The Gordon Research Conference (GRC) on 2004 Gordon Research Conference on Reversible Associations in Structure & Molecular Biology was held at Four Points Sheraton, CA, 1/25-30/2004. The Conference was well attended with 82 participants (attendees list attached). The attendees represented the spectrum of endeavor in this field coming from academia, industry, and government laboratories, both U.S. and foreign scientists, senior researchers, young investigators, and students.

This Gordon conference will cover the areas of structural, functional and evolutionary genomics. It will take a systematic approach to genomics, examining the evolution of proteins, protein functional sites, protein-protein interactions, regulatory networks, and metabolic networks. Emphasis will be placed on what we can learn from comparative genomics and entire genomes and proteomes.

This report is about 3D Arcing for Offset Measurements with a Hamar Laser on 7th International workshop on accelerator alignment.

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Prior to and during the design of the APS's Access Control Interlock System (ACIS), an effort was made to insure that the design complied with the relevant DOE and ANL requirements as well as those set forth in other recognized documents then in circulation. A paragraph-by-paragraph listing of the requirements (in some cases, recommended practices) and the corresponding ACIS design features was compiled for use by the review committees then in place. This tabulation was incorporated in the APS Safety Analysis Document (SAD) as Appendix A. With the evolutionary changes that have occurred to the APS and to the documents referenced, some of the details of these compliances have evolved as well. It has been decided to maintain the SAD as a ''living'' document, editing it in close time proximity to the evolving APS. Since Appendix A depicted the ACIS's original design compliance to an also-evolving set of documents, it was decided to remove Appendix A but to retain it as a reference document. This LS Note now contains that set of original design compliances. As the APS and the ACIS continue to evolve, the changes made will be subject to internal review and approval and will always be subject …

Evaluation of the fabrication processes involved in the manufacture of waste containers is important as these processes can have an effect on the metallurgical structure of an alloy. Since material properties such as strength, toughness, aging kinetics and corrosion resistance are all dependent on the microstructure, it is important that prototypes be built and evaluated for processing effects on the performance of the material. Of particular importance are welds, which have an as-cast microstructure with chemical segregation and precipitation of complex phases resulting from the welding process. The work presented in this report focuses on the effects of processes such as solution annealing, stress mitigation, and welding on the kinetics of precipitation and corrosion properties. For a waste package lifetime of thousands of years, it is impossible to test directly in the laboratory the behavior of Alloy 22 under expected repository conditions. The changes that may occur in these materials must be accelerated. For phase-stability studies this is achieved by accelerating the phase transformations by increasing test temperatures above those anticipated in the proposed repository. For these reasons, Alloy 22 characterization specimens are currently being aged at Lawrence Livermore National Laboratory (LLNL) Aging Facilities for times from 1 hour to …

Aging and weathering can reduce the solar reflectance of cool roofing materials. This paper summarizes laboratory measurements of the solar spectral reflectance of unweathered, weathered, and cleaned samples collected from single-ply roofing membranes at various sites across the United States. Fifteen samples were examined in each of the following six conditions: unweathered; weathered; weathered and brushed; weathered, brushed and then rinsed with water; weathered, brushed, rinsed with water, and then washed with soap and water; and weathered, brushed, rinsed with water, washed with soap and water, and then washed with an algaecide. Another 25 samples from 25 roofs across the United States and Canada were measured in their unweathered state, weathered, and weathered and wiped. We document reduction in reflectivity resulted from various soiling mechanisms and provide data on the effectiveness of various cleaning approaches. Results indicate that although the majority of samples after being washed with detergent could be brought to within 90% of their unweathered reflectivity, in some instances an algaecide was required to restore this level of reflectivity.

The major objective of this study was to identify and analyze signal transduction factors that function with the CR4 receptor kinase. We pursued this analysis in Arabidopsis. Analysis of other members of the ACR4 related receptor (CRR) family produced biochemical evidence consistent with some of them functioning in ACR4 signal transduction. Yeast 2-hybrid identified six proteins that interact with the cytoplasmic domain of ACR4, representing putative downstream signal transduction components. The interactions for all 6 proteins were verified by in vitro pull down assays. Five of the interacting proteins were phosphorylated by ACR4. We also identified candidate interactors with the extracellular TNFR domain. We hypothesize this may be the ligand binding domain for ACR4. In one approach, yeast 2-hybrid was again used and five candidate proteins identified. Nine additional candidates were identified in a genome wide scan of Arabidopsis amino acid sequences that threaded onto the TNF structure.

This procedure is written as general guidance for the measurement of elemental isotopic composition by plasma-source inorganic mass spectrometry. Analytical methods for uranium and plutonium are given as examples.

This chapter describes procedures for the collection and analysis of samples of various matrices for the purpose of determining the presence of chemical agents in a civilian setting. This appendix is intended to provide the reader with sufficient information to make informed decisions about the sampling and analysis process and to suggest analytical strategies that might be implemented by the scientists performing sampling and analysis. This appendix is not intended to be used as a standard operating procedure to provide detailed instructions as to how trained scientists should handle samples. Chemical agents can be classified by their physical and chemical properties. Table 1 lists the chemical agents considered by this report. In selecting sampling and analysis methods, we have considered procedures proposed by the Organization for Prohibition of Chemical Weapons (OPCW), the U. S. Environmental Protection Agency (EPA), and peer-reviewed scientific literature. EPA analytical methods are good resources describing issues of quality assurance with respect to chain-of-custody, sample handling, and quality control requirements.

The recent advent of parallel machines with tens of thousands of processors is presenting new challenges for obtaining scalability. A particular challenge for large-scale scientific software is determining the inter-processor communications required by the computation when a global description of the data is unavailable or too costly to store. We present a type of rendezvous algorithm that determines communication partners in a scalable manner by assuming the global distribution of the data. We demonstrate the scaling properties of the algorithm on up to 32,000 processors in the context of determining communication patterns for a matrix-vector multiply in the hypre software library. Our algorithm is very general and is applicable to a variety of situations in parallel computing.

This document is the first of two volumes describing the ATF2 project. The present volume discusses the technical justification for ATF2 and presents a design description. Since the International Committee for Future Accelerator (ICFA) decision on the choice of technology, a world-wide collaboration on the design of the International Linear Collider (ILC) has rapidly progressed [1]. The formation of the Global Design Effort (GDE) will accelerate the work towards a final design. An important technical challenge is obviously the high gradient acceleration but what is similarly challenging is the collision of extremely small beams of a few nanometer size. The latter challenge has three distinct issues: creating small emittance beams, preserving the emittance during acceleration and transport, and focusing the beams to nanometers. Most studies have been done using computer simulations but many issues still remain that require experimental verification. Accelerator Test Facility (ATF) at KEK was built to create small emittance beams, and succeeded in obtaining an emittance that almost satisfies the ILC requirements [2]. In this proposal we present a project, ATF2, which addresses the focusing of the beam into a nanometer spot. The ATF2 project will extend the extraction beamline of the ATF with an ILC-type final …

Adequate path calibrations are crucial for improving the accuracy of seismic event location and origin time, size, and mechanism, as required for CTBT monitoring. There is considerable information on structure in broadband seismograms that is currently not fully utilized. The limitations have been largely theoretical. the development and application to solid earth problems of powerful numerical techniques, such as the Spectral Element Method (SEM), has opened a new era, and theoretically, it should be possible to compute the complete predicted wavefield accurately without any restrictions on the strength or spatial extent of heterogeneity. This approach requires considerable computational power, which is currently not fully reachable in practice. We propose an approach which relies on a cascade of increasingly accurate theoretical approximations for the computation of the seismic wavefield to develop a model of regional structure for the area of Eurasia located between longitudes of 30 and 150 degrees E, and latitudes of -10 to 60 degrees North. The selected area is particularly suitable for the purpose of this experiment, as it is highly heterogeneous, presenting a challenge for calibration purposes, but it is well surrounded by earthquake sources and, even though they are sparsely distributed, a significant number of high …

Adequate path calibrations are crucial for improving the accuracy of seismic event location and origin time, size, and mechanism, as required for CTBT monitoring. There is considerable information on structure in broadband seismograms that is currently not fully utilized. The limitations have been largely theoretical. the development and application to solid earth problems of powerful numerical techniques, such as the Spectral Element Method (SEM), has opened a new era, and theoretically, it should be possible to compute the complete predicted wavefield accurately without any restrictions on the strength or spatial extent of heterogeneity. This approach requires considerable computational power, which is currently not fully reachable in practice. We propose an approach which relies on a cascade of increasingly accurate theoretical approximations for the computation of the seismic wavefield to develop a model of regional structure for the area of Eurasia located between longitudes of 30 and 150 degrees E, and latitudes of -10 to 60 degrees North. The selected area is particularly suitable for the purpose of this experiment, as it is highly heterogeneous, presenting a challenge for calibration purposes, but it is well surrounded by earthquake sources and, even though they are sparsely distributed, a significant number of high …

Adequate path calibrations are crucial for improving the accuracy of seismic event location and origin time, size, and mechanism, as required for CTBT monitoring. There is considerable information on structure in broadband seismograms that is currently not fully utilized. The limitations have been largely theoretical. the development and application to solid earth problems of powerful numerical techniques, such as the Spectral Element Method (SEM), has opened a new era, and theoretically, it should be possible to compute the complete predicted wavefield accurately without any restrictions on the strength or spatial extent of heterogeneity. This approach requires considerable computational power, which is currently not fully reachable in practice. We propose an approach which relies on a cascade of increasingly accurate theoretical approximations for the computation of the seismic wavefield to develop a model of regional structure for the area of Eurasia located between longitudes of 30 and 150 degrees E, and latitudes of -10 to 60 degrees North. The selected area is particularly suitable for the purpose of this experiment, as it is highly heterogeneous, presenting a challenge for calibration purposes, but it is well surrounded by earthquake sources and, even though they are sparsely distributed, a significant number of high …

Common Internet services can be reliably distinguished based solely upon the locations of clusters in traffic-based features (ratios of inbound to outbound packets, ratios of packets to payloads, etc.) This capability has value in revealing the nature of ''hidden'' (tunneled) services and in detecting anomalous changes to known services. We provide measures of session capture volumes sufficient to make confidence-level assertions regarding ''unknown'' services, and outline a throughput system for providing alarms for service anomalies.

Hydrocarbon synthesis from photocatalytic reactions of CO{sub 2} and H{sub 2}O over various catalysts has been studied by UV-visible light. The quantum efficiencies suggest that Pd/TiO{sub 2} sol gel exhibits the highest activity for hydrocarbon synthesis from photocatalytic reactions. The in situ IR was able to monitor the adsorbed hydrocarbon species. The UV-visible, IR spectroscopy and XRD techniques were used to characterize the catalysts to obtain the information of properties of the process and catalyst before/after reaction. The UV-visible spectroscopy provides the information about the surface band gap energy of each catalyst. In situ UV-visible studies reveals that TiO{sub 2}-supported catalysts require the higher energy (i.e. shorter wavelength) to pass through the water-thin film deposited on the surface to activate the photocatalytic reaction. XRD data show there is changes in the crystal structure of TiO{sub 2} sol gel from photon energy during photo reaction. Studies on photocatalytic oxidation of methylene blue show that the photocatalytic oxidation rate is significantly higher than the photocatalytic reduction rate on TiO{sub 2} based catalysts. The information from this study can lead to a better understanding of the nature of the catalysts and photoreaction processes, which might provide the information to develop better catalysts and …

Grid convergence is often assumed as a given during computational analyses involving discretization of an assumed continuum process. In practical use of finite difference and finite element analyses, perfect grid convergence is rarely achieved or assured, and this fact must be addressed to make statements about model validation or the use of models in risk analysis. We have previously provided a 4-step quantitative implementation for a quantitative V&V process. One of the steps in the 4-step process is that of Solution Verification. Solution Verification is the process of assuring that a model approximating a physical reality with a discretized continuum (e.g. finite element) code converges in each discretized domain to a converged answer on the quantity of subsequent validation interest. The modeling reality is that often we are modeling a problem with a discretized code because it is neither continuous spatially (e.g. contact and impact) nor smooth in relevant physics (e.g. shocks, melting, etc). The typical result is a non-monotonic convergence plot that can lead to spurious conclusions about the order of convergence, and a lack of means to estimate residual solution verification error or uncertainty at confidence. We compare ten techniques for grid convergence assessment, each formulated to enable …

Compatibility and outgassing studies of non-nuclear materials were carried out in support of the W80 Life Extension Program. These studies included small-scale laboratory experiments as well as participation in Sandia's Materials Aging and Compatibility test (MAC-1). Analysis of the outgassing signature of removable epoxy foam (REF) revealed unusually high levels of volatile organic compounds in the material. REF was replaced with the polyurethane PMDI. Laboratory compatibility tests of high priority materials were performed and revealed incompatibilities between Viton A (LX-07 binder) and syntactic polysulfide as well as Viton A and REF. With the removal of REF from the system, the incompatibility with Viton A is not an issue. In the case of the viton/polysulfide, both of these materials have a history of reliability in the stockpile, and the observed results, while scientifically interesting, appear to be a laboratory anomaly. Participation in the MAC-1 test led to a detailed study of Viton A degradation. At elevated temperatures up to 70 C, the Viton A samples darkened and exhibited increased crosslinking. Laboratory experiments were pursued to correlate the observed changes to exposure to specific compounds that were present in the MAC-1 canister atmospheres. Exposure to siloxanes resulted in changes similar to those …

Concentrations of eleven potential environmental contaminants (metals) in the blood and retrice feathers of fledged-Hatch Year and adult loggerhead shrikes (Lanius ludovicianus) were examined at Lawrence Livermore National Laboratory's Site 300 and a control site, in San Joaquin and Contra Costa Counties, California. The purpose of this pilot study was to determine, through non-lethal means, if loggerhead shrikes are exposed to metals at Site 300 and whether specific demographic variables (i.e., clutch size, fledgling success, etc.) are affected. Loggerhead shrikes at Site 300 had higher blood concentrations of metals, especially birds on the west side of the site, when compared to control site birds. Metal concentrations in the feathers of control site birds tended to be higher than Site 300 shrikes. Blood concentrations of metals in loggerhead shrikes from both Site 300 and the control site were well below the Most Tolerant Dietary Level (MTDL) for domestic birds for all metals except selenium. Clutch size was similar to other populations but one deformed embryo was discovered in a failed egg. The results of this pilot study suggest further work is needed to understand possible synergistic effects related to other contaminants of concern found at Site 300 and overall population variability.

Urban areas tend to have higher air temperatures than their rural surroundings as a result of gradual surface modifications that include replacing the natural vegetation with buildings and roads. The term ''Urban Heat Island'' describes this phenomenon. The surfaces of buildings and pavements absorb solar radiation and become extremely hot, which in turn warm the surrounding air. Cities that have been ''paved over'' do not receive the benefit of the natural cooling effect of vegetation. As the air temperature rises, so does the demand for air-conditioning (a/c). This leads to higher emissions from power plants, as well as increased smog formation as a result of warmer temperatures. In the United States, we have found that this increase in air temperature is responsible for 5-10% of urban peak electric demand for a/c use, and as much as 20% of population-weighted smog concentrations in urban areas. Simple ways to cool the cities are the use of reflective surfaces (rooftops and pavements) and planting of urban vegetation. On a large scale, the evapotranspiration from vegetation and increased reflection of incoming solar radiation by reflective surfaces will cool a community a few degrees in the summer. As an example, computer simulations for Los Angeles, …

The properties of pentaamine (5-cyano-2H-tetrazolato-N2) cobalt (III) perchlorate (CP), which was first synthesized in 1968, continues to be of interest for predicting behavior in handling, shipping, aging, and thermal cook-off situations. We report coefficient of thermal expansion (CTE) values over four specific temperature ranges, decomposition kinetics using linear heating rates, and the reaction to three different types of stimuli: impact, spark, and friction. The CTE was measured using a Thermal Mechanical Analyzer (TMA) for samples that were uniaxially compressed at 10,000 psi and analyzed over a dynamic temperature range of -20 C to 70 C. Using differential scanning calorimetry, DSC, CP was decomposed at linear heating rates of 1, 3, and 7 C/min and the kinetic triplet calculated using the LLNL code Kinetics05. Values are also reported for spark, friction, and impact sensitivity.

Mechanically alloyed oxide dispersion strengthened (ODS) Fe-Cr-Al alloy thin walled tubes and sheets, produced via powder processing and consolidation methodologies, are promising materials for eventual use at temperatures up to 1200 C in the power generation industry, far above the temperature capabilities of conventional alloys. Target end-uses range from gas turbine combustor liners to high aspect ratio (L/D) heat exchanger tubes. Grain boundary creep processes at service temperatures, particularly those acting in the hoop direction, are the dominant failure mechanisms for such components. The processed microstructure of ODS alloys consists of high aspect ratio grains aligned parallel to the tube axis, a result of dominant axial metal flow which aligns the dispersoid particles and other impurities in the longitudinal direction. The dispersion distribution is unaltered on a micro scale by recrystallization thermal treatments, but the high aspect ratio grain shape typically obtained limits transverse grain spacing and consequently the hoop creep response. Improving hoop creep in ODS-alloy components will require understanding and manipulating the factors that control the recrystallization behavior, and represents a critical materials design and development challenge that must be overcome in order to fully exploit the potential of ODS alloys. The objectives of this program are to …

A new Timing and Synchronization System component, the Universal Networked Timer (UNT), is under development at the National Spherical Torus Experiment (NSTX). The UNT is a second-generation multifunction timing device that emulates the timing functionality and electrical interfaces originally provided by various CAMAC modules. Using Field Programmable Gate Array (FPGA) technology, each of the UNT's eight channels can be dynamically programmed to emulate a specific CAMAC module type. The timer is compatible with the existing NSTX timing and synchronization system and will also support a (future) clock system with extended performance. To assist system designers and collaborators, software will be written to integrate the UNT with EPICS, MDSplus, and LabVIEW. This paper will describe the timing capabilities, hardware design, programming/software support, and the current status of the Universal Networked Timer at NSTX.