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.

A new three-dimensional visualization engine has been developed for the MARS14 code system. It is based on the OPENINVENTOR graphics library and integrated with the MARS built-in two-dimensional Graphical-User Interface, MARS-GUI-SLICE. The integrated package allows thorough checking of complex geometry systems and their fragments, materials, magnetic fields, particle tracks along with a visualization of calculated 2-D histograms. The algorithms and their optimization are described for two geometry classes along with examples in accelerator and detector applications.

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 …

The Henry's law type constants of OH and HO{sub 2} have not been experimentally determined for obvious reasons: it is extremely difficult to measure the concentrations of these reactive species in either the gas phase or the aqueous phase, let alone simultaneously in both phases. At a more fundamental level, because these radicals react rapidly in both phases, compared with mass-transfer rates characterizing typical laboratory multi-phase systems, the gas-liquid equilibrium which is necessary for such measurements to be feasible is typically not attainable. Consequently, the Henry's law constants of these radicals are traditionally evaluated from the free energy of solution, {Delta}{sub sol}G{sup 0}(X) accompanying the process of transferring a molecule X from the gas phase, denoted g, to the aqueous phase, a, i.e. X{sub g} {rightleftharpoons} X{sub a} (9.10); using the equation {Delta}{sub sol}G{sup o}(X) = -RT ln k{sub H} (9.11); {Delta}{sub sol}G{sup o}(X) is defined as {Delta}{sub sol}G{sup o}(X) = {Delta}{sub f}G{sup o}(X){sub a} - {Delta}{sub f}G{sup o}(X){sub g} (9.12) where the free energies of formation of X in the gas phase and in the aqueous phase are typically evaluated using thermochemical cycles.

High-pressure, high-temperature scanning tunneling microscopy (HPHTSTM) was used to study adsorbate structures and reactions on single crystal model catalytic systems. Studies of the automobile catalytic converter reaction [CO + NO {yields} 1/2 N{sub 2} + CO{sub 2}] on Rh(111) and ethylene hydrogenation [C{sub 2}H{sub 4} + H{sub 2} {yields} C{sub 2}H{sub 6}] on Rh(111) and Pt(111) elucidated information on adsorbate structures in equilibrium with high-pressure gas and the relationship of atomic and molecular mobility to chemistry. STM studies of NO on Rh(111) showed that adsorbed NO forms two high-pressure structures, with the phase transformation from the (2 x 2) structure to the (3 x 3) structure occurring at 0.03 Torr. The (3 x 3) structure only exists when the surface is in equilibrium with the gas phase. The heat of adsorption of this new structure was determined by measuring the pressures and temperatures at which both (2 x 2) and (3 x 3) structures coexisted. The energy barrier between the two structures was calculated by observing the time necessary for the phase transformation to take place. High-pressure STM studies of the coadsorption of CO and NO on Rh(111) showed that CO and NO form a mixed (2 x 2) structure …

As the Barrel Tile Calorimeter is constructed, the support saddles and the modules will be subjected to different forces, stresses, and deflections than when completely assembled. The purpose of this analysis is to examine the forces, stresses, and deflections acting on the support saddles and modules at various stages of assembly. The nominal weight of a barrel module is 20 tons. CERN Document number ATL-LB-EA-0001 'Summary of the Structural Analysis of the Barrel Support Saddles' describes in detail the structural analysis of the saddles and the completed barrel assembly. These calculations followed Eurocode 3. This paper examined several load cases which occur during the assembly of the Barrel. The following are the main conclusions: (1) The assembly is not stable until 18 modules are in place, and only then can the support cradle be removed; (2) The forces between modules are nominal and are far less that the forces in the completed cylinder with 64 modules in place and the cryostat load applied; (3) All of the stresses in the connections between modules are within acceptable limits; and (4) The interface between the cryostat supports and the cryostat move approximately 1.0 mm in the X and Y directions when the …

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.

As part of the U.S. National Spent Nuclear Fuel Program, aluminide fuels (UAl{sub x}) are being tested under conditions that might exist in the proposed repository at Yucca Mountain, Nevada. Intermittent drip tests at 90 C were completed for up to 183 days on partially declad, unirradiated, low-enriched UAl{sub x} samples. Through 183 days of exposure to modified water from the J-13 well at 90 C, the fuel coupon remained in good mechanical condition. Only a tarnishing of the surface was observed and no spalled products were found in the fuel holder. The mechanism for alteration is consistent with that observed from dry oxidation experiments on UAl{sub x} (for the initial corrosion) and humid UO{sub 2} oxidation (for the subsequent paragenesis). Specifically, solid-state conversion of UAl{sub x} into UO{sub 2} and oxidized Al is followed by further oxidation, dissolution of the uranium, and reprecipitation as uranyl oxyhydroxides. The release rate of uranium varied from 0.23 to 2.9 mg/m{sup 2}/day (avg. = 0.97 mg U/m{sup 2}/day) depending on the specimen and test interval, but was similar in magnitude to that observed in earlier flow-through and drip tests with irradiated UAl{sub x} and UO{sub 2}. Most (mean=87%) of the released uranium sorbed …

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 …

The Maine Yankee (MY) nuclear power plant is undergoing the process of decontamination and decommissioning (D&D). Part of the process requires analyses that demonstrate that any radioactivity that remains after D&D will not cause exposure to radioactive contaminants to exceed acceptable limits. This requires knowledge of the distribution of radionuclides in the remaining material and their potential release mechanisms from the material to the contacting groundwater. In this study the concern involves radionuclide contamination in activated concrete in the ICI Sump below the containment building. Figures 1-3 are schematic representations of the ICI Sump. Figure 2 and 3 contain the relevant dimensions needed for the analysis. The key features of Figures 2 and 3 are the 3/8-inch carbon steel liner that isolates the activated concrete from the pit and the concrete wall, which is between 7 feet and 7 feet 2 inches thick. During operations, a small neutron flux from the reactor activated the carbon steel liner and the concrete outside the liner. Current MY plans call for filling the ICI sump with compacted sand.

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.

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This documentation describes the procedures and methods used to measure total carbon dioxide (TCO{sub 2}) total alkalinity (TALK), and partial pressure of CO{sub 2} (pCO{sub 2}) at hydrographic stations on the North Atlantic Ocean sections AR24, A24, A20, and A22 during the R/V Knorr Cruises 147-2, 151-2, 151-3, and 151-4 in 1996 and 1997. Conducted as part of the World Ocean Circulation Experiment (WOCE), the expeditions began at Woods Hole, Massachusetts, on October 24, 1996, and ended at Woods Hole on September 3, 1997. Instructions for accessing the data are provided. A total of 5,614 water samples were analyzed for discrete TCO{sub 2} using two single-operator multiparameter metabolic analyzers (SOMMAs) coupled to a coulometer for extracting and detecting CO{sub 2}. The overall accuracy of the TCO{sub 2} determination was {+-} 1.59 {micro}mol/kg. The TALK was determined in a total of 6,088 discrete samples on all sections by potentiometric titration using an automated titration system developed at the University of Miami. The accuracy of the TALK determination was {+-} 3 {micro}mol/kg. A total of 2,465 discrete water samples were collected for determination of pCO{sub 2} in seawater on sections A24, A20, and A22. The pCO{sub 2} was measured by means of …

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).

A new method of processing multivariate response data to extract chemical information has been developed. Sensor array response patterns are transformed into a vector containing values for solvation parameter descriptors of the detected vapor's properties. These results can be obtained by using a method similar to classical least squares, and equations have been derived for mass-transducing sensors or volume-transducing sensors. Polymer-coated acoustic wave devices are an example of mass-transducing sensors. However, some acoustic wave sensors, such as polymer-coated surface acoustic wave (SAW) devices give responses resulting from both mass-loading and decreases in modulus. The latter effect can be modeled as a volume effect. In this paper we derive solutions for obtaining descriptor values from arrays of mass-plus-volume-transducing sensors. Simulations were performed to investigate the effectiveness of these solutions and to compare them with solutions for purely mass-transducing sensor arrays. It is concluded that this new method of processing sensor array data can be applied to SAW sensor arrays even when the modulus changes contribute to the responses. The simulations show that good estimations of vapor descriptors can be obtained by using a closed form estimation approach that is similar to the closed form solution for purely mass-transducing sensor arrays. Estimations …

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.