Membrane proteins make up a diverse and important subset of proteins for which structural information is limited. In this study, chemical cross-linking and mass spectrometry were used to explore the structure of the G-protein-coupled photoreceptor bovine rhodopsin in the dark-state conformation. All experiments were performed in rod outer segment membranes using amino acid 'handles' in the native protein sequence and thus minimizing perturbations to the native protein structure. Cysteine and lysine residues were covalently cross-linked using commercially available reagents with a range of linker arm lengths. Following chemical digestion of cross-linked protein, cross-linked peptides were identified by accurate mass measurement using liquid chromatography-fourier transform mass spectrometry and an automated data analysis pipeline. Assignments were confirmed and, if necessary, resolved, by tandem MS. The relative reactivity of lysine residues participating in cross-links was evaluated by labeling with NHS-esters. A distinct pattern of cross-link formation within the C-terminal domain, and between loop I and the C-terminal domain, emerged. Theoretical distances based on cross-linking were compared to inter-atomic distances determined from the energy-minimized X-ray crystal structure and Monte Carlo conformational search procedures. In general, the observed cross-links can be explained by re-positioning participating side-chains without significantly altering backbone structure. One exception, between C3 …

Pendeo-epitaxy has been applied to nonpolar a-plane GaN layers in order to observe if such process will lead to defect reduction in comparison with direct growth on this plane. Uncoalesced and coalesced a-plane GaN layers with thicknesses 2{micro}m and 12{micro}m, respectively have been studied by conventional and high resolution electron microscopy. The following structural defects have been observed in pendeo-epitaxial layers: (1) basal stacking faults, (2) threading dislocations and (3) prismatic stacking faults. Drastic decrease of threading dislocation density and stacking faults have been observed in 'wing' areas with respect to 'seed' areas. Cross-section images reveal cracks and voids at the areas where two coalesced wings meet each other. High resolution electron microscopy shows that the majority of stacking faults are low-energy planar defects of the types I{sub 1}, I{sub 2} and I{sub 3}. The I{sub 3} type basal stacking fault, predicted theoretically, has been observed experimentally for the first time.

This paper reports on the global potential for carbonsequestration in forest plantations, and the reduction of carbonemissions from deforestation, in response to six carbon price scenariosfrom 2000 to 2100. These carbon price scenarios cover a range typicallyseen in global integrated assessment models. The world forest sector wasdisaggregated into tenregions, four largely temperate, developedregions: the European Union, Oceania, Russia, and the United States; andsix developing, mostly tropical, regions: Africa, Central America, China,India, Rest of Asia, and South America. Three mitigation options -- long-and short-rotation forestry, and the reduction of deforestation -- wereanalyzed using a global dynamic partial equilibrium model (GCOMAP). Keyfindings of this work are that cumulative carbon gain ranges from 50.9 to113.2 Gt C by 2100, higher carbon prices early lead to earlier carbongain and vice versa, and avoided deforestation accounts for 51 to 78percent of modeled carbon gains by 2100. The estimated present value ofcumulative welfare change in the sector ranges from a decline of $158billion to a gain of $81 billion by 2100. The decline is associated witha decrease in deforestation.

For astrophysical applications, as well as modeling laser-produced plasmas, there is a continual need for equation-of-state data over a wide domain of physical conditions. This paper presents algorithmic aspects for computing the Helmholtz free energy of plasma electrons for temperatures spanning from a few Kelvin to several KeV, and densities ranging from essentially isolated ion conditions to such large compressions that most bound orbitals become delocalized. The objective is high precision results in order to compute pressure and other thermodynamic quantities by numerical differentiation. This approach has the advantage that internal thermodynamic self-consistency is ensured, regardless of the specific physical model, but at the cost of very stringent numerical tolerances for each operation. The computational aspects we address in this paper are faced by any model that relies on input from the quantum mechanical spectrum of a spherically symmetric Hamiltonian operator. The particular physical model we employ is that of INFERNO; of a spherically averaged ion embedded in jellium. An overview of PURGATORIO, a new implementation of the INFERNO equation of state model, is presented. The new algorithm emphasizes a novel decimation scheme for automatically resolving the structure of the continuum density of states, circumventing limitations of the pseudo-R matrix …

Clostridial neurotoxins, such as botulinum and tetanus, are generally thought to invade neural cells through a process of high affinity binding mediated by gangliosides, internalization via endosome formation, and subsequent membrane penetration of the catalytic domain activated by a pH drop in the endosome. This surface recognition and internalization process is still not well understood with regard to what specific membrane features the toxins target, the intermolecular interactions between bound toxins, and the molecular conformational changes that occur as a result of pH lowering. In an effort to elucidate the mechanism of tetanus toxin binding and permeation through the membrane a simple yet representative model was developed that consisted of the ganglioside G{sub tlb} incorporated in a bilayer of cholesterol and DPPC (dipalmitoylphosphatidyl choline). The bilayers were stable over time yet sensitive towards the binding and activity of whole toxin. A liposome leakage study at constant pH as well as with a pH gradient, to mimic the processes of the endosome, was used to elucidate the effect of pH on the toxin's membrane binding and permeation capability. Topographic imaging of the membrane surface, via in situ tapping mode AFM, provided nanoscale characterization of the toxin's binding location and pore formation …

We investigate the potential for CO2 monitoring in thenear-surface environment as an approach to exploration for hiddengeothermal systems. Numerical simulations of CO2 migration from a modelhidden geothermal system show that CO2 concentrations can reach highlevels in the shallow subsurface even for relatively low CO2 fluxes.Therefore, subsurface measurements offer an advantage over above-groundmeasurements which are affected by winds that rapidly disperse CO2. Tomeet the challenge of detecting geothermal CO2 emissions within thenatural background variability of CO2, we propose an approach thatintegrates available detection and monitoring techniques with statisticalanalysis and modeling.

Semiconductor bridges (SCBs) are commonly used as initiators for explosive and pyrotechnic devices. Their advantages include reduced voltage and energy requirements and exceptional safety features. Moreover, the design of systems which implement SCBs can be expedited using electrical simulation software. Successful use of this software requires that certain parameters be correctly chosen. In this paper, we explain how these parameters can be identified using optimization. We describe the problem focusing on the application of a direct optimization method for its solution, and present some numerical results.

This report contains the summary of the 'Magnetophoretic Bead Trapping in a High-Flowrate Biological Detection System' LDRD project 74795. The objective of this project is to develop a novel biodetection system for high-throughput sample analysis. The chief application of this system is in detection of very low concentrations of target molecules from a complex liquid solution containing many different constituents--some of which may interfere with identification of the target molecule. The system is also designed to handle air sampling by using an aerosol system (for instance a WESP - Wet Electro-Static Precipitator, or an impact spray system) to get air sample constituents into the liquid volume. The system described herein automatically takes the raw liquid sample, whether air converted or initially liquid matrix, and mixes in magnetic detector beads that capture the targets of interest and then performs the sample cleanup function, allowing increased sensitivity and eliminating most false positives and false negatives at a downstream detector. The surfaces of the beads can be functionalized in a variety of ways in order to maximize the number of targets to be captured and concentrated. Bacteria and viruses are captured using antibodies to surface proteins on bacterial cell walls or viral particle …

The objective of this LDRD was to develop microdevice strategies for dealing with samples to be examined in biological detection systems. This includes three sub-components: namely, microdevice fabrication, sample delivery to the microdevice, and sample processing within the microdevice. The first component of this work focused on utilizing Sandia's surface micromachining technology to fabricate small volume (nanoliter) fluidic systems for processing small quantities of biological samples. The next component was to develop interfaces for the surface-micromachined silicon devices. We partnered with Micronics, a commercial company, to produce fluidic manifolds for sample delivery to our silicon devices. Pressure testing was completed to examine the strength of the bond between the pressure-sensitive adhesive layer and the silicon chip. We are also pursuing several other methods, both in house and external, to develop polymer-based fluidic manifolds for packaging silicon-based microfluidic devices. The second component, sample processing, is divided into two sub-tasks: cell collection and cell lysis. Cell collection was achieved using dielectrophoresis, which employs AC fields to collect cells at energized microelectrodes, while rejecting non-cellular particles. Both live and dead Staph. aureus bacteria have been collected using RF frequency dielectrophoresis. Bacteria have been separated from polystyrene microspheres using frequency-shifting dielectrophoresis. Computational modeling was …

Description. Individual raw data streams from instrumentation at the Atmospheric Radiation Measurement (ARM) Program Climate Research Facility (ACRF) fixed and mobile sites are collected and sent to the Data Management Facility (DMF) at Pacific Northwest National Laboratory for processing in near real time. Raw and processed data are then sent daily to the ACRF Archive, where they are made available to users. For each instrument, we calculate the ratio of the actual number of data records received daily at the Archive to the expected number of data records. The results are tabulated by (1) individual data stream, site, and month for the current year and (2) site and fiscal year dating back to 1998. The United States Department of Energy requires national user facilities to report time-based operating data. The requirements concern the actual hours of operation (ACTUAL); the estimated maximum operation or uptime goal (OPSMAX), which accounts for planned downtime; and the VARIANCE [1 – (ACTUAL/OPSMAX)], which accounts for unplanned downtime. The OPSMAX time for this second quarter for the Southern Great Plains (SGP) site is 2052 hours (0.95 × 2,160 hours this quarter). The annual OPSMAX for the North Slope Alaska (NSA) site is 1944 hours (0.90 × …

This report presents a modification of a previous model for the statistical distribution of linear antenna impedance. With this modification a simple formula is determined which yields accurate results for all ratios of modal spectral width to spacing. It is shown that the reactance formula approaches the known unit Lorentzian in the lossless limit.

The formulation, implementation and usage of a numerical solution verification code is described. This code uses the Richardson extrapolation procedure to estimate the order of accuracy and error of a computational program solution. It evaluates multiple solutions performed in numerical grid convergence studies to verify a numerical algorithm implementation. Analyses are performed on both structured and unstructured grid codes. Finite volume and finite element discretization programs are examined. Two and three-dimensional solutions are evaluated. Steady state and transient solution analysis capabilities are present in the verification code. Multiple input data bases are accepted. Benchmark options are included to allow for minimal solution validation capability as well as verification.

A growing trend in developing large and complex applications on today's Teraflop scale computers is to integrate stand-alone and/or semi-independent program components into a comprehensive simulation package. One example is the Community Climate System Model which consists of atmosphere, ocean, land-surface and sea-ice components. Each component is semi-independent and has been developed at a different institution. We study how this multi-component, multi-executable application can run effectively on distributed memory architectures. For the first time, we clearly identify five effective execution modes and develop the MPH library to support application development utilizing these modes. MPH performs component-name registration, resource allocation and initial component handshaking in a flexible way.

The CABle ANAlysis (CABANA) portion of the EMPHASIS suite is designed specifically for the simulation of cable SGEMP. The code can be used to evaluate the response of a specific cable design to threat or to compare and minimize the relative response of difference designs. This document provides user-specific information to facilitate the application of the code to cables of interest.

Symbioses between cnidarians and dinoflagellates in the genus Symbiodinium are widespread in the marine environment. The importance of this symbiosis to reef-building corals and reef nutrient and carbon cycles is well documented, but little is known about the mechanisms by which the partners establish and regulate the symbiosis. Because the dinoflagellate symbionts live inside the cells of their host coral, the interactions between the partners occur on cellular and molecular levels, as each partner alters the expression of genes and proteins to facilitate the partnership. These interactions can examined using high-throughput techniques that allow thousands of genes to be examined simultaneously. We are developing the groundwork so that we can use DNA microarray profiling to identify genes involved in the Montastraea faveolata and Acropora palmata symbioses. Here we report results from the initial steps in this microarray initiative, that is, the construction of cDNA libraries from 4 of 16 target stages, sequencing of 3450 cDNA clones to generate Expressed Sequenced Tags (ESTs), and annotation of the ESTs to identify candidate genes to include in the microarrays. An understanding of how the coral-dinoflagellate symbiosis is regulated will have implications for atmospheric and ocean sciences, conservation biology, the study and diagnosis of …

The Container Analysis Fire Environment (CAFE) computer code has been developed to model all relevant fire physics for predicting the thermal response of massive objects engulfed in large fires. It provides realistic fire thermal boundary conditions for use in design of radioactive material packages and in risk-based transportation studies. The CAFE code can be coupled to commercial finite-element codes such as MSC PATRAN/THERMAL and ANSYS. This coupled system of codes can be used to determine the internal thermal response of finite element models of packages to a range of fire environments. This document is a user manual describing how to use the three-dimensional version of CAFE, as well as a description of CAFE input and output parameters. Since this is a user manual, only a brief theoretical description of the equations and physical models is included.

Arc and glow discharges are defined based on their cathode processes. Arcs are characterized by collective electron emission, which can be stationary with hot cathodes (thermionic arcs), or non-stationary with cold cathodes (cathodic arcs). A brief review on cathodic arc properties serves as the starting point to better understand arcing phenomena in sputtering. Although arcing occurs in both metal and reactive sputtering, it is more of an issue in the reactive case. Arcing occurs if sufficiently high field strength leads to thermal runaway of an electron emission site. The role of insulating layers and surface potential adjustment through current leakage is highlighted. In the situation of magnetron sputtering with ''racetrack'', the need for a model with two spatial dimensions is shown. In many cases, arcing is initiated by breakdown of dielectric layers and inclusions. It is most efficiently prevented if formation and excessive charge-up of dielectric layers and inclusions can be avoided.

This is the eighth Quarterly Report for this project. The background and technical justification for the project are described, including potential benefits of reducing fuel moisture, prior to firing in a pulverized coal boiler. Analyses were performed to determine the effects of coal product moisture on unit performance. Results are given showing how the coal product moisture level affects parameters such as boiler efficiency, power required to drive the fluidizing air fan, other station service power needed for fans and pulverizers, net unit heat rate, thermal energy rejected by the cooling tower, and stack emissions.

The KDP crystals present in the final optics assembly at the National Ignition Facility (NIF) are used for conversion of infrared laser light beam into ultraviolet. The conversion is highest for a certain incident angle, the alignment of which is determined from the position of the back reflection beam, which exhibits a distinct characteristics shape. When a phase plate device is introduced before the final assembly to increase the uniformity of the beam, the back reflection pattern changes drastically. The algorithm which is best for tracking the special shaped beam is no longer suitable to track the phase modified beam. The work presented here discusses our detection schemes for both the situations. In particular, we demonstrate how the algorithm senses the modified beam using a newly proposed criterion of ''correlation peak pedestal area'' and execute an alternate algorithm in real time without operator intervention. This new algorithm continuously tracks the beam pattern to guarantee reliable and repeatable sensing. Results from simulation and real world implementation of the algorithm at the NIF facility are presented.

This report describes a system level study on the use of a swarm of sea gliders to detect, confirm and kill littoral submarine threats. The report begins with a description of the problem and derives the probability of detecting a constant speed threat without networking. It was concluded that glider motion does little to improve this probability unless the speed of a glider is greater than the speed of the threat. Therefore, before detection, the optimal character for a swarm of gliders is simply to lie in wait for the detection of a threat. The report proceeds by describing the effect of noise on the localization of a threat once initial detection is achieved. This noise is estimated as a function of threat location relative to the glider and is temporally reduced through the use of an information or Kalman filtering. In the next section, the swarm probability of confirming and killing a threat is formulated. Results are compared to a collection of stationary sensors. These results show that once a glider has the ability to move faster than the threat, the performance of the swarm is equal to the performance of a stationary swarm of gliders with confirmation and …

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Matrix diffusion is an important mechanism for solutetransport in fractured rock. We recently conducted a literature survey onthe effective matrix diffusion coefficient, Dem, a key parameter fordescribing matrix diffusion processes at the field scale. Forty fieldtracer tests at 15 fractured geologic sites were surveyed and selectedfor study, based on data availability and quality. Field-scale Dem valueswere calculated, either directly using data reported in the literature orby reanalyzing the corresponding field tracer tests. Surveyed dataindicate that the effective-matrix-diffusion-coefficient factor FD(defined as the ratio of Dem to the lab-scale matrix diffusioncoefficient [Dem]of the same tracer) is generally larger than one,indicating that the effective matrix diffusion coefficient in the fieldis comparatively larger than the matrix diffusion coefficient at therock-core scale. This larger value could be attributed to the manymass-transfer processes at different scales in naturally heterogeneous,fractured rock systems. Furthermore, we observed a moderate trend towardsystematic increase in the emDFmDDF value with observation scale,indicating that the effective matrix diffusion coefficient is likely tobe statistically scale dependent. The FD value ranges from 1 to 10,000for observation scales from 5 to 2,000 m. At a given scale, the FD valuevaries by two orders of magnitude, reflecting the influence of differingdegrees of fractured rock heterogeneity at different …

This report describes Phase III of a project entitled Innovative Applications of Energy Storage in a Restructured Electricity Marketplace. For this study, the authors assumed that it is feasible to operate an energy storage plant simultaneously for two primary applications: (1) energy arbitrage, i.e., buy-low-sell-high, and (2) to reduce peak loads in utility ''hot spots'' such that the utility can defer their need to upgrade transmission and distribution (T&D) equipment. The benefits from the arbitrage plus T&D deferral applications were estimated for five cases based on the specific requirements of two large utilities operating in the Eastern U.S. A number of parameters were estimated for the storage plant ratings required to serve the combined application: power output (capacity) and energy discharge duration (energy storage). In addition to estimating the various financial expenditures and the value of electricity that could be realized in the marketplace, technical characteristics required for grid-connected distributed energy storage used for capacity deferral were also explored.

Thermal property measurements of 18650 cells for the Space Shuttle Orbiter Advanced Hydraulic Power System (AHPS, formerly known as EAPU) have been performed. Cells were measured from three commercial manufacturers: E-One MOLI (12 cells), Panasonic (5 cells) and Sanyo (5 cells). Thermal property measurements of the MOLI 18650 cells included measurements of specific heat, self discharge (microcalorimetry), overcharge response and thermal runaway by accelerating rate calorimetry (ARC). The Panasonic and Sanyo cells were measured only for thermal runaway response in the ARC at increasing states of charge (3.8V, 4.0V, 4.2V, 4.3V).