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Environmental contamination with a variety of pollutants hasprompted the development of effective bioremediation strategies. But howcan these processes be best monitored and controlled? One avenue underinvestigation is the development of stress response systems as tools foreffective and general process control. Although the microbial stressresponse has been the subject of intensive laboratory investigation, theenvironmental reflection of the laboratory response to specific stresseshas been little explored. However, it is only within an environmentalcontext, in which microorganisms are constantly exposed to multiplechanging environmental stresses, that there will be full understanding ofmicrobial adaptive resiliency. Knowledge of the stress response in theenvironment will facilitate the control of bioremediation and otherprocesses mediated by complex microbial communities.

Modern single molecule fluorescence microscopy offers new, highly quantitative ways of studying the systems biology of cells while keeping the cells healthy and alive in their natural environment. In this context, a quantum optical technique, photon antibunching, has found a small niche in the continuously growing applications of single molecule techniques to small molecular complexes. Here, we review some of the most recent applications of photon antibunching in biophotonics, and we provide a guide for how to conduct photon antibunching experiments at the single molecule level by applying techniques borrowed from time-correlated single photon counting. We provide a number of new examples for applications of photon antibunching to the study of multichromophoric molecules and small molecular complexes.

Inverse Compton scattering of high-power laser pulses on relativistic electron bunches represents an attractive method for high-brightness, quasi-monoenergetic {gamma}-ray production. The efficiency of {gamma}-ray generation via inverse Compton scattering is severely constrained by the small Thomson scattering cross section. Furthermore, repetition rates of high-energy short-pulse lasers are poorly matched with those available from electron accelerators, resulting in low repetition rates for generated {gamma}-rays. Laser recirculation has been proposed as a method to address those limitations, but has been limited to only small pulse energies and peak powers. Here we propose and experimentally demonstrate an alternative method for laser pulse recirculation that is uniquely capable of recirculating short pulses with energies exceeding 1 J. Inverse Compton scattering of recirculated Joule-level laser pulses has a potential to produce unprecedented peak and average {gamma}-ray brightness in the next generation of sources.

Recent experiments with high Z disks on the Argus facility have exteanded our knowledge of the temperature (inferred from the slope of the hard x-ray spectrum) of laser generated suprathermal electrons, from the previous regime of 1 less than or equal to Z less than or equal to 30 to the Z approx. = 80 regime. The systematic rise of temperature with Z is theoretically analyzed. We believe that material albedoes (electron reflectivity) which increase with Z can account for this behavior, since electrons can make multiple passes through the region of resonant electric fields and are thus reheated. We treat this effect quantitatively and obtain reasonable agreement with experiment. The effects of magnetic fields and filamentation are also examined.

Fragmentation of free liquids in Inertial Confinement Fusion reactors could determine the upper bound on reactor pulse rate because increased surface area will enhance the cooling and condensation of coolant ablated by the fusion x rays. Relaxation from the suddenly (neutron) heated state will move a liquid into the negative pressure region under the liquid-vapor P-V dome. The resulting expansion in a diverging geometry will hydrodynamically force the liquid to fragment, with vapor then forming from the new surfaces to fill the cavities. An energy minimization model is used to determine the fragment size that produces the least amount of non-fragment-center-of-mass energy; i.e., the sum of the surface and dilational kinetic energies. This model predicts fragmentation dependence on original system size and amount of isochoric heating as well as liquid density, Grueneisen parameter, surface tension, and sound speed. A two dimensional molecular dynamics code was developed to test the model at a microscopic scale for the Lennard-Jones fluid with its two adjustable constants chosen to represent lithium.

Fifteen ICF power reactor design studies published since 1980 are reviewed to illuminate the design trends they represent. There is a clear, continuing trend toward making ICF reactors inherently safer and environmentally benign. Since this trend accentuates inherent advantages of ICF reactors, we expect it to be further emphasized in the future. An emphasis on economic competitiveness appears to be a somewhat newer trend. Lower cost of electricity, smaller initial size (and capital cost), and more affordable development paths are three of the issues being addressed with new studies.

In response to the increasing severity of target surface finish requirements for laser fusion experiments, it has become necessary to examine spherical targets in the Scanning Electron Microscope, prior to laser irradiation, on an orderly nondestructive basis. We have developed a new sample manipulation technique which rolls a thin wall sphere through 4..pi.. steradians, minimizes damage and allows easy recovery. The sphere is placed between two parallel plane surfaces formed in conductively coated silicone rubber on the ends of capillaries. Mechanical slides cause the capillaries to translate laterally and roll the ball bringing the entire surface of the sphere into a position for examination. Resolutions comparable with traditional mounting techniques are attained. A side looking, Si(Li) detector increases the utility of the system by allowing simultaneous energy dispersive x-ray microanalysis. The entire detector assembly slips between the secondary electron detector and the sphere rolling capillaries to collect x-rays from the target.

A method for obtaining a constitutive relation that relates the flow stress to the equivalent plastic strain is developed. The method uses simple tension test data to suggest a functional form. This form is then used as a constitutive model in a computer program that simulates the tension test. The calculated results are compared with the experimental results and the functional form is refined until agreement is obtained between calculations and experiments. The importance of knowing the relationship between the flow stress and the plastic strain is discussed. A work hardening function is calibrated for 6061 T6 aluminum.

We have previously reported the delay and reduction of the hydriding of uranium by implantation of oxygen. The reduced hydriding was attributed to the presence of the uranium oxide layer created near room temperature. In this paper we present results for the layers formed by implantation of 80 keV C/sup +/ to a dose of 8E17 C/cm/sup 2/. The carbide layers formed were characterized by Auger electron spectroscopy, Rutherford backscattering, and glancing angle x-ray diffraction. Hydriding properties of both non-implanted and implanted uranium were measured for 76 Torr hydrogen at 130/sup 0/C. The implanted specimens had significantly longer incubation times for the start of the reaction after exposure to hydrogen and less area participating in the reaction.

Tool Gear is a software infrastructure for developing performance analysis and other tools. Unlike existing integrated toolkits, which focus on providing a suite of capabilities, Tool Gear is designed to help tool developers create new tools quickly. It combines dynamic instrumentation capabilities with an efficient database and a sophisticated and extensible graphical user interface. This paper describes the design of Tool Gear and presents examples of tools that have been built with it.

We find the annihilation rate of positronium (Ps) within silica sodalite. Positron density and the electronic density seen by positrons are compared with a semi-empirical ''free volume'' model.

Multilateral mechanisms for the fuel cycle are seen as a potentially important way to create an industrial infrastructure that will support a renaissance and at the same time not contribute to the risk of nuclear proliferation. In this way, international nuclear fuel cycle centers for enrichment can help to provide an assurance of supply of nuclear fuel that will reduce the likelihood that individual states will pursue this sensitive technology, which can be used to produce nuclear material directly usable nuclear weapons. Multinational participation in such mechanisms can also potentially promote transparency, build confidence, and make the implementation of IAEA safeguards more effective or more efficient. At the same time, it is important to ensure that there is no dissemination of sensitive technology. The Russian Federation has taken a lead role in this area by establishing an International Uranium Enrichment Center (IUEC) for the provision of enrichment services at its uranium enrichment plant located at the Angarsk Electrolysis Chemical Complex (AECC). This paper describes how the IUEe is organized, who its members are, and the steps that it has taken both to provide an assured supply of nuclear fuel and to ensure protection of sensitive technology. It also describes the …

We present a search for the decay B{sup +} {yields} {ell}{sup +} {nu}{sub {ell}} ({ell} = {tau}, {mu}, or e) in (458.9 {+-} 5.1) x 10{sup 6} {Upsilon}(4S) decays recorded with the BABAR detector at the SLAC PEP-IIB-Factory. A sample of events with one reconstructed exclusive semi-leptonic B decay (B{sup -} {yields} D{sup 0} {ell}{sup -}{bar {nu}}X) is selected, and in the recoil a search for B{sup +} {yields} {ell}{sup +}{nu}{sub {ell}} signal is performed. The {tau} is identified in the following channels: {tau}{sup +} {yields} e{sup +}{nu}{sub e}{nu}{sub {tau}}, {tau}{sup +} {yields} {mu}{sup +}{nu}{sub {mu}}{nu}{sub {tau}}, {tau}{sup +} {yields} {pi}{sup +}{nu}{sub {tau}}, and {tau}{sup +} {yields} {pi}{sup +}{pi}{sup 0}{nu}{sub {tau}}. The analysis strategy and the statistical procedure is set up for branching fraction extraction or upper limit determination. We determine from the dataset a preliminary measurement of {Beta}(B{sup +} {yields} {tau}{sup +}{nu}{sub {tau}}) = (1.8 {+-} 0.8 {+-} 0.1) x 10{sup -4}, which excludes zero at 2.4{sigma}, and f{sub B} = 230 {+-} 57 MeV. Combination with the hadronically tagged measurement yields {Beta}(B{sup +} {yields} e{sup +}{nu}{sub e}) = (1.8 {+-} 0.6) x 10{sup -4}. We also set preliminary limits on the branching fractions at {Beta}(B{sup +} {yields} e{sup …

Pyrosequencing technologies such as 454/Roche and Solexa/Illumina vastly lower the cost of nucleotide sequencing compared to the traditional Sanger method, and thus promise to greatly expand the number of sequenced eukaryotic genomes. However, the new technologies also bring new challenges such as shorter reads and new kinds and higher rates of sequencing errors, which complicate genome assembly and gene prediction. At JGI we are deploying 454 technology for the sequencing and assembly of ever-larger eukaryotic genomes. Here we describe our first whole-genome annotation of a purely 454-sequenced fungal genome that is larger than a yeast (>30 Mbp). The pezizomycotine (filamentous ascomycote) Aspergillus carbonarius belongs to the Aspergillus section Nigri species complex, members of which are significant as platforms for bioenergy and bioindustrial technology, as members of soil microbial communities and players in the global carbon cycle, and as agricultural toxigens. Application of a modified version of the standard JGI Annotation Pipeline has so far predicted ~;;10k genes. ~;;12percent of these preliminary annotations suffer a potential frameshift error, which is somewhat higher than the ~;;9percent rate in the Sanger-sequenced and conventionally assembled and annotated genome of fellow Aspergillus section Nigri member A. niger. Also,>90percent of A. niger genes have potential homologs …

Historically, the estuarine portions of the Savannah River have been considered to be the only portion of the river in which significant amounts of striped bass (Morone saxatilis) spawning normally occur. A reexamination of data from 1983 through 1985 shows a region between River Kilometers 144 and 253 where significant numbers of striped bass eggs and larvae occur with estimated total egg production near that currently produced in the estuarine reaches. It appears possible that there are two separate spawning populations of striped bass in the Savannah River.

The Heavy-Ion Fusion Sciences Virtual National Laboratory is pursuing an approach to target heating experiments in the warm dense matter regime, using space-charge-dominated ion beams that are simultaneously longitudinally bunched and transversely focused. Longitudinal beam compression by large factors has been demonstrated in the Neutralized Drift Compression Experiment (NDCX) with controlled ramps and forced neutralization. Using an injected 30 mA K{sup +} ion beam with initial kinetic energy 0.3 MeV, axial compression leading to {approx}50X current amplification and simultaneous radial focusing to a few mm have led to encouraging energy deposition approaching the intensities required for eV-range target heating experiments. We discuss the status of several improvements to NDCX to reach the necessary higher beam intensities, including: beam diagnostics, greater axial compression via a longer velocity ramp; and plasma injection improvements to establish a plasma density always greater than the beam density, expected to be > 10{sup 13} cm{sup -3}.

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TOUGH2{_}MP, the parallel version TOUGH2 code, has been enhanced by implementing more efficient communication schemes. This enhancement is achieved through reducing the amount of small-size messages and the volume of large messages. The message exchange speed is further improved by using non-blocking communications for both linear and nonlinear iterations. In addition, we have modified the AZTEC parallel linear-equation solver to nonblocking communication. Through the improvement of code structuring and bug fixing, the new version code is now more stable, while demonstrating similar or even better nonlinear iteration converging speed than the original TOUGH2 code. As a result, the new version of TOUGH2{_}MP is improved significantly in its efficiency. In this paper, the scalability and efficiency of the parallel code are demonstrated by solving two large-scale problems. The testing results indicate that speedup of the code may depend on both problem size and complexity. In general, the code has excellent scalability in memory requirement as well as computing time.

Obtaining precise values of the undulator parameter, K, is critical for producing high-gain FEL radiation. At the LCLS [1], where the FEL wavelength reaches down to 1.5 {angstrom}, the relative precision of K must satisfy ({Delta}K/K){sub rms} {approx}< 0.015% over the full length of the undulator. Transverse misalignments, construction errors, radiation damage, and temperature variations all contribute to errors in the mean K values among the undulator segments. It is therefore important to develop some means to measure relative K values, after installation and alignment. We propose a method using the angle-integrated spontaneous radiation spectrum of two nearby undulator segments, and the natural shot-to-shot energy jitter of the electron beam. Simulation of this scheme is presented using both ideal and measured undulator fields. By ''leap-frogging'' to different pairs of segments with extended separations we hope to confirm or correct the values of K, including proper tapering, over the entire 130-m long LCLS undulator.

This paper presents the dynamic simulation of the 6M drum with a locking-ring type closure subjected to a 4.9-foot drop. The drum is filled with water to 98 percent of overflow capacity. A three dimensional finite-element model consisting of metallic, liquid and rubber gasket components is used in the simulation. The water is represented by a hydrodynamic material model in which the material's volume strength is determined by an equation of state. The explicit numerical method based on the theory of wave propagation is used to determine the combined structural response to the torque load for tightening the locking-ring closure and to the impact load due to the drop.

A numerical technique has been developed to simulate the structural responses of radioactive material packaging components requiring closure-tightening torque to the scenarios of the hypothetical accident conditions (HAC) defined in the Code of Federal Regulations Title 10 part 71 (10CFR 71). A rigorous solution to this type of problem poses a considerable mathematical challenge. Conventional methods for evaluating the residue stresses due to the torque load are either inaccurate or not applicable to dynamic analyses. In addition, the HAC events occur sequentially and the cumulative damage to the package needs to be evaluated. Commonly, individual HAC events are analyzed separately and the cumulative damage is not addressed. As a result, strict compliance of the package with the requirements specified in 10CFR 71 is usually demonstrated by physical testing. The proposed technique utilizes the combination of kinematic constraints, rigid-body motions and structural deformations to overcome some of the difficulties encountered in modeling the effect of cumulative damage in numerical solutions. The analyses demonstrating use of this technique were performed to determine the cumulative damage of torque preload, a 30-foot drop, a 30-foot dynamic crush and a 40-inch free fall onto a mild steel pipe.

The Linac Coherent Light Source (LCLS) will be the world's first x-ray free-electron laser (FEL) when it becomes operational in 2009. The LCLS is currently in the construction phase. The beam position monitor (BPM) system planned for the LCLS undulator will incorporate a high-resolution X-band cavity BPM system described in this paper. The BPM system will provide high-resolution measurements of the electron beam trajectory on a pulse-to-pulse basis and over many shots. The X-band cavity BPM size, simple fabrication, and high resolution make it an ideal choice for LCLS beam position detection. We will discuss the system specifications, design, and prototype test results.