The transient deflagration code DPAC (Deflagration Pressure Analysis Code) has been upgraded for use in modeling hydrogen deflagration transients. The upgraded code is benchmarked using data from vented hydrogen deflagration tests conducted at the HYDRO-SC Test Facility at the University of Pisa. DPAC originally was written to calculate peak deflagration pressures for deflagrations in radioactive waste storage tanks and process facilities at the Savannah River Site. Upgrades include the addition of a laminar flame speed correlation for hydrogen deflagrations and a mechanistic model for turbulent flame propagation, incorporation of inertial effects during venting, and inclusion of the effect of water vapor condensation on vessel walls. In addition, DPAC has been coupled with CEA, a NASA combustion chemistry code. The deflagration tests are modeled as end-to-end deflagrations. The improved DPAC code successfully predicts both the peak pressures during the deflagration tests and the times at which the pressure peaks.

Packaging options are evaluated for compliance with safety requirements for shipment of mixed actinide oxides packaged in a 9975 Primary Containment Vessel (PCV). Radiolytic gas generation rates, PCV internal gas pressures, and shipping windows (times to reach unacceptable gas compositions or pressures after closure of the PCV) are calculated for shipment of a 9975 PCV containing a plastic bottle filled with plutonium and uranium oxides with a selected isotopic composition. G-values for radiolytic hydrogen generation from adsorbed moisture are estimated from the results of gas generation tests for plutonium oxide and uranium oxide doped with curium-244. The radiolytic generation of hydrogen from the plastic bottle is calculated using a geometric model for alpha particle deposition in the bottle wall. The temperature of the PCV during shipment is estimated from the results of finite element heat transfer analyses.

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These presentation visuals introduce the National Center for Nuclear Security. Its chartered mission is to enhance the Nation’s verification and detection capabilities in support of nuclear arms control and nonproliferation through R&D activities at the NNSS. It has three focus areas: Treaty Verification Technologies, Nonproliferation Technologies, and Technical Nuclear Forensics. The objectives of nuclear forensics are to reduce uncertainty in the nuclear forensics process & improve the scientific defensibility of nuclear forensics conclusions when applied to nearsurface nuclear detonations. Research is in four key areas: Nuclear Physics, Debris collection and analysis, Prompt diagnostics, and Radiochemistry.

Interaction of a high intensity laser with matter may generate an ionizing radiation hazard. Very limited studies have been made, however, on the laser-induced radiation protection issue. This work reviews available literature on the physics and characteristics of laser-induced X-ray hazards. Important aspects include the laser-to-electron energy conversion efficiency, electron angular distribution, electron energy spectrum and effective temperature, and bremsstrahlung production of X-rays in the target. The possible X-ray dose rates for several femtosecond Ti:sapphire laser systems used at SLAC, including the short pulse laser system for the Matter in Extreme Conditions Instrument (peak power 4 TW and peak intensity 2.4 x 10{sup 18} W/cm{sup 2}) were analysed. A graded approach to mitigate the laser-induced X-ray hazard with a combination of engineered and administrative controls is also proposed.

Using four genomes: Chamydomonas reinhardtii, Agaricus bisporus, Aspergillus carbonarius, and Sporotricum thermophile with EST coverage of 2.9x, 8.9x, 29.5x, and 46.3x respectively, we identified 11 alternative splicing (AS) types that were dominated by intron retention (RI; biased toward short introns) and found 15, 35, 52, and 63percent AS of multiexon genes respectively. Genes with AS were more ancient, and number of AS correlated with number of exons, expression level, and maximum intron length of the gene. Introns with tendency to be retained had either stop codons or length of 3n+1 or 3n+2 presumably triggering nonsense-mediated mRNA decay (NMD), but introns retained in major isoforms (0.2-6percent of all introns) were biased toward 3n length and stop codon free. Stopless introns were biased toward phase 0, but 3n introns favored phase 1 that introduced more flexible and hydrophilic amino acids on both ends of introns which would be less disruptive to protein structure. We proposed a model in which minor RI intron could evolve into major RI that could facilitate intron loss through exonization.

Using the integral field spectrograph OSIRIS, on the Keck II telescope, broad near-infrared H and K-band spectra of the young exoplanet HR8799b have been obtained. In addition, six new narrow-band photometric measurements have been taken across the H and K bands. These data are combined with previously published photometry for an analysis of the planet's atmospheric properties. Thick photospheric dust cloud opacity is invoked to explain the planet's red near-IR colors and relatively smooth near-IR spectrum. Strong water absorption is detected, indicating a Hydrogen-rich atmosphere. Only weak CH{sub 4} absorption is detected at K band, indicating efficient vertical mixing and a disequilibrium CO/CH{sub 4} ratio at photospheric depths. The H-band spectrum has a distinct triangular shape consistent with low surface gravity. New giant planet atmosphere models are compared to these data with best fitting bulk parameters, T{sub eff} = 1100K {+-} 100 and log(g) = 3.5 {+-} 0.5 (for solar composition). Given the observed luminosity (log L{sub obs}/L{sub {circle_dot}} {approx} -5.1), these values correspond to a radius of 0.75 R{sub Jup{sub 0.12}{sup +0.17}} and mass {approx} 0.72 M{sub Jup{sub -0.6}{sup +2.6}} - strikingly inconsistent with interior/evolution models. Enhanced metallicity (up to {approx} 10 x that of the Sun) along with …

A new tool, DUK, is developed to perform matching task. Matching is to find whether a query sequence partially or totally matches given reference sequences or not. Matching is similar to alignment. Indeed many traditional analysis tasks like contaminant removal use alignment tools. But for matching, there is no need to know which bases of a query sequence matches which position of a reference sequence, it only need know whether there exists a match or not. This subtle difference can make matching task much faster than alignment. DUK is accurate, versatile, fast, and has efficient memory usage. It uses Kmer hashing method to index reference sequences and Poisson model to calculate p-value. DUK is carefully implemented in C++ in object oriented design. The resulted classes can also be used to develop other tools quickly. DUK have been widely used in JGI for a wide range of applications such as contaminant removal, organelle genome separation, and assembly refinement. Many real applications and simulated dataset demonstrate its power.

Manual library construction is a limiting factor in Illumina sequencing. Constructing libraries by hand is costly, time-consuming, low-throughput, and ergonomically hazardous, and constructing multiple libraries introduces risk of library failure due to pipetting errors. The ability to construct multiple libraries simultaneously in automated fashion represents significant cost and time savings. Here we present a strategy to construct up to 96 unamplified indexed libraries using Illumina TruSeq reagents and a Biomek FX robotic platform. We also present data to indicate that this library construction method has little or no risk of cross-contamination between samples.

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We examine a double trace deformation of SU(N) Yang-Mills theory which, for large N and large volume, is equivalent to unmodified Yang-Mills theory up to O(1/N{sup 2}) corrections. In contrast to the unmodified theory, large N volume independence is valid in the deformed theory down to arbitrarily small volumes. The double trace deformation prevents the spontaneous breaking of center symmetry which would otherwise disrupt large N volume independence in small volumes. For small values of N, if the theory is formulated on R{sup 3} x S{sup 1} with a sufficiently small compactification size L, then an analytic treatment of the non-perturbative dynamics of the deformed theory is possible. In this regime, we show that the deformed Yang-Mills theory has a mass gap and exhibits linear confinement. Increasing the circumference L or number of colors N decreases the separation of scales on which the analytic treatment relies. However, there are no order parameters which distinguish the small and large radius regimes. Consequently, for small N the deformed theory provides a novel example of a locally four-dimensional pure gauge theory in which one has analytic control over confinement, while for large N it provides a simple fully reduced model for Yang-Mills theory. …

We propose and analyze a new tool to help solve sparse linear least-squares problems min{sub x} {parallel}Ax-b{parallel}{sub 2}. Our method is based on a sparse QR factorization of a low-rank perturbation {cflx A} of A. More precisely, we show that the R factor of {cflx A} is an effective preconditioner for the least-squares problem min{sub x} {parallel}Ax-b{parallel}{sub 2}, when solved using LSQR. We propose applications for the new technique. When A is rank deficient we can add rows to ensure that the preconditioner is well-conditioned without column pivoting. When A is sparse except for a few dense rows we can drop these dense rows from A to obtain {cflx A}. Another application is solving an updated or downdated problem. If R is a good preconditioner for the original problem A, it is a good preconditioner for the updated/downdated problem {cflx A}. We can also solve what-if scenarios, where we want to find the solution if a column of the original matrix is changed/removed. We present a spectral theory that analyzes the generalized spectrum of the pencil (A*A,R*R) and analyze the applications.

This Report is Description of Sensory Transduction in Microorganisms at Gordon Conference.

In this paper, we present the recent results of our research on the ultra-high power fast silicon RF switch and its application on active X-Band RF pulse compression systems. This switch is composed of a group of PIN diodes on a high purity silicon wafer and has achieved a switching time of 300ns. The wafer is inserted into a cylindrical waveguide operating in the TE01 mode. Switching is performed by injecting carriers into the bulk silicon through a high current pulse. The RF energy is stored in a room-temperature, high-Q 375 ns delay line; it is then extracted out of the line in a short time using the switch. The pulse compression system has achieved a gain of 8, which is the ratio between output and input power.

The Linac Coherent Light Source (LCLS) is a SASE x-ray Free-Electron Laser (FEL) based on the final kilometer of the Stanford Linear Accelerator. One of the most critical diagnostic devices is the bunch length monitor (BLM), which is to be installed right after each compressor utilizing coherent radiation from the last bending magnet. We describe the components and the optical layout of such a BLM. Based on the setup geometry, we discuss some issues about the coherent radiation signal.

The Linac Coherent Light Source (LCLS) is a SASE x-ray Free-Electron Laser (FEL) based on the final kilometer of the Stanford Linear Accelerator. Such an FEL requires a high energy, high brightness electron beam to drive the FEL instability to saturation. When fed by an RF-photocathode gun, and modified to include two bunch compressor chicanes, the SLAC linac will provide such a high quality beam at 14 GeV and 1-{micro}m normalized emittance. In this paper, we report on recent linac studies, including beam stability and tolerances, longitudinal and transverse feedback systems, conventional and time-resolved diagnostics, and beam collimation systems. Construction and installation of the injector through first bunch compressor will be completed by December 2006, and electron commissioning is scheduled to begin in January of 2007.

The long-term corrosion test facility (LTCTF) at the Lawrence Livermore National Laboratory (LLNL) consisted of 22 vessels that housed more than 7,000 corrosion test specimens from carbon steels to highly corrosion resistant materials such Alloy 22 and Ti Grade 7. The specimens from LTCTF range from standard weight-loss coupons to U-bend specimens for testing susceptibility to environmentally assisted cracking. Each vessel contained approximately 1000 liters of concentrated brines at 60 C or 90 C. The LTCTF started its operations in late 1996. The thousands of specimens from the LTCTF were removed in August-September 2006. The specimens are being catalogued and stored for future characterization. Previously removed specimens (e.g. 1 and 5 years) are also archived for further studies.

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We present an analysis of inclusive {Omega}{sub c}{sup 0} baryon production and decays in 230.5 fb{sup -1} of data recorded with the BABAR detector at the PEP-II asymmetric-energy e{sup +}e{sup -} collider at the Stanford Linear Accelerator Center. {Omega}{sub c}{sup 0} baryons are reconstructed in four final states ({Omega}{sup -}{pi}{sup +}, {Omega}{sup -}{pi}{sup +}{pi}{sup 0}, {Omega}{sup -}{pi}{sup +}{pi}{sup +}{pi}{sup -}, {Xi}{sup -}K{sup -}{pi}{sup +}{pi}{sup +}) and the ratios of branching fractions for these final states are measured. We also measure the momentum spectrum of the {Omega}{sub c}{sup 0} baryons in the e{sup +}e{sup -} center-of-mass frame. From the spectrum, they observe {Omega}{sub c}{sup 0} production from B decays and in c{bar c} events, and extract the two rates of production.

A study of breakdown mechanism has been initiated at the Argonne Wakefield Accelerator (AWA). Breakdown may include several factors such as local field enhancement, explosive electron emission, Ohmic heating, tensile stress produced by electric field, and others. The AWA is building a dedicated facility to test various models for breakdown mechanisms and to determine the roles of different factors in the breakdown. We plan to trigger breakdown events with a high-powered laser at various wavelengths (IR to UV) to determine the role of explosive electron emission in the breakdown process. Another experimental idea follows from the recent work on a Schottky-enabled photoemission in an RF photoinjector [1] that allows us to determine in situ the field enhancement factor on a cathode surface. Monitoring the field enhancement factor before and after the breakdown can shed some light on a number of observations such as the crater formation process.

Solvation of small and large clusters are studied by simulation, considering a range of solvent-solute attractive energy strengths. Over a wide range of conditions, both for solvation in the Lennard-Jones liquid and in the SPC model of water, it is shown that the mean solvent density varies linearly with changes in solvent-solute adhesion or attractive energy strength. This behavior is understood from the perspective of Weeks theory of solvation [Ann. Rev. Phys. Chem. 2002, 53, 533] and supports theories based upon that perspective.

There is renewed interest in the United States (U.S.) to construct new Generation III and III+ reactors within the next decade and Generation IV reactors in the future. Licensing by the U.S. Nuclear Regulatory Commission (NRC) is a significant consideration and these new plants may pose new challenges. One such challenge is the advances in human factors engineering (HFE) methods that are used. These methods are used to design and evaluate the HFE aspects of a plant, such as the human-system interface (HSI). These methods are important because NRC HFE reviews are design process oriented, thus, the criteria are mostly technology neutral with regard to reactor design.[1] However, the HFE review criteria are not neutral with respect to the HFE methods that are used as part of the design process This will be important for new reactor reviews because the diversity of reactor types, HSIs, and operational concepts will increase, especially for Generation III+ and IV plants. Thus the NRC is conducting research to identify advances in HFE methods and to develop additional guidance to address their review.