In this paper, we evaluate Titanium's usability as a high-level parallel programming language through a case study, where we implement a subset of Chombo's functionality in Titanium. Chombo is a software package applying the Adaptive Mesh Refinement methodology to numerical Partial Differential Equations at the production level. In Chombo, the library approach is used to parallel programming (C++ and Fortran, with MPI), whereas Titanium is a Java dialect designed for high-performance scientific computing. The performance of our implementation is studied and compared with that of Chombo in solving Poisson's equation based on two grid configurations from a real application. Also provided are the counts of lines of code from both sides.

Over the past few years, the emphasis in heavy ion target design has moved from the distributed radiator target to the 'hybrid' target because the hybrid target allows a larger beam focal spot than the distributed radiator ({approx} 5 mm radius rather than {approx} 2 mm radius). The larger spot relaxes some of the requirements on the driver, but introduces some new target physics issues. Most notable is the use of shine shields and shims in the hohlraum to achieve symmetry rather than achieving symmetry by beam placement. The shim is a thin layer of material placed on or near the capsule surface to block a small amount of excess radiation. While we have been developing this technique for the heavy ion hybrid target, the technique can be used in any indirect drive target. We have begun testing the concept of a shim to improve symmetry using a double-ended z-pinch hohlraum on the Sandia Z-machine. Experiments using shimmed thin wall capsules have shown that we can reverse the sign of a P{sub 2} asymmetry and significantly reduce the size of a P{sub 4} asymmetry. These initial experiments demonstrate the concept of a shim as another method for controlling early time …

Article about the Women on their Toes benefit, the Austin Museum of Art's annual Art Ball, and other events around Austin, Texas.

Summary: ANDY (seArch coordination aND analYsis) is a set ofPerl programs and modules for distributing large biological databasesearches, and in general any sequence of commands, across the nodes of aLinux computer cluster. ANDY is compatible with several commonly usedDistributed Resource Management (DRM) systems, and it can be easilyextended to new DRMs. A distinctive feature of ANDY is the choice ofeither dedicated or fair-use operation: ANDY is almost as efficient assingle-purpose tools that require a dedicated cluster, but it runs on ageneral-purpose cluster along with any other jobs scheduled by a DRM.Other features include communication through named pipes for performance,flexible customizable routines for error-checking and summarizingresults, and multiple fault-tolerance mechanisms. Availability: ANDY isfreely available and may be obtained fromhttp://compbio.berkeley.edu/proj/andy; this site also containssupplemental data and figures and amore detailed overview of thesoftware.

Our previous atomic force microscopy (AFM) studies successfully visualized native Bacillus atrophaeus spore coat ultrastructure and surface morphology. We have shown that the outer spore coat surface is formed by a crystalline array of {approx}11 nm thick rodlets, having a periodicity of {approx}8 nm. We present here further AFM ultrastructural investigations of air-dried and fully hydrated spore surface architecture. In the rodlet layer, planar and point defects, as well as domain boundaries, similar to those described for inorganic and macromolecular crystals, were identified. For several Bacillus species, rodlet structure assembly and architectural variation appear to be a consequence of species-specific nucleation and crystallization mechanisms that regulate the formation of the outer spore coat. We propose a unifying mechanism for nucleation and self-assembly of this crystalline layer on the outer spore coat surface.

A new facility for high-pressure diffraction and spectroscopy using diamond anvil high-pressure cells has been built at the Advanced Light Source on Beamline 12.2.2. This beamline benefits from the hard X-radiation generated by a 6 Tesla superconducting bending magnet (superbend). Useful x-ray flux is available between 5 keV and 35 keV. The radiation is transferred from the superbend to the experimental enclosure by the brightness preserving optics of the beamline. These optics are comprised of: a plane parabola collimating mirror (M1), followed by a Kohzu monochromator vessel with a Si(111) crystals (E/{Delta}E {approx} 7000) and a W/B{sub 4}C multilayer (E/{Delta}E {approx} 100), and then a toroidal focusing mirror (M2) with variable focusing distance. The experimental enclosure contains an automated beam positioning system, a set of slits, ion chambers, the sample positioning goniometry and area detectors (CCD or image-plate detector). Future developments aim at the installation of a second end station dedicated for in situ laser-heating on one hand and a dedicated high-pressure single-crystal station, applying both monochromatic as well as polychromatic techniques.

An analytical formulation of conductivity bounds by Bergman and Milton is used in a different way to obtain rigorous bounds on the real transport coefficients (electrical conductivity, thermal conductivity, and/or fluid permeability) of a fluid-saturated porous medium. These bounds do not depend explicitly on the porosity, but rather on two formation factors--one associated with the pore space and the other with the solid frame. Hashin-Shtrikman bounds for transport in random polycrystals of porous-material laminates will also be discussed.

With the emergence of structural genomics, more effort is being invested into developing methods that incorporate basic crystallographic knowledge to enhance decision making procedures (e.g. Panjikar, 2005). A key area where some crystallographic knowledge is often vital for the smooth progress of structure solution is that of judging the quality or characteristics of an X-ray dataset. For instance, detecting the presence of anisotropic diffraction or twinning while a crystal is on the beam line, may allow the user to change the data collection strategy in order to obtain a better or a more complete data set. In post-collection analyses, the presence of (for instance) non-crystallographic translational symmetry might help the user (or program!) to solve the structure more easily. Of course, the identification of problems is by no means a guarantee that the problems can be overcome, but knowledge of the idiosyncrasies of a given X-ray data set permits the user or software pipeline to tailor the structure solution and refinement procedures to increase the chances of success. In this report, a number of routines are presented that assist the user in detecting specific problems or features within a given dataset. The routines are made available via the open source …

Experimental methods of measuring intermolecular interactions have had several recent developments which have improved our understanding of chemical forces. First, they allowed direct exploration of the role that different functionalities, solvents and environmental variables play in shaping the strength of intermolecular interactions. Chemical force microscopy approach, in particular, became an extremely effective tool for exploring the contributions of each of these factors. Second, CFM studies clearly debunked the naive notion that intermolecular interaction strength is determined only by the nature of the interacting groups. These studies showed that the interaction strength between two chemical species must always considered in context of the environment surrounding these species. Third, CFM studies highlighted the critical role solvent plays in shaping intermolecular interactions in condensed phases. Emerging kinetic view of the intermolecular interactions introduced a completely new paradigm for understanding these interactions. Kinetic modeling showed that the measured interactions strength depends not only on the energy landscape of the system, but also on the loading history prior to the bond break-up. This new paradigm refocused our attention to the energy landscape as a fundamental characteristic of the interaction. Moreover, dynamic force spectroscopy, derived from kinetic models, allowed direct characterization of the geometry of the …

The thermal stability of high explosive (HE) and its compatibility with other materials are of critical importance in storage and handling practices. These properties are measured at Lawrence Livermore National Laboratory using the chemical reactivity test (CRT). The CRT measures the total amount of gas evolved from a material or combination of materials after being heat treated for a designated period of time. When the test result is compared to a threshold value, the relative thermal stability of an HE or the compatibility of an HE with other materials is determined. We describe the CRT testing apparatus, the experimental procedure, and the comparison methodology and provide examples and discussion of results.

New corrosion-resistant, iron-based amorphous metals have been identified from published data or developed through combinatorial synthesis, and tested to determine their relative corrosion resistance. Many of these materials can be applied as coatings with advanced thermal spray technology. Two compositions have corrosion resistance superior to wrought nickel-based Alloy C-22 (UNS N06022) in some very aggressive environments, including concentrated calcium-chloride brines at elevated temperature. One of these compositions, SAM1651, is discussed in detail to illustrate the promise of this general class of materials.

Alloy 22 (N06022) is a nickel (Ni) based alloy containing nominally 22% Chromium (Cr), 13% Molybdenum (Mo) and 3% tungsten (W). Alloy 22 is highly resistant to general and localized corrosion such as pitting corrosion and stress corrosion cracking. Due to the formation of a stable passive film, when Alloy 22 is immersed in certain electrolytes, its corrosion potential (E{sub corr}) increases and its corrosion rate (CR) decreases as a function of the immersion time. This paper discusses the evolution of E{sub corr} and corrosion rate (CR) of creviced Alloy 22 specimens in six different mixtures of sodium chloride (NaCl) and potassium nitrate (KNO{sub 3}) at 100 C. Two types of specimens were used, polished as-welded (ASW) and as-welded solution plus heat-treated (ASW+SHT). The latter contained the black annealing oxide film on the surface. Results show that, for the two type of materials, as the immersion time increases, E{sub corr} increased and the CR decreased. Even for concentrated brine solutions at 100 C the CR was < 50 nm/year after more than 100 days immersion.

We present an efficient easily implemented method for loading cryogenic fluids in a large volume press. We specifically apply this method to the high-pressure synthesis of an extended solid derived from CO using a Paris-Edinburgh cell. This method employs cryogenic cooling of Bridgman type WC anvils well insulated from other press components, condensation of the load gas within a brass annulus surrounding the gasket between the Bridgman anvils. We demonstrate the viability of the described approach by synthesizing macroscopic amounts (several milligrams) of polymeric CO-derived material, which were recovered to ambient conditions after compression of pure CO to 5 GPa or above.

We show that the solid lower bound of about 10{sup -44} cm{sup 2} is obtained for the cross section between the supersymmetric dark matter and nucleon in a theory in which the supersymmetric fine-tuning problem is solved without extending the Higgs sector at the weak scale. This bound arises because of relatively small superparticle masses and a fortunate correlation that the two dominant diagrams for the dark matter detection always interfere constructively if the constraint from the b {yields} s{gamma} measurements is obeyed. It is, therefore, quite promising in the present scenario that the supersymmetric dark matter is discovered before the LHC, assuming that the dark matter is the lightest supersymmetric particle.

Savannah River Site Building 235-F was being considered for future plutonium storage and stabilization missions but the Defense Nuclear Facilities Safety Board (DNFSB) noted that large quantities of Plutonium-238 left in cells and gloveboxes from previous operations posed a potential hazard to both the existing and future workforce. This material resulted from the manufacture of Pu-238 heat sources used by the NASA space program to generate electricity for deep space exploration satellites. A multi-disciplinary team was assembled to propose a cost- effective solution to mitigate this legacy source term which would facilitate future DOE plutonium storage activities in 235-F. One aspect of this study involved an evaluation of commercially available radiological decontamination techniques to remove the legacy Pu-238 and fixative coatings that could stabilize any residual Pu-238 following decontamination activities. Four chemical methods were identified as most likely to meet decontamination objectives for this project and are discussed in detail. Short and long term fixatives will be reviewed with particular attention to the potential radiation damage caused by Pu-238, which has a high specific activity and would be expected to cause significant radiation damage to any coating applied. Encapsulants that were considered to mitigate the legacy Pu-238 will also be …

Initiated in 1992, the DECOVALEX project is an international collaboration for advancing the understanding and modeling of coupled thermo-hydro-mechanical (THM) processes in geologic systems. The project has made important scientific achievements through three stages and is progressing in its fourth stage. It has played a key role in the development of mathematical modeling and in situ testing of coupled THM processes in fractured rock and buffer/backfill materials, a subject of importance for performance assessment of radioactive waste geologic repositories. This paper summarizes studies under the most recent stage of the project, DECOVALEX III (2000-2003). These studies include those of two major field experiments: (a) the FEBEX experiment at Grimsel, Switzerland, investigating coupled THM processes in a crystalline rock-bentonite system, and (b) the Drift Scale Test (DST) experiment at Yucca Mountain, Nevada, investigating coupled THM processes in unsaturated tuff. These are two of the largest multiyear heater tests undertaken to date for the study of coupled THM processes in geological systems. In addition, three so-called benchmark tests are also studied to evaluate the impact of coupled THM processes under different scenarios and geometries. Within the DECOVALEX project, multiple research teams participated in each of the studies, using different approaches and computer …

The strong focusing VISA undulator is presented in this report. The proposed FEL will operate at the 1 {micro}m water window. Extensive simulations were performed to optimize an FEL amplifier based on the two-meter long VISA undulator which has a period of 1.8 cm and an undulator parameter K = 1.26. The betatron function inside the VISA undulator is about 30 cm. For an electron beam with a peak current {approx}1 kA and a normalized emittance of 5 mm-mrad, the FEL peak power can exceed 1 GW within the 2 m VISA undulator using a 5 kW peak power seed laser. Such a device can produce a megawatt of average power for a 700 MHz rep rate. The transverse distribution of the FEL radiation along the undulator, as well as after the undulator, is explored by numerical simulation. The FEL power density at 5 m downstream from the undulator is less than 100 kW/cm{sup 2} for this MW-class FEL. We will also discuss the feasibility of an experimental demonstration of the laser seeded FEL amplifier based on the 2-m VISA undulator at the NSLS Source Development Lab (SDL).

The 3.2 giga-pixel LSST camera will produce over half a petabyte of raw images every month. This data needs to be reduced in under a minute to produce real-time transient alerts, and then cataloged and indexed to allow efficient access and simplify further analysis. The indexed catalogs alone are expected to grow at a speed of about 600 terabytes per year. The sheer volume of data, the real-time transient alerting requirements of the LSST, and its spatio-temporal aspects require cutting-edge techniques to build an efficient data access system at reasonable cost. As currently envisioned, the system will rely on a database for catalogs and metadata. Several database systems are being evaluated to understand how they will scale and perform at these data volumes in anticipated LSST access patterns. This paper describes the LSST requirements, the challenges they impose, the data access philosophy, and the database architecture that is expected to be adopted in order to meet the data challenges.

There is much demand for chemical kinetic models to represent practical fuels such as gasoline, diesel and aviation fuel. These blended fuels contain hundreds of components whose identity and amounts are often unknown. A chemical kinetic mechanism that would represent the oxidation of all these species with accompanying chemical reactions is intractable with current computational capabilities, chemical knowledge and manpower resources. The use of surrogate fuels is an approach to make the development of chemical kinetic mechanisms for practical fuels tractable. A surrogate fuel model consists of a small number of fuel components that can be used to represent the practical fuel and still predict desired characteristics of the practical fuel. These desired fuel characteristics may include ignition behavior, burning velocity, fuel viscosity, fuel vaporization, and fuel emissions (carbon monoxide, hydrocarbons, soot and nitric oxides). Gasoline consists of many different classes of hydrocarbons including n-alkanes, alkenes, iso-alkanes, cycloalkanes, cycloalkenes, and aromatics. One approach is to use a fuel surrogate that has a single component from each class of hydrocarbon in gasoline so that the unique molecular structure of each class is represented. This approach may lead to reliable predictions of many of the combustion properties of the practical fuel. In …

Diamond has a unique combination of physical properties for the inertial confinement fusion ablator application, such as appropriate optical properties, high atomic density, high yield strength, and high thermal conductivity. Here, we present a feasible concept to fabricate diamond ablator shells. The fabrication of diamond capsules is a multi-step process, which involves diamond chemical vapor deposition on silicon mandrels followed by polishing, microfabrication of holes, and removing of the silicon mandrel by an etch process. We also discuss the pros and cons of coarse-grained optical quality and nanocrystalline chemical vapor deposition diamond films for the ablator application.

In-situ x-ray diffraction studies of iron under shock conditions confirm unambiguously a phase change from the bcc ({alpha}) to hcp ({var_epsilon}) structure. Previous identification of this transition in shock-loaded iron has been inferred from the correlation between shock wave-profile analyses and static high-pressure x-ray measurements. This correlation is intrinsically limited because dynamic loading can markedly affect the structural modifications of solids. The in-situ measurements are consistent with a uniaxial collapse along the [001] direction and shuffling of alternate (110) planes of atoms, and in good agreement with large-scale non-equilibrium molecular dynamics simulations.

Managing subsurface damage during the shaping process and removing subsurface damage during the polishing process is essential in the production of low damage density optical components, such as those required for use on high peak power lasers. Removal of subsurface damage, during the polishing process, requires polishing to a depth which is greater than the depth of the residual cracks present following the shaping process. To successfully manage, and ultimately remove subsurface damage, understanding the distribution and character of fractures in the subsurface region introduced during fabrication process is important. We have characterized the depth and morphology of subsurface fractures present following fixed abrasive and loose abrasive grinding processes. At shallow depths lateral cracks and an overlapping series of trailing indentation fractures were found to be present. At greater depths, subsurface damage consists of a series of trailing indentation fractures. The area density of trailing fractures changes as a function of depth, however the length and shape of individual cracks remain nearly constant for a given grinding process. We have developed and applied a model to interpret the depth and crack length distributions of subsurface surface damage in terms of key variables including abrasive size and load.

To qualify the performance of non-actinic inspection tools, a novel EUV mask inspection system has been installed at the Advanced Light Source (ALS) synchrotron facility at Lawrence Berkeley National Laboratory. Similar to the older generation actinic mask inspection tool, the new system can operate in scanning mode, when mask blanks are scanned for defects using 13.5-nm in-band radiation to identify and map all locations on the mask that scatter a significant amount of EUV light. By modifying and optimizing beamline optics (11.3.2 at ALS) and replacing K-B focusing mirrors with a high quality Schwarzschild illuminator, the new system achieves an order of magnitude improvement on in-band EUV flux density at the mask, enabling faster scanning speed and higher sensitivity to smaller defects. Moreover, the system can also operate in imaging mode, when it becomes a zone-plate-based full-field EUV microscope with spatial resolution better than 100 nm. The microscope utilizes an off-axis setup, making it possible to obtain bright field images over a field-of-view of 5 x 5 {micro}m.

The effect of zirconia phase on the activity and selectivityof Cu/ZrO2 for the hydrogenation of CO has been investigated. Relativelypure t-ZrO2 and m-ZrO2 were prepared with high surface areas (~; 145m2/g). Copper was then deposited onto the surface of these materials byeither incipient-wetness impregnation or deposition-precipitation. For afixed Cu surface area, Cu/m-ZrO2 was tenfold more active for methanolsynthesis than Cu/t-ZrO2 from a feed of 3/1 H2/CO at 3.0 MPa andtemperatures between 473 and 523 K. Cu/m-ZrO2 also exhibited a higherselectivity to methanol. Increasing the Cu surface area on m-ZrO2resulted in further improvement in activity with minimal change inselectivity. Methanol productivity increased linearly for both Cu/t-ZrO2and Cu/m-ZrO2 with increasing Cu surface area. The difference in inherentactivity of each phase paralleled the stronger and larger CO adsorptioncapacity of the Cu/m-ZrO2 as quantified by CO-TPD. The higher COadsorption capacity of Cu/m-ZrO2 is attributed to the presence of a highconcentration of anionic vacancies on the surface of m-ZrO2. Suchvacancies expose cus-Zr4+ cations, which act as Lewis acid centers andenhance the Bronsted acidity of adjacent Zr-OH groups. The presence ofcus-Zr4+ sites and adjacent Bronsted acidic Zr-OH groups contributes tothe adsorption of CO as HCOO-Zr groups, which are the initial precursorsto methanol.