing theories for the unusual magnetism in these materials are ruled out by the lack of temperature dependence of the measured intermediate valence. These results have implications for understanding chemical bonding not only in organolanthanide complexes but also for f-element chemistry in general, as well as understanding magnetic interactions in nanoparticles and devices.

The Human Resources Staffing Plan quantified the equivalent staffing needs required for the Tank Farm Contractor (TFC) and its subcontractors to execute the readiness to proceed baseline between FY 2000-2008. The TFC staffing needs were assessed along with the staffings needs of Fluor Hanford and the privatization contractor. The plan then addressed the staffing needs and recruitment strategies required to execute the baseline.