The polymerase chain reaction (PCR) stands among the keystone technologies for analysis of biological sequence data. PCR is used to amplify DNA, to generate many copies from as little as a single template. This is essential, for example, in processing forensic DNA samples, pathogen detection in clinical or biothreat surveillance applications, and medical genotyping for diagnosis and treatment of disease. It is used in virtually every laboratory doing molecular, cellular, genetic, ecologic, forensic, or medical research. Despite its ubiquity, we lack the precise predictive capability that would enable detailed optimization of PCR reaction dynamics. In this LDRD, we proposed to develop Virtual PCR (VPCR) software, a computational method to model the kinetic, thermodynamic, and biological processes of PCR reactions. Given a successful completion, these tools will allow us to predict both the sequences and concentrations of all species that are amplified during PCR. The ability to answer the following questions will allow us both to optimize the PCR process and interpret the PCR results: What products are amplified when sequence mixtures are present, containing multiple, closely related targets and multiplexed primers, which may hybridize with sequence mismatches? What are the effects of time, temperature, and DNA concentrations on the concentrations …

We have studied the spin relaxation in diluted spin ice Ho{sub 2-x} Y{sub x} Ti{sub 2}O{sub 7} by means of neutron spin echo spectroscopy. Remarkably, the geometrical frustration is not relieved by doping with non-magnetic Y, and the dynamics of the freezing is unaltered in the spin echo time window up to x {approx_equal} 1.6. At higher doping with non-magnetic Y (x {ge} 1.6) a new relaxation process at relatively high temperature (up to at least T {approx_equal} 55 K) appears which is more than 10 times faster than the thermally activated main relaxation process. We find evidence that over the whole range of composition all Ho spins participate in the dynamics. These results are compared to a.c. susceptibility measurements of the diluted Ho and Dy spin ice systems. X-ray absorption fine structure (EXAFS) spectra and x-ray diffraction show that the samples are structurally well ordered.

Large-scale scientific computation and all of the disciplines that support and help validate it have been placed at the focus of Lawrence Livermore National Laboratory (LLNL) by the Advanced Simulation and Computing (ASC) program of the National Nuclear Security Administration (NNSA) and the Scientific Discovery through Advanced Computing (SciDAC) initiative of the Office of Science of the Department of Energy (DOE). The maturation of simulation as a fundamental tool of scientific and engineering research is underscored in the President's Information Technology Advisory Committee (PITAC) June 2005 finding that ''computational science has become critical to scientific leadership, economic competitiveness, and national security''. LLNL operates several of the world's most powerful computers--including today's single most powerful--and has undertaken some of the largest and most compute-intensive simulations ever performed, most notably the molecular dynamics simulation that sustained more than 100 Teraflop/s and won the 2005 Gordon Bell Prize. Ultrascale simulation has been identified as one of the highest priorities in DOE's facilities planning for the next two decades. However, computers at architectural extremes are notoriously difficult to use in an efficient manner. Furthermore, each successful terascale simulation only points out the need for much better ways of interacting with the resulting avalanche of …

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This report is one of the major products and deliverables of the Groundwater Remediation and Closure Assessment Projects detailed work plan for FY 2006, and reflects the requirements of The Groundwater Performance Assessment Project Quality Assurance Plan (PNNL-15014). This report presents the results of groundwater and vadose zone monitoring and remediation for fiscal year 2005 on the U.S. Department of Energy's Hanford Site, Washington. The most extensive contaminant plumes in groundwater are tritium, iodine-129, and nitrate, which all had multiple sources and are very mobile in groundwater. The largest portions of these plumes are migrating from the central Hanford Site to the southeast, toward the Columbia River. Carbon tetrachloride and associated organic constituents form a relatively large plume beneath the west-central part of the Hanford Site. Hexavalent chromium is present in plumes beneath the reactor areas along the river and beneath the central part of the site. Strontium-90 exceeds standards beneath all but one of the reactor areas. Technetium-99 and uranium plumes exceeding standards are present in the 200 Areas. A uranium plume underlies the 300 Area. Minor contaminant plumes with concentrations greater than standards include carbon-14, cesium-137, cis-1,2-dichloroethene, cyanide, fluoride, plutonium, and trichloroethene. Monitoring for the Comprehensive Environmental Response, …

On September 15, 2005, the House of Representatives approved H. Res. 437, which created the Select Bipartisan Committee to Investigate the Preparation for and Response to Hurricane Katrina (“the Select Committee”). According to the resolution, the Committee was charged with conducting “a full and complete investigation and study and to report its findings to the House not later than February 15, 2006, regarding— (1) the development, coordination, and execution by local, State, and Federal authorities of emergency response plans and other activities in preparation for Hurricane Katrina; and (2) the local, State, and Federal government response to Hurricane Katrina.” The Committee presents the report narrative and the findings that stem from it to the U.S. House of Representatives and the American people for their consideration. Members of the Select Committee agree unanimously with the report and its findings. Other Members of Congress who participated in the Select Committee’s hearings and investigation but were not official members of the Select Committee, while concurring with a majority of the report’s findings, have presented additional views as well, which we offer herein on their behalf. First and foremost, this report is issued with our continued thoughts and prayers for Katrina’s victims. Their families. …

Welcome to the 2006 joint meeting of the fourth Genomics:GTL Contractor-Grantee Workshop and the six Metabolic Engineering Working Group Inter-Agency Conference. The vision and scope of the Genomics:GTL program continue to expand and encompass research and technology issues from diverse scientific disciplines, attracting broad interest and support from researchers at universities, DOE national laboratories, and industry. Metabolic engineering's vision is the targeted and purposeful alteration of metabolic pathways to improve the understanding and use of cellular pathways for chemical transformation, energy transduction, and supramolecular assembly. These two programs have much complementarity in both vision and technological approaches, as reflected in this joint workshop. GLT's challenge to the scientific community remains the further development and use of a broad array of innovative technologies and computational tools to systematically leverage the knowledge and capabilities brought to us by DNA sequencing projects. The goal is to seek a broad and predictive understanding of the functioning and control of complex systems--individual microbes, microbial communities, and plants. GTL's prominent position at the interface of the physical, computational, and biological sciences is both a strength and challenge. Microbes remain GTL's principal biological focus. In the complex 'simplicity' of microbes, they find capabilities needed by DOE and …

Sum frequency generation (SFG), a second-order nonlinear optical process, is electric-dipole forbidden in systems with inversion symmetry. As a result, it has been used to study chiral media and interfaces, systems intrinsically lacking inversion symmetry. This thesis describes recent progresses in the applications of and new insights into SFG from chiral media and interfaces. SFG from solutions of chiral amino acids is investigated, and a theoretical model explaining the origin and the strength of the chiral signal in electronic-resonance SFG spectroscopy is discussed. An interference scheme that allows us to distinguish enantiomers by measuring both the magnitude and the phase of the chiral SFG response is described, as well as a chiral SFG microscope producing chirality-sensitive images with sub-micron resolution. Exploiting atomic and molecular parity nonconservation, the SFG process is also used to solve the Ozma problems. Sum frequency vibrational spectroscopy is used to obtain the adsorption behavior of leucine molecules at air-water interfaces. With poly(tetrafluoroethylene) as a model system, we extend the application of this surface-sensitive vibrational spectroscopy to fluorine-containing polymers.

The complexes [Ce(tmtaa)2], [Ce(tmtaa)(tmtaaH)]and[Ce2(tmtaa)3(thf)2]are obtained from Ce[N(SiMe3)2]3 and tmtaaH2, themacrocyclic ligand 6,8,15,17-tetramethyldibenzotetraaza[14]-annulene,depending on the stoichiometry, solvent and temperature. The crystalstructure of Ce(tmtaa)2 is isostructural with Zr(tmtaa)2, howevermagnetic susceptibility measurements in the range 5-300 K show thatCe(tmtaa)2 is not diamagnetic, but is a temperature-independentparamagnet (TIP), similar to Ce(cot)2, cerocene.

The purpose of this SAND Report is to document efforts in the extraction and failure analyses of sleeve-style Lightning Arrestor Connectors (LACs). Several MC3080 and MC3079 LACs were recovered from the field and tested as part of the Enhanced Surveillance Campaign. A portion of these LACs failed retesting. Terry Ernest (01733), the LAC Component Engineer, provided eleven MC3080 LACs for evaluation where four of the LACs failed IR/DCW and one failed FRB requirements. The extraction of rutile sleeves from failed LACs was required to determine the source of failure. Rutile sleeves associated with connector function failures were examined for cracks, debris as well as any other anomalies which could have caused the LAC to not function properly. Sleeves that failed FRB or that experienced high FRB exhibited high symmetry, smooth surface, long-flow amicon, and slightly over-sized inside diameter. LACs that failed DCW or IR requirements had rutile sleeves that exhibited breakdown tracks.

This paper assesses relevant knowledge within the alternative fuels community and recommends transitional strategies and tactics that will further the hydrogen transition in the transportation sector.

Detailed statistical analysis of the experimental data from testing of alumina-loaded epoxy (ALOX) composites was conducted to better understand influences of the selected compositional properties on the compressive strength of these ALOX composites. Analysis of variance (ANOVA) for different models with different sets of parameters identified the optimal statistical model as, y{sub l} = -150.71 + 29.72T{sub l} + 204.71D{sub l} + 160.93S{sub 1l} + 90.41S{sub 2l}-20.366T{sub l}S{sub 2l}-137.85D{sub l}S{sub 1l}-90.08D{sub l}S{sub 2l} where y{sub l} is the predicted compressive strength, T{sub l} is the powder type, D{sub l} is the density as the covariate for powder volume concentration, and S{sub il}(i=1,2) is the strain rate. Based on the optimal statistical model, we conclude that the compressive strength of the ALOX composite is significantly influenced by the three main factors examined: powder type, density, and strain rate. We also found that the compressive strength of the ALOX composite is significantly influenced by interactions between the powder type and the strain rate and between the powder volume concentration and the strain rate. However, the interaction between the powder type and the powder volume concentration may not significantly influence the compressive strength of the ALOX composite.

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The Modular Caustic-Side Solvent Extraction (CSSX) Unit (MCU) and the Salt Waste Processing Facility (SWPF) will produce a Deactivated Salt Solution (DSS) that will go to the Saltstone Production Facility (SPF). Recent information indicates that solvent entrainment in the DSS is larger than expected. The main concern is with Isopar{reg_sign} L, the diluent in the solvent mixture, and its flammability in the saltstone vault. If it is assumed that all the Isopar{reg_sign} L is released instantaneously into the vault from the curing grout before each subsequent pour; the Isopar{reg_sign} L in the vault headspace is well mixed; and each pour displaces an equivalent volume of headspace, the allowable concentration of Isopar{reg_sign} L in the DSS sent to SPF has been calculated at approximately 4 ppm. The amount allowed would be higher, if the release from grout were significantly less. The Savannah River National Laboratory was tasked with determining the release of Isopar{reg_sign} L from saltstone prepared with a simulated DSS with Isopar{reg_sign} L concentrations ranging from 50 mg/L to 200 mg/L in the salt fraction and with test temperatures ranging from ambient to 95 C. The results from the curing of the saltstone showed that the Isopar{reg_sign} L release data …

This report talks about Characterization And Monitoring Of Natural Attenuation Of Chlorinated Solvents In Ground Water: A Systems Approach

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1995 Army Team Lead Desk Material - 1991 BRAC Commission Final Report.

This report represents the proceedings of a conference held on February 16, 2006, at the Texas A&M University-Corpus Christi campus regarding Texas Gulf Coast aquifers.