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.

The increased use of object-oriented toolkits in large-scale scientific simulation presents new opportunities and challenges for the use of automatic (or algorithmic) differentiation (AD) techniques, especially in the context of optimization. Because object-oriented toolkits use well-defined interfaces and data structures, there is potential for simplifying the AD process. Furthermore, derivative computation can be improved by exploiting high-level information about numerical and computational abstractions. However, challenges to the successful use of AD with these toolkits also exist. Among the greatest challenges is balancing the desire to limit the scope of the AD process with the desire to minimize the work required of a user. They discuss their experiences in integrating AD with the PETSc, PVODE, and TAO toolkits and the plans for future research and development in this area.

Experimental tests have been undertaken to determine safe levels of laser exposure on bare high explosive (HE) samples and on common metals used in intimate contact with HE. Laser light is often focused on bare HE and upon metals in contact with HE during alignment procedures and experimental metrology experiments. This paper looks at effects caused by focusing laser beams at high energy densities directly onto the surface of various bare HE samples. Laser energy densities (fluence) exceeding 19 kilowatts/cm{sup 2} using a 5-milliwatt, 670 nm, cw laser diode were generated by focusing the laser down to a spot size diameter of 4 microns. Upon careful inspection, no laser damage was observed in any of the HE samples illuminated at this fluence level. Direct laser exposure of metals directly contacting HE surfaces was also tested. Laser energy densities (fluence) varying from 188 Watts/cm{sup 2} to 12.7 KW/cm{sup 2} were generated using an 11-Watt, 532 nm frequency-doubled Nd:YAG cw laser with focal spot size diameters as small as 100 microns. These measurements look at the temperature rise of the surface of the metal in contact with HE when laser energy is incident on the opposite side of the metal. The temperature …

Coscheduling is essential for obtaining good performance in a time-shared symmetric multiprocessor (SMP) cluster environment. However, the most common technique, gang scheduling, has limitations such as poor scalability and vulnerability to faults mainly due to explicit synchronization between its components. A decentralized approach called dynamic coscheduling (DCS) has been shown to be effective for network of workstations (NOW), but this technique is not suitable for the workloads on a very large SMP-cluster with thousands of processors. Furthermore, its implementation can be prohibitively expensive for such a large-scale machine. In this paper, we propose a novel coscheduling technique based on the DCS approach which can achieve coscheduling on very large SMP-clusters in a scalable, efficient, and cost-effective way. In the proposed technique, each local scheduler achieves coscheduling based upon message traffic between the components of parallel jobs. Message trapping is carried out at the user-level, eliminating the need for unsupported hardware or device-level programming. A sending process attaches its status to outgoing messages so local schedulers on remote nodes can make more intelligent scheduling decisions. Once scheduled, processes are guaranteed some minimum period of time to execute. This provides an opportunity to synchronize the parallel job's components across all nodes and …

Pulsed lasers offer the capability of rapid material removal. Here we present simulations of steel coupon tests by two solid state heat capacity lasers built at LLNL. Operating at 1.05 pm, these deliver pulse energies of about 80 J at 10 Hz, and about 500 J at 20 Hz. Each is flashlamp-pumped. The first laser was tested at LLNL, while the second laser has been delivered to HELSTF, White Sands Missile Range. Liquid ejection appears to be an important removal mechanism. We have modeled these experiments via a time-dependent code called THALES, which describes heat transport, melting, vaporization, and the hydrodynamics of liquid, vapor, and air. It was previously used, in a less advanced form, to model drilling by copper vapor lasers [1] . It was also used to model vaporization in beam dumps for a high-power laser [2]. The basic model is in 1D, while the liquid hydrodynamics is handled in 2D.

We have directly observed motion of inorganic nanoparticles during fluid evaporation using a Transmission Electron Microscope. Tracking real-time diffusion of both spherical (5-15 nm) and rod-shaped (5x10 nm) gold nanocrystals in a thin-film of water-15percentglycerol reveals complex movements, such as rolling motions coupled to large-step movements and macroscopic violations of the Stokes-Einstein relation for diffusion. As drying patches form during the final stages of evaporation, particle motion is dominated by the nearby retracting liquid front.

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}.

Magnetic susceptibility measurements and X-ray data confirm that tert-butyl substituted manganocenes [(Me{sub 3}C){sub n}C{sub 5}H{sub 5-n}]{sub 2}Mn (n= 1, 2) follow the trend previously observed with the methylated manganocenes, i.e., electron donating groups attached to the Cp ring stabilize the low-spin (LS) electronic ground state relative to Cp{sub 2}Mn and exhibit higher spin-crossover (SCO) temperatures. However, introducing three CMe3 groups on each ring gives a temperature invariant high-spin (HS) state manganocene. The origin of the high-spin state in [1,2,4-(Me{sub 3}C){sub 3}C{sub 5}H{sub 2}]{sub 2}Mn is due to the significant bulk of the [1,2,4-(Me{sub 3}C){sub 3}C{sub 5}H{sub 2}]{sup -} ligand, which is sufficient to generate severe inter-ring steric strain that prevents the realization of the low-spin state. Interestingly, the spin transition in [1,3-(Me{sub 3}C){sub 2}C{sub 5}H{sub 3}]{sub 2}Mn is accompanied by a phase transition resulting in a significant irreversible hysteresis ({Delta}T{sub c} = 16 K). This structural transition was also observed by extended X-ray absorption fine-structure (EXAFS) measurements. Magnetic susceptibility studies and X-ray diffraction data on SiMe{sub 3} substituted manganocenes [(Me{sub 3}Si){sub n}C{sub 5}H{sub 5-n}]{sub 2}Mn (n= 1, 2, 3) show high-spin configuration in these cases. Although tetra- and hexasubstituted manganocenes are high-spin at all accessible temperatures, the disubstituted manganocenes exhibit …

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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.

Large-scale carbon capture and sequestration (CCS) projects involving annual injections of millions of tons of CO2 are a key infrastructural element needed to substantially reduce greenhouse gas emissions. The large rate and volume of injection will induce pressure and stress gradients within the formation that could activate existing fractures and faults, or drive new fractures through the caprock. We will present results of an ongoing investigation to identify conditions that will activate existing fractures/faults or make new fractures within the caprock using the Livermore Distinct Element Code (LDEC). LDEC is a multiphysics code, developed at LLNL, capable of simulating dynamic fracture of rock masses under a range of conditions. As part of a recent project, LDEC has been extended to consider fault activation and dynamic fracture of rock masses due to pressurization of the pore-space. We will present several demonstrations of LDEC functionality and an application of LDEC to a CO2 injection scenario. We present results from our investigations of Teapot Dome using LDEC to study the potential for fault activation during injection. Using this approach, we built finite element models of the rock masses surrounding bounding faults and explicitly simulated the compression and shear on the fault interface. A …

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.

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.

Fire barriers, and physical separation are key components in managing the fire risk in Nuclear Facilities. The expected performance of these features have often been predicted using rules-of-thumb or expert judgment. These approaches often lack the convincing technical bases that exist when addressing other Nuclear Facility accident events. This paper presents science-based approaches to demonstrate the effectiveness of fire separation methods.

A large fraction of the anticipated source detections by the Gamma-ray Large Area Space Telescope (GLAST-LAT) will initially be unidentified. We argue that traditional approaches to identify individuals and/or populations of gamma ray sources will encounter procedural limitations. Those limitations are discussed on the background of source identifications from EGRET observations. Generally, our ability to classify (faint) source populations in the anticipated GLAST dataset with the required degree of statistical confidence will be hampered by sheer source wealth. A new paradigm for achieving the classification of gamma ray source populations is discussed.

Successful implementation of both the nuclear safety program and fire protection program is best accomplished using a coordinated process that relies on sound technical approaches. When systematically prepared, the documented safety analysis (DSA) and fire hazard analysis (FHA) can present a consistent technical basis that streamlines implementation. If not coordinated, the DSA and FHA can present inconsistent conclusions, which can create unnecessary confusion and can promulgate a negative safety perception. This paper will compare the scope, purpose, and analysis techniques for DSAs and FHAs. It will also consolidate several lessons-learned papers on this topic, which were prepared in the 1990s.