Molecular dynamics (MD) simulations were carried out on the DNA oligonucleotide GGGAACAACTAG:CTAGTTGTTCCC in its native form and with guanine in the central G19:C6 base pair replaced by 8-oxoguanine (8oxoG). A box of explicit water molecules was used for solvation and Na+ counterions were added to neutralize the system. The direction and magnitude of global bending were assessed by a technique used previously to analyze simulations of DNA containing a thymine dimer. The presence of 8oxoG did not greatly affect the magnitude of DNA bending; however, bending into the major groove was significantly more probable when 8oxoG replaced G19. Crystal structures of glycosylases bound to damaged-DNA substrates consistently show a sharp bend into the major groove at the damage site. We conclude that changes in bending dynamics that assist the formation of this kink are a part of the mechanism by which glycosylases of the base excision repair pathway recognize the presence of 8oxoG in DNA.

The term beta-beam has been coined for the production of a pure beam of electron neutrinos or their antiparticles through the decay of radioactive ions circulating in a storage ring. This concept requires radioactive ions to be accelerated to a Lorentz gamma of 150 for {sup 6}He and 60 for {sup 18}Ne. The neutrino source itself consists of a storage ring for this energy range, with long straight sections in line with the experiment(s). Such a decay ring does not exist at CERN today, nor does a high-intensity proton source for the production of the radioactive ions. Nevertheless, the existing CERN accelerator infrastructure could be used as this would still represent an important saving for a beta-beam facility. This paper outlines the first study, while some of the more speculative ideas will need further investigations.

Caching techniques have been used to improve the performance gap of storage hierarchies in computing systems. In data intensive applications that access large data files over wide area network environment, such as a data grid,caching mechanism can significantly improve the data access performance under appropriate workloads. In a data grid, it is envisioned that local disk storage resources retain or cache the data files being used by local application. Under a workload of shared access and high locality of reference, the performance of the caching techniques depends heavily on the replacement policies being used. A replacement policy effectively determines which set of objects must be evicted when space is needed. Unlike cache replacement policies in virtual memory paging or database buffering, developing an optimal replacement policy for data grids is complicated by the fact that the file objects being cached have varying sizes and varying transfer and processing costs that vary with time. We present an accurate model for evaluating various replacement policies and propose a new replacement algorithm referred to as ''Least Cost Beneficial based on K backward references (LCB-K).'' Using this modeling technique, we compare LCB-K with various replacement policies such as Least Frequently Used (LFU), Least Recently …

Possibilities to accumulate antiprotons in the Recycler are considered for three different cases: with current stochastic cooling, with upgraded stochastic cooling and with electron cooling. With stochastic cooling only, even upgraded, Recycler looks hardly useful. However, with electron cooling at its goal parameters and reasonably good vacuum in the Recycler, this machine would be efficient.

The National Nuclear Security Administration is developing methods for nonproliferation assessments to support the development and implementation of U.S. nonproliferation policy. This paper summarizes the key results of that effort. Proliferation resistance is the degree of difficulty that a nuclear material, facility, process, or activity poses to the acquisition of one or more nuclear weapons. A top-level measure of proliferation resistance for a fuel cycle system is developed here from a hierarchy of metrics. At the lowest level, intrinsic and extrinsic barriers to proliferation are defined. These barriers are recommended as a means to characterize the proliferation characteristics of a fuel cycle. Because of the complexity of nonproliferation assessments, the problem is decomposed into: metrics to be computed, barriers to proliferation, and a finite set of threats. The spectrum of potential threats of nuclear proliferation is complex and ranges from small terrorist cells to industrialized countries with advanced nuclear fuel cycles. Two general categories of methods have historically been used for nonproliferation assessments: attribute analysis and scenario analysis. In the former, attributes of the systems being evaluated (often fuel cycle systems) are identified that affect their proliferation potential. For a particular system under consideration, the attributes are weighted subjectively. In …

Astronomical applications of adaptive optics at Lawrence Livermore National Laboratory (LLNL) has a history that extends from 1984. The program started with the Lick Observatory Adaptive Optics system and has progressed through the years to lever-larger telescopes: Keck, and now the proposed CELT (California Extremely Large Telescope) 30m telescope. LLNL AO continues to be at the forefront of AO development and science.

Alloying III-V compounds with small amounts of nitrogen leads to dramatic reduction of the fundamental band-gap energy in the resulting dilute nitride alloys. The effect originates from an anti-crossing interaction between the extended conduction-band states and localized N states. The interaction splits the conduction band into two nonparabolic subbands. The downward shift of the lower conduction subband edge is responsible for the N-induced reduction of the fundamental band-gap energy. The changes in the conduction band structure result in significant increase in electron effective mass and decrease in the electron mobility, and lead to a large enhance of the maximum doping level in GaInNAs doped with group VI donors. In addition, a striking asymmetry in the electrical activation of group IV and group VI donors can be attributed to mutual passivation process through formation of the nearest neighbor group-IV donor nitrogen pairs.

The CDF experiment's Silicon Vertex Trigger is a system of 150 custom 9U VME boards that reconstructs axial tracks in the CDF silicon strip detector in a 15 {mu}sec pipeline. SVT's 35 {mu}m impact parameter resolution enables CDF's Level 2 trigger to distinguish primary and secondary particles, and hence to collect large samples of hadronic bottom and charm decays. We review some of SVT's key design features. Speed is achieved with custom VLSI pattern recognition, linearized track fitting, pipelining, and parallel processing. Testing and reliability are aided by built-in logic state analysis and test-data sourcing at each board's input and output, a common inter-board data link, and a universal ''Merger'' board for data fan-in/fan-out. Speed and adaptability are enhanced by use of modern FPGAs.

A demonstration of Fluidized Bed Steam Reforming (FBSR) was recently completed on a Hanford Low Activity Waste (LAW) simulant. This technology produced stable mineral phases (feldspathoids) when co-fired with clay. The mineral phases are cage structured and were determined to retain anions as well as cations such as Re (simulant for Tc) in the mineral cages. The FBSR mineral waste form exhibited incongruent leaching characteristics during Product Consistency Testing (PCT or ASTM C1285). FBSR mineral waste forms are EPA regulatory compliant at the Universal Treatment Standard (UTS) making delisting an attractive option for this waste form.

We present a calculation of the charmonium spectrum with three flavors of dynamical staggered quarks from gauge configurations that were generated by the MILC collaboration. We use the Fermilab action for the valence charm quarks. Our calculation of the spin-averaged 1P-1S and 2S-1S splittings yields a determination of the strong coupling, with {alpha}{sub {ovr MS}}(M{sub Z}) = 0.119(4).

In previous studies we have investigated after-burning effects of a fuel-rich explosive (TNT). In that case the detonation only releases about 30 % of the available energy, but generates a hot cloud of fuel that can burn in the ambient air, thus evoking an additional energy release that is distributed in space and time. The current series of small-scale experiments can be looked upon as a natural generalization of this mechanism: a booster charge disperses a (non-explosive) fuel, provides mixing with air and - by means of the hot detonation products - energy to ignite the fuel. The current version of our miniature Shock-Dispersed-Fuel (SDF) charges consists of a spherical booster charge of 0.5 g PETN, embedded in a paper cylinder of approximately 2.2 cm3, which is filled with powdered fuel compositions. The main compositions studied up to now contain aluminum powder, hydrocarbon powders like polyethylene or sucrose and/or carbon particles. These charges were studied in three different chambers of 4-1, 6.6-1 and 40.5-1 volume. In general, the booster charge was sufficient to initiate burning of the fuel. This modifies the pressure signatures measured with a number of wall gages and increases the quasi-static overpressure level obtained in the chambers. …

High-resolution computer simulations produce large volumes of data. As a first step in the analysis of these data, supervised machine learning techniques can be used to retrieve objects similar to a query that the user finds interesting. These objects may be characterized by a large number of features, some of which may be redundant or irrelevant to the similarity retrieval problem. This paper presents a comparison of six dimensionality reduction algorithms on data from a fluid mixing simulation. The objective is to identify methods that efficiently find feature subsets that result in high accuracy rates. Our experimental results with single- and multi-resolution data suggest that standard forward feature selection produces the smallest feature subsets in the shortest time.

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Cloud parameterizations in large-scale models often try to predict the amount of sub-grid scale variability in cloud properties to address the significant non-linear effects of radiation and precipitation. Statistical cloud schemes provide an attractive framework to self-consistently predict the variability in radiation and microphysics but require accurate predictions of the width and asymmetry of the distribution of cloud properties. Data from the Atmospheric Radiation Measurement (ARM) program are used to assess the variability in boundary layer cloud properties for a well- mixed stratocumulus observed at the Oklahoma ARM site during the March 2000 Intensive Observing Period. Cloud boundaries, liquid water content, and liquid water path are retrieved from the millimeter wavelength cloud radar and the microwave radiometer. Balloon soundings, aircraft data, and satellite observations provide complementary views on the horizontal cloud inhomogeneity. It is shown that the width of the liquid water path probability distribution function is consistent with a model in which horizontal fluctuations in liquid water content are vertically coherent throughout the depth of the cloud. Variability in cloud base is overestimated by this model, however; perhaps because an additional assumption that the variance of total water is constant with altitude throughout the depth of the boundary layer …

Herein we compare three functional families for afterglow morphologies: the homogeneous afterglow with constant shock surface energy density, the structured afterglow for which the energy density decays as a power-law as a function of viewer angle, and the gaussian afterglow which has an exponential decay of energy density with viewer angle. We simulate observed lightcurves and polarization curves for each as seen from a variety of observer vantage points. We find that the homogeneous jet is likely inconsistent with observations and suggest that the future debate on the structure of afterglow jets will be between the other two candidates.

An improved version of the focusing magnet for a Heavy Ion Fusion (HIF) accelerator was designed, built and tested in 2002-2003. This quadrupole has higher focusing power and lower error field than the previous version of the focusing quadrupoles successfully built and tested in 2001. We discuss the features of the new design, selected fabrication issues and test results.

The development of high-temperature electrochemical devices such as oxygen and hydrogen separators, fuel gas reformers, solid oxide fuel cells, and chemical sensors is part of a rapidly expanding segment of the solid state technology market. These devices employ an ionic conducting ceramic as the active membrane that establishes the electrochemical potential of the device, either under voltage (i.e. to carry out gas separation) or under chemical gradient (to develop an electrical potential and thereby generate electrical power). Because the device operates under an ionic gradient that develops across the electrolyte, hermiticity across this layer is paramount. That is, not only must this thin ceramic membrane be dense with no interconnected porosity, but it must be connected to the rest of the device, typically constructed from a heat resistant alloy, with a high-temperature, gas-tight seal. A significant engineering challenge in fabricating these devices is how to effectively join the thin electrochemically active membrane to the metallic body of the device such that the resulting seal is hermetic, rugged, and stable during continuous high temperature operation. Active metal brazing is the typical method of joining ceramic and metal engineering components. It employs a braze alloy that contains one or more reactive elements, …

This paper presents information and data relative to recent advances in the development at Oak Ridge National Laboratory of porous inorganic membranes for high-temperature hydrogen separation. The Inorganic Membrane Technology Laboratory, which was formerly an organizational element of Bechtel Jacobs Company, LLC, was formally transferred to Oak Ridge National Laboratory on August 1, 2002, as a result of agreements reached between Bechtel Jacobs Company, the management and integration contractor at the East Tennessee Technology Park (formerly the Oak Ridge Gaseous Diffusion Plant or Oak Ridge K-25 Site); UT-Battelle, the management and operating contractor of Oak Ridge National Laboratory; and the U.S. Department of Energy (DOE) Oak Ridge Operations Office. Research emphasis during the last year has been directed toward the development of high-permeance (high-flux) and high-separation-factor metal-supported membranes. Performance data for these membranes are presented and are compared with performance data for membranes previously produced under this program and for membranes produced by other researchers. New insights into diffusion mechanisms are included in the discussion. Fifteen products, many of which are the results of research sponsored by the DOE Fossil Energy Advanced Research Materials Program, have been declared unclassified and have been approved for commercial production.

Successful development of metallic filters with high temperature oxidation/corrosion resistance for fly ash capture is a key to enabling advanced coal combustion and power generation technologies. Compared to ceramic filters, metallic filters can offer increased resistance to impact and thermal fatigue, greatly improving filter reliability. A beneficial metallic filter structure, composed of a thin-wall (0.5mm) tube with uniform porosity (about 30%), is being developed using a unique spherical powder processing and partial sintering approach, combined with porous sheet rolling and resistance welding. Alloy choices based on modified superalloys, e.g., Ni-16Cr-4.5Al-3Fe (wt.%), are being tested in porous and bulk samples for oxide (typically alumina) scale stability in simulated oxidizing/sulfidizing atmospheres found in PFBC and IGCC systems at temperatures up to 850 C. Recent ''hanging o-ring'' exposure tests in actual combustion systems at a collaborating DOE site (EERC) have been initiated to study the combined corrosive effects from particulate deposits and hot exhaust gases. New studies are exploring the correlation between sintered microstructure, tensile strength, and permeability of porous sheet samples.

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Using ion implantation followed by pulsed-laser melting (PLM), we have synthesized ferromagnetic films of Ga{sub 1-x}Mn{sub x}As. Ion-channeling experiments reveal that these films are single crystalline and have high Mn substitutionality while variable temperature resistivity measurements reveal the strong Mn-hole interactions characteristic of carrier-mediated ferromagnetism in homogeneous DMS's. We have observed Curie temperatures (T{sub C}'s) of approximately 80 K for films with substitutional Mn concentrations of x=0.04. The use of n-type counter doping as a means of increasing Mn substitutionality and T{sub c} is explored by co-implantation of Mn and Te into GaAs. In Ga{sub 1-x}Mn{sub x}P samples synthesized using our technique, the implanted layer regrows as an epitaxial single crystal capped by a highly defective surface layer. These samples display ferromagnetism with T{sub c} {approx} 23 K.

The electrical resistivity of rock cores under conditions representative of geothermal reservoirs is strongly influenced by the state and phase (liquid/vapor) of the pore fluid. In fractured samples, phase change (vaporization/condensation) can result in resistivity changes that are more than an order of magnitude greater than those measured in intact samples. These results suggest that electrical resistivity monitoring of geothermal reservoirs may provide a useful tool for remotely detecting the movement of water and steam within fractures, the development and evolution of fracture systems and the formation of steam caps. We measured the electrical resistivity of cores of welded tuff containing fractures of various geometries to investigate the resistivity contrast caused by active boiling and to determine the effects of variable fracture dimensions and surface area on water extraction from the matrix. We then used the Nonisothermal Unsaturated Flow and Transport model (NUFT) (Nitao, 1998) to simulate the propagation of boiling fronts through the samples. The simulated saturation profiles combined with previously reported measurements of resistivity-saturation curves allow us to estimate the evolution of the sample resistivity as the boiling front propagates into the rock matrix. These simulations provide qualitative agreement with experimental measurements suggesting that our modeling approach may …

We present an improved analytical expression for the x-ray dynamic structure factor from a dense plasma which includes the effects of weakly bound electrons. This result can be applied to describe scattering from low to moderate Z plasmas, and it covers the entire range of plasma conditions that can be found in inertial confinement fusion experiments, from ideal to degenerate up to moderately coupled systems. We use our theory to interpret x-ray scattering experiments from solid density carbon plasma and to extract accurate measurements of electron temperature, electron density and charge state. We use our experimental results to validate various equation-of-state models for carbon plasmas.

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