Publications

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The use of chemical imaging of secondary ion mass spectrometry (SIMS) data for self-modeling image analysis (SIA) has special challenges because of the following reasons: (a) At higher counting rates, the data are non-linear. (b) The heteroscedastic nature of the noise causes structure in the data which gives rise to extra components. (c) There is a high amount of noise in SIMS data and outliers often cause problems. This paper will discuss an adaptation of a pre-processing method to correct for heteroscedastic noise and a method to minimize the effect of outlying pixels. Examples will be given of the following: (a) Different mixtures of palmitic and stearic acid on aluminum foil. (b) A film coating of polyvinyl acetate (PVA) and polystyrene (PS). (c) A sample of copper and nickel and a fused layer. Copyright © 2008 John Wiley & Sons, Ltd.

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This workshop is the fourth one of a series that includes the Neutrino Geophysics Conference at Honolulu, Hawaii, which I attended in 2005. This workshop was organized by the Astro-Particle and Cosmology laboratory in the recently opened Condoret building of the University of Paris. More information, including copies of the presentations, on the workshop is available on the website: www.apc.univ-paris7.fr/AAP2007/. The workshop aims at opening neutrino physics to various fields such that it can be applied in geosciences, nuclear industry (reactor and spent fuel monitoring) and non-proliferation. The workshop was attended by over 60 people from Europe, USA, Asia and Brazil. The meeting was also attended by representatives of the Comprehensive nuclear-Test Ban Treaty (CTBT) and the International Atomic Energy Agency (IAEA). The workshop also included a workshop dinner on board of a river boat sailing the Seine river.

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Hyperspectral imaging confocal microscopy (HSI-CM) is a powerful tool for the analysis of cellular processes such as the immune response. HSI-CM is a data rich technique that routinely generates two-way data having a spectral domain and an image or concentration domain. Using a variety of modifications to the instrument or experimental protocols, one can readily produce three-way data with HSI-CM. These data are often amenable to trilinear analysis. For example we have used a time series of 18 images acquired during photobleaching of the fluorophores in an effort to identify fluorescence resonance energy transfer (FRET). The resulting images represent intensity as a function of concentration, wavelength and photodegradation in time, to which we apply our techniques of trilinear decomposition. We have successfully employed trilinear decomposition of photobleaching spectral image data from fixed A549 cells transfected with yellow and green fluorescent proteins (YFP and GFP) as molecular probes of cellular proteins involved in the cellular immune response. While useful in the interpretation biological processes, the size of the data generated with the HSI-CM can be difficult to manage computationally. The 208 x 204 x 512 x 18 elements in the image data require careful processing and efficient analysis algorithms. Accordingly, we have implemented fast algorithms that can quickly perform the trilinear decomposition. In this paper we describe how three-way data are produced and the methods we have used to process them. Specifically, we show that co-adding spectra in a spatial neighborhood is a highly effective method for improving the performance of these algorithms without sacrificing resolution. Copyright © 2008 John Wiley & Sons, Ltd.

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Towards developing rapid and portable diagnostics for detecting zoonotic diseases, we have developed microchip-based electrophoretic immunoassays for sensitive and rapid detection of viruses. Two types of microchip-based electrophoretic immunoassays were developed. The initial assay used open channel electrophoresis and laser-induced fluorescence detection with a labeled antibody to detect influenza virus. However, this assay did not have adequate sensitivity to detect viruses at relevant concentrations for diagnostic applications. Hence, a novel assay was developed that allows simultaneous concentration and detection of viruses using a microfluidic chip with an integrated nanoporous membrane. The size-exclusion properties of the in situ polymerized polyacrylamide membrane are exploited to simultaneously concentrate viral particles and separate the virus/fluorescent antibody complex from the unbound antibody. The assay is performed in two simple steps-addition of fluorescently labeled antibodies to the sample, followed by concentration of antibody-virus complexes on a porous membrane. Excess antibodies are removed by electrophoresis through the membrane and the complex is then detected downstream of the membrane. This new assay detected inactivated swine influenza virus at a concentration four times lower than that of the open-channel electrophoresis assay. The total assay time, including device regeneration, is six minutes and requires <50 μl of sample. The filtration effect of the polymer membrane eliminates the need for washing, commonly required with surface-based immunoassays, increasing the speed of the assay. This assay is intended to form the core of a portable device for the diagnosis of high-consequence animal pathogens such as foot-and-mouth disease. The electrophoretic immunoassay format is rapid and simple while providing the necessary sensitivity for diagnosis of the illness state. This would allow the development of a portable, cost-effective, on-site diagnostic system for rapid screening of large populations of livestock, including sheep, pigs, cattle, and potentially birds. © The Royal Society of Chemistry.

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This paper introduces and develops the concept of "Type X" and "Type Y" errors in model validation and calibration, and their implications on extrapolative prediction. Type X error is non-detection of model bias because it is effectively hidden by the uncertainty in the experiments. Possible deleterious effects of Type X error can be avoided by mapping uncertainty into the model until it envelopes the potential model bias, but this likely assigns a larger uncertainty than is needed to account for the actual bias (Type Y error). A philosophy of Best Estimate + Uncertainty modeling and prediction is probably best supported by taking the conservative choice of guarding against Type X error while accepting the downside of incurring Type Y error. An associated methodology involving data-and model-conditioning is presented and tested on a simple but rich test problem. The methodology is shown to appropriately contend with model bias under conditions of systematic experimental input uncertainty in the test problem. The methodology effectively bounds the uncertain model bias and brings a correction into the model that extrapolates very well under a large variety of extrapolation conditions. The methodology has been straightforwardly applied to considerably more complex real problems where system response is likewise jointly monotonic in the input uncertainties. The methodology also allows for other types of systematic and random uncertainty in the experiments and model as discussed herein. Copyright © 2008 SAE International.

We demonstrate the first high-speed second-order silicon microdisk bandpass switch. The switch, constructed of a pair of 3μm radii active microdisks possesses ~40GHz flat-top passbands, a 4.2THz free-spectral-range, and a 2.4ns switching time. © 2008 Optical Society of America.

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Predicting and controlling the evolution of materials microstructure is one of the central challenges of materials science. The simulation of microstructural evolution requires a detailed knowledge of the properties, including energies and mobilities, of interfaces in the material. We present the results of molecular dynamics simulations of these interfacial properties for a large set of boundaries.

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This paper reports post-CMOS compatible aluminum nitride dual mode resonator filters that realize 4th order band-pass filters in a single resonator device. Dual mode filters at 106 MHz operating in their fundamental mode are reported with insertion losses as low as 5.5 dB when terminated with 150 Ω. A notching technique is demonstrated for varying the 3 dB bandwidth of these filters from 0.15 to 0.7%, overcoming a significant limitation of previous work. Dual mode filters operating at their 5th and 10th overtones are reported scaling the operating frequencies of this class of device to 0.55 and 1.1 GHz.

Electrothermal actuation has been used in microelectromechanical systems where low actuation voltage and high contact force are required. Power consumption to operate electrothermal actuators has typically been higher than with electrostatic actuation. A method of designing and processing electrothermal actuators is presented that leads to an order of magnitude reduction in required power while maintaining the low voltage, high force advantages. The substrate was removed beneath the actuator beams, thereby discarding the predominant power loss mechanism and reducing the required actuation power by an order of magnitude. Measured data and theoretical results from electrothermally actuated switches are presented to confirm the method. © 2008 Society of Photo-Optical Instrumentation Engineers.

This work presents a new type of MEMS resonator based on launching an acoustic wave around a ring. Its maximum frequency is set by electrode spacing and can therefore provide a means for developing resonators with center frequencies in the GHz. In addition since the center frequency is dependent on the average radius it is not subject to lithographic process variations in ring width. We have demonstrated several Ring Waveguide (RWG) Resonators with center frequencies at 484 MHz and 1 GHz. In addition we have demonstrated a 4th order filter based on a RWG design.

The thermodynamics and kinetics of hydrogen dissolved in structural metals is often not addressed when assessing phenomena associated with hydrogen-assisted fracture. Understanding the behavior of hydrogen atoms in a metal lattice, however, is important for interpreting materials properties measured in hydrogen environments, and for designing structurally efficient components with extended lifecycles. The assessment of equilibrium hydrogen contents and hydrogen transport in steels is motivated by questions raised in the safety, codes and standards community about mixtures of gases containing hydrogen as well as the effects of stress and hydrogen trapping on the transport of hydrogen in metals. More broadly, these questions are important for enabling a comprehensive understanding of hydrogen-assisted fracture. We start by providing a framework for understanding the thermodynamics of pure gaseous hydrogen and then we extend this to treat mixtures of gases containing hydrogen. An understanding of the thermodynamics of gas mixtures is necessary for analyzing concepts for transitioning to a hydrogen-based economy that incorporate the addition of gaseous hydrogen to existing energy carrier systems such as natural gas distribution. We show that, at equilibrium, a mixture of gases containing hydrogen will increase the fugacity of the hydrogen gas, but that this increase is small for practical systems and will generally be insufficient to substantially impact hydrogen-assisted fracture. Further, the effects of stress and hydrogen trapping on the transport of atomic hydrogen in metals are considered. Tensile stress increases the amount of hydrogen dissolved in a metal and slightly increases hydrogen diffusivity. In some materials, hydrogen trapping has very little impact on hydrogen content and transport, while other materials show orders of magnitude increases of hydrogen content and reductions of hydrogen diffusivity. © 2008 Materials Research Society.

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We demonstrate high-speed switching of a symmetric self-electrooptic effect device (S-SEED) operating at 1550 nm. Transitions faster than 10 ps are observed, verifying the suitability of this technology for integrated logic operations beyond 40 GHz. © 2008 Optical Society of America.

Stable and accurate numerical modeling of seismic wave propagation in the vicinity of high-contrast interfaces is achieved with straightforward modifications to the conventional, rectangular-staggered-grid, finite-difference (FD) method. Improvements in material parameter averaging and spatial differencing of wavefield variables yield high-quality synthetic seismic data.

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Packet switched data communication networks that use distributed processing architectures have the potential to simplify the design and development of new and increasingly sophisticated satellite payloads. Distributed network architectures can improve system reliability and capability and reduce size, weight, and power when compared to current architectures. This study performed a broad review of network characteristics and architectures for use on-board future satellite payloads. The concepts of topology selection, commercially available communication protocols, and architecture modeling and simulation were studied, and the results are presented in this paper. Copyright © 2008 by the American Institute of Aeronautics and Astronautics, Inc.

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Micro- and nanofluidics pose a series of significant challenges for science-based modeling. Key among those are the wide separation of length- and timescales between interface phenomena and bulk flow and the spatially heterogeneous solution properties near solid-liquid interfaces. It is not uncommon for characteristic scales in these systems to span nine orders of magnitude from the atomic motions in particle dynamics up to evolution of mass transport at the macroscale level, making explicit particle models intractable for all but the simplest systems. Recently, atomistic-to-continuum (A2C) multiscale simulations have gained a lot of interest as an approach to rigorously handle particle-level dynamics while also tracking evolution of large-scale macroscale behavior. While these methods are clearly not applicable to all classes of simulations, they are finding traction in systems in which tight-binding, and physically important, dynamics at system interfaces have complex effects on the slower-evolving large-scale evolution of the surrounding medium. These conditions allow decomposition of the simulation into discrete domains, either spatially or temporally. In this paper, we describe how features of domain decomposed simulation systems can be harnessed to yield flexible and efficient software for multiscale simulations of electric field-driven micro- and nanofluidics. © 2008 - IOS Press and the authors. All rights reserved.

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We will present our recent progress on 1) waveguide-based sensor arrays that can operate as high density immunoassay sensors for detection of proteins and other biomolecules in solution, 2) metamaterial and plasmonic-based chem-bio sensors. © 2008 Optical Society of America.

We present a mesh optimization algorithm for adaptively improving the finite element interpolation of a function of interest. The algorithm minimizes an objective function by swapping edges and moving nodes. Numerical experiments are performed on model problems. The results illustrate that the mesh optimization algorithm can reduce the W1,∞ semi-norm of the interpolation error. For these examples, the L2, L∞, and H1 norms decreased also.

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This paper presents a new method for handling non-conforming hexahedralto- hexahedral interfaces. One or both of the adjacent hexahedralmeshes are locally modified to create a one-to-onemapping between between themesh nodes and quadrilaterals at the interface allowing a conforming mesh to be created. In the finite element method, non-conforming interfaces are currently handled using constraint conditions such as gapelements, tied contacts, or multi-point constraints. By creating a conforming mesh, the need for constraint conditions is eliminated resulting in a smoother, more precise numerical solution. The method presented in this paper uses hexahedral dual operations, including pillowing, sheet extraction, dicing and column collapse operations, to affect the local mesh modifications. In addition, an extension to pillowing, called sheet inflation, is introduced to handle the insertion of self-intersecting and self-touching sheets. The quality of the resultant conforming hexahedral mesh is high and the increase in number of elements is moderate.

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A sub-scale experiment has been conducted to study the trailing vortex shed from a tapered fin installed on a wind tunnel wall to represent missile configurations. Stereoscopic particle image velocimetry measurements have been acquired in the near-field for several locations downstream of the fin tip and at different fin angles of attack. The vortex's tangential velocity is found to decay with downstream distance while its radius increases, but the vortex core circulation remains constant. Circulation and tangential velocity rise greatly for increased fin angle of attack, but the radius is approximately constant or slightly decreasing. The vortex axial velocity is always a deficit, whose magnitude diminishes with downstream distance and smaller angle of attack. No variation with Mach number can be discerned in the normalized velocity data. Vortex roll-up is observed to be largely complete by about four root chord lengths downstream of the fin trailing edge. Prior to this point, the vortex is asymmetric in the tangential velocity but the core radius stays nearly constant. Vortical rotation draws low-speed turbulent fluid from the wind tunnel wall boundary layer into the vortex core, which appears to hasten vortex decay and produce a larger axial velocity deficit than might be expected. Self-similarity of the vortex is established even while it is still rolling up. Attempts to normalize vortex properties by the fin's lift coefficient proved unsuccessful.

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Advances in high-performance computational capabilities enable scientific simulations with increasingly realistic physical representations. This situation is especially true of turbulent combustion involving multiscale interactions between turbulent flow, complex chemical reaction, and scalar transport. A fundamental understanding of combustion processes is crucial to the development and optimization of next-generation combustion technologies operating with alternative fuels, at higher pressures, and under less stable operating conditions, such as highly dilute, stratified mixtures. Direct numerical simulations (DNS) of turbulent combustion resolving all flow and chemical features in canonical configurations are used to improve fundamental understanding of complex flow processes and to provide a database for the development and validation of combustion models. A description of the DNS solver and its optimization for use in massively parallel simulations is presented. Recent DNS results from a series of three combustion configurations are presented: soot formation and transport in a nonpremixed ethylene jet flame, the effect of fuel stratification in methane Bunsen flames, and extinction and reignition processes in nonpremixed ethylene jet flames. © 2008 IOP Publishing Ltd.

Error in Particle Image Velocimetry (PIV) interrogation due to velocity gradients in turbulent flows was studied for both classical and advanced algorithms. Classical algorithms are considered to be digital cross-correlation analysis including discrete window offsets and, for the present work, advanced algorithms are those using image deformation to compensate for velocity gradients. Synthetic PIV simulations revealed substantial negative biases in the turbulent stress for classical algorithms even for velocity gradients within recommended PIV design limits. This bias worsens if the distribution of velocity gradients has a nonzero mean, and error in the mean velocity may be introduced as well. Conversely, advanced algorithms do not exhibit this bias error if the velocity gradients are linear. Nonlinear velocity gradients increase the error in classical algorithms and a significant negative bias in the turbulent stress arises for the advanced algorithm as well. Two experimental data sets showed substantially lower turbulent stresses for the classical algorithm compared with the advanced algorithm, as predicted. No new experimental design rules for advanced algorithms are yet proposed, but any such recommendation would concern second-order velocity derivatives rather than first order.

We have demonstrated purification of proteins in a simple aqueous two-phase extraction process in a microfluidic device. The laminar flows inherent to microchannels allows us to perform a binary split of a complex cell lysate sample, in an open channel with no chromatography support and no moving parts. This mild process allows recovery of functional proteins with a modest increase in purity. Aromatic-rich fusion tags are used to drive partitioning of enzymes in a generic PEG-salt two-phase system. Addition of affinity ligands to the PEG phase allows us to exploit other popular fusion tags, such as polyhistidine tags and GST-tags. © 2008 CBMS.

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We demonstrate the power of our technique for establishing and immobilizing well-defined polymer gradients in microchannels by fabricating two miniaturized analytical platforms: microscale immobilized pH gradients (μIPGs) for rapid and high resolution isoelectric focusing (IEF) applications, and polyacrylamide porosity gradients to achieve microscale pore limit electrophoresis (μPLE) in which species are separated based on molecular size by driving them toward the pore size at which migration ceases. Both separation techniques represent the first microscale implementation of their respective methodologies.

Simulations of water at hydrophilic self-assembled monolayer (SAM) surfaces are especially relevant for biological interfaces. Well-defined, atomically smooth surfaces that can be continuously varied are possible with SAMs. These characteristics enable more accurate measurements than many other surfaces with the added advantage of tailoring the surface to treat specific chemical groups. A fundamental question is how solid surfaces affect the structure and dynamics of water. Measurements of the structure and dynamics of water at solid surfaces have improved significantly, but there remain differences among the experiments. In this article, the authors review simulations of water at the interface with hydrophilic SAMs. These simulations find that while the interfacial water molecules are slower than the bulk water molecules, the interfacial dynamics remains that of a liquid. A major biological application of SAMs is for making coatings resistant to protein adsorption. SAMs terminated with ethylene glycol monomers have proven to be excellent at resisting protein adsorption. Understanding the mechanisms behind this resistance remains an unresolved issue. Recent simulations suggest a new perspective of the role of interfacial water and the inseparable interplay between the SAM and the water. © 2008 American Vacuum Society.

A Brain-Emulating Cognition and Control Architecture (BECCA) is presented. It is consistent with the hypothesized functions of pervasive intra-cortical and cortico-subcortical neural circuits. It is able to reproduce many salient aspects of human voluntary movement and motor learning. It also provides plausible mechanisms for many phenomena described in cognitive psychology, including perception and mental modeling. Both "inputs" (afferent channels) and "outputs"' (efferent channels) are treated as neural signals; they are all binary (either on or off) and there is no meaning, information, or tag associated with any of them. Although BECCA initially has no internal models, it learns complex interrelations between outputs and inputs through which it bootstraps a model of the system it is controlling and the outside world. BECCA uses two key algorithms to accomplish this: S-Learning and Context-Based Similarity (CBS).

We describe a novel approach to fabricate high-aspect-ratio membranes in microchannels by direct laser scanning, and demonstrate >10-fold improvement in sample preconcentration speed by achieving lower fM detection of proteins within 5 minutes. The integrated device can be used for continuous sample preparation, injection, preconcentration, and biochemical binding/reaction applications. © 2008 CBMS.

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A sub-scale experiment has been constructed using fins mounted on one wall of a transonic wind tunnel to investigate the influence of fin trailing vortices upon downstream control surfaces. Data are collected using a fin balance instrumenting the downstream fin to measure the aerodynamic forces of the interaction, combined with stereoscopic Particle Image Velocimetry to determine vortex properties. The fin balance data show that the response of the downstream fin essentially is shifted from the baseline single-fin data dependent upon the angle of attack of the upstream fin. Freestream Mach number and the spacing between fins have secondary effects. The velocimetry shows that the vortex strength increases markedly with upstream fin angle of attack, though even an uncanted fin generates a noticeable wake. No variation with Mach number can be discerned in the normalized velocity data. Correlations between the force data and the velocimetry suggest that the interaction is fundamentally a result of an angle of attack superposed upon the downstream fin by the vortex shed from the upstream fin tip. The Mach number influence arises from differing vortex lift on the leading edge of the downstream fin even when the impinging vortex is Mach invariant.

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An experiment was conducted comparing the effectiveness of individual versus group electronic brainstorming in addressing real-world "wickedly difficult" challenges. Previous laboratory research has engaged small groups of students in answering questions irrelevant to an industrial setting. The current experiment extended this research to larger, real-world employee groups engaged in addressing organizationrelevant challenges. Within the present experiment, the data demonstrated that individuals performed at least as well as groups in terms of number of ideas produced and significantly (p<.02) outperformed groups in terms of the quality of those ideas (as measured along the dimensions of originality, feasibility, and effectiveness).

Tuberculosis (TB), caused by the bacterium Mycobacterium tuberculosis (Mtb), is a growing international health crisis. Mtb is able to persist in host tissues in a nonreplicating persistent (NRP) or latent state. This presents a challenge in the treatment of TB. Latent TB can re-activate in 10% of individuals with normal immune systems, higher for those with compromised immune systems. A quantitative understanding of latency-associated virulence mechanisms may help researchers develop more effective methods to battle the spread and reduce TB associated fatalities. Leveraging BioXyce's ability to simulate whole-cell and multi-cellular systems we are developing a circuit-based framework to investigate the impact of pathogenicity-associated pathways on the latency/reactivation phase of tuberculosis infection. We discuss efforts to simulate metabolic pathways that potentially impact the ability of Mtb to persist within host immune cells. We demonstrate how simulation studies can provide insight regarding the efficacy of potential anti-TB agents on biological networks critical to Mtb pathogenicity using a systems chemical biology approach. © 2008 IEEE.

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We develop an approach for estimating model parameters which result in the "best distribution fit" between experimental and simulation data. Best distribution fit means matching moments of experimental data to those of a simulation (and possibly matching a full probability distribution). This approach extends typical nonlinear least squares methods which identify parameters maximizing agreement between experimental points and computational simulation results. Several analytic formulations for the distribution matching problem are provided, along with results for solving test problems and comparisons of this parameter estimation technique with a deterministic least squares approach. Copyright © 2008 by the American Institute of Aeronautics and Astronautics, Inc.

We describe a novel approach to fabricate high-aspect-ratio membranes in microchannels by direct laser scanning, and demonstrate >10-fold improvement in sample preconcentration speed by achieving lower fM detection of proteins within 5 minutes. The integrated device can be used for continuous sample preparation, injection, preconcentration, and biochemical binding/reaction applications. © 2008 CBMS.

The rich history of scalable computing research owes much to a rapid rise in computing platform scale in terms of size and speed. As platforms evolve, so must algorithms and the software expressions of those algorithms. Unbridled growth in scale inevitably leads to complexity. This special issue grapples with two facets of this complexity: scalable execution and scalable development. The former results from efficient programming of novel hardware with increasing numbers of processing units (e.g., cores, processors, threads or processes). The latter results from efficient development of robust, flexible software with increasing numbers of programming units (e.g., procedures, classes, components or developers). The progression in the above two parenthetical lists goes from the lowest levels of abstraction (hardware) to the highest (people). This issue's theme encompasses this entire spectrum. The lead author of each article resides in the Scalable Computing Research and Development Department at Sandia National Laboratories in Livermore, CA. Their co-authors hail from other parts of Sandia, other national laboratories and academia. Their research sponsors include several programs within the Department of Energy's Office of Advanced Scientific Computing Research and its National Nuclear Security Administration, along with Sandia's Laboratory Directed Research and Development program and the Office of Naval Research. The breadth of interests of these authors and their customers reflects in the breadth of applications this issue covers. This article demonstrates how to obtain scalable execution on the increasingly dominant high-performance computing platform: a Linux cluster with multicore chips. The authors describe how deep memory hierarchies necessitate reducing communication overhead by using threads to exploit shared register and cache memory. On a matrix-matrix multiplication problem, they achieve up to 96% parallel efficiency with a three-part strategy: intra-node multithreading, non-blocking inter-node message passing, and a dedicated communications thread to facilitate concurrent communications and computations. On a quantum chemistry problem, they spawn multiple computation threads and communication threads on each node and use one-sided communications between nodes to minimize wait times. They reduce software complexity by evolving a multi-threaded factory pattern in C++ from a working, message-passing program in C.

Reaction dynamics in exothermic Co/Al multilayer foils are studied with high speed digital photography. Unsteady, spin-like reaction propagation is observed in which the net synthesis of a foil is accomplished through advancing transverse bands that propagate perpendicular to the net reaction direction. This unsteady behavior is connected to the final reacted foil surface morphology that exhibits periodic structures. The evolution of the reaction front shape and corresponding surface morphology are discussed with respect to Co/Al foil characteristics. © 2009 Materials Research Society.

The monolithic nature of transportation technologies offers opportunities for significant improvements in efficiency of 25-50% through strategic technical investments in both advanced fuels and new low-temperature engine concepts. The application of direct numerical simulation (DNS) provides a way to study fundamental issues related to small-scale combustion processes in well-defined canonical configurations, whereas the application of large eddy simulation (LES) provides a formal treatment of the full range of time and length scales that exist in turbulent reacting flows, and thus provides a direct link to experimental studies of relevant combustion devices. In the present study, through DOE INCITE and Oak Ridge National Laboratory 250 Tflop Transition-to-Operations grants in 2008, DNS is performed to understand how a lifted autoignitive flame is stabilized, and LES is performed to understand the high-pressure injection and mixing processes in internal combustion engines. Understanding of these and other fundamental issues is needed to develop robust and reliable ignition and combustion models for the combustion regimes observed under low-temperature combustion engine environments using alternative fuels. © 2008 IOP Publishing Ltd.

A coupled Euler-Lagrange solution approach is used to model the response of a buried reinforced concrete structure subjected to a close-in detonation of a high explosive charge. The coupling algorithm is discussed along with a set of benchmark calculations involving detonations in clay and sand.

The disturbed rock zone constitutes an important geomechanical element of the Waste Isolation Pilot Plant. The science and engineering underpinning the disturbed rock zone provide the basis for evaluating ongoing operational issues and their impact on performance assessment. Contemporary treatment of the disturbed rock zone applied to the evaluation of the panel closure system and to a new mining horizon improves the level of detail and quantitative elements associated with a damaged zone surrounding the repository openings. Technical advancement has been realized by virtue of ongoing experimental investigations and international collaboration. Initial sections summarize and document theoretical and experimental results, which quantify characteristics of the disturbed rock zone as applied to nuclear waste repositories in salt. This information is then applied to operational issues pertaining to recertification of the repository. © 2008 ASCE.

A total system performance assessment (TSPA) model has been developed to analyze the ability of the natural and engineered barriers of the Yucca Mountain repository to isolate nuclear waste over the period following repository closure. The principal features of the engineered barrier system are emplacement tunnels (or "drifts") containing a two-layer waste package (WP) for waste containment and a titanium drip shield to protect the WP from seeping water and falling rock. The 25-mm-thick outer shell of the WP is composed of Alloy 22, a highly corrosion-resistant nickel-based alloy. There are five nominal degradation modes of the Alloy 22: general corrosion, microbially influenced corrosion, stress corrosion cracking, early failure due to manufacturing defects, and localized corrosion (LC). This paper specifically examines the incorporation of the Alloy 22 LC model into the Yucca Mountain TSPA model, particularly the abstraction and modeling methodology, as well as issues dealing with scaling, spatial variability, uncertainty, and coupling to other submodels that are part of the total system model, such as the submodel for seepage water chemistry.

Future energy systems based on gasification of coal or biomass for co-production of electrical power and fuels may require gas turbine operation on unusual gaseous fuel mixtures. In addition, global climate change concerns may dictate the generation of a CO2 product stream for end-use or sequestration, with potential impacts on the oxidizer used in the gas turbine. In this study the operation at atmospheric pressure of a small, optically accessible swirl-stabilized premixed combustor, burning fuels ranging from pure methane to conventional and H2-rich and H2-lean syngas mixtures is investigated. Both air and CO2-diluted oxygen are used as oxidizers. CO and NOx emissions for these flames have been determined from the lean blowout limit to slightly rich conditions (1.03). In practice, CO2-diluted oxygen systems will likely be operated close to stoichiometric conditions to minimize oxygen consumption while achieving acceptable NOx performance. The presence of hydrogen in the syngas fuel mixtures results in more compact, higher temperature flames, resulting in increased flame stability and higher NOx emissions. Consistent with previous experience, the stoichiometry of lean blowout decreases with increasing H2 content in the syngas. Similarly, the lean stoichiometry at which CO emissions become significant decreases with increasing H2 content. For the mixtures investigated, CO emissions near the stoichiometric point do not become significant until 0.95. At this stoichiometric limit, CO emissions rise more rapidly for combustion in O2-CO2 mixtures than for combustion in air.

Understanding the relationship between chemical structure and function is a ubiquitous problem within the fields of chemistry and biology. Simulation approaches attack the problem utilizing physics to understand a given process at the particle level. Unfortunately, these approaches are often too expensive for many problems of interest. Informatics approaches attack the problem with empirical analysis of descriptions of chemical structure. The issue in these methods is how to describe molecules in a manner that facilitates accurate and general calculation of molecular properties. Here, we present a novel approach that utilizes aspects of simulation and informatics in order to formulate structure-property relationships. We show how supervised learning can be utilized to overcome the sampling problem in simulation approaches. Likewise, we show how learning can be achieved based on molecular descriptions that are rooted in the physics of dynamic intermolecular forces. We apply the approach to three problems including the analysis of corticosteroid binding globulin ligand binding affinity, identification of formylpeptide receptor ligands, and identification of resveratrol analogues capable of inhibiting activation of transcription factor nuclear factor kappaB. © 2008 American Chemical Society.

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In part I of this study we introduced a 17-parameter model that can predict heart rate regulation during postural change from sitting to standing. In this subsequent study, we focus on the 17 model parameters needed to adequately represent the observed heart rate response. In part I and in previous work (Olufsen et al. 2006), we estimated the 17 model parameters by minimizing the least squares error between computed and measured values of the heart rate using the Nelder-Mead method (a simplex algorithm). In this study, we compare the Nelder-Mead optimization method to two sampling methods: the implicit filtering method and a genetic algorithm. We show that these off-the-shelf optimization methods can work in conjunction with the heart rate model and provide reasonable parameter estimates with little algorithm tuning. In addition, we make use of the thousands of points sampled by the optimizers in the course of the minimization to perform an overall analysis of the model itself. Our findings show that the resulting least-squares problem has multiple local minima and that the non-linear-least squares error can vary over two orders of magnitude due to the complex interaction between the model parameters, even when provided with reasonable bound constraints. © Springer Science+Business Media, LLC 2007.

A method to measure interfacial mechanical properties at high temperatures and in a controlled atmosphere has been developed to study anodized aluminum surface coatings at temperatures where the interior aluminum alloy is molten. This is the first time that the coating strength has been studied under these conditions. We have investigated the effects of ambient atmosphere, temperature, and surface finish on coating strength for samples of aluminum alloy 7075. Surprisingly, the effective Young's modulus or strength of the coating when tested in air was twice as high as when samples were tested in an inert nitrogen or argon atmosphere. Additionally, the effective Young's modulus of the anodized coating increased with temperature in an air atmosphere but was independent of temperature in an inert atmosphere. The effect of surface finish was also examined. Sandblasting the surface prior to anodization was found to increase the strength of the anodized coating with the greatest enhancement noted for a nitrogen atmosphere. Machining marks were not found to significantly affect the strength.

Current published models for predicting squeeze film damping (SFD), which are based on different assumptions, give widely different results in the free-molecule regime. The work presented here provides experimental data for validating SFD models in that regime. The test device was an almost rectangular micro plate supported by beam springs. The structure was base-excited. The rigid plate oscillated vertically while staying parallel to the substrate. The velocities of the plate and of the substrate were measured with a laser Doppler vibrometer and a microscope. The damping ratio was calculated by performing modal analysis of the frequency response functions. The test structures were contained in a vacuum chamber with air pressures controlled to provide a five-order-of-magnitude range of Knudsen numbers. The damping coefficients from the measurements were compared with predictions from various published models. The results show that the continuum-base Reynolds equation predicts squeeze-film damping accurately if used with correct boundary conditions. The accuracy of molecular-based models depends heavily on the assumptions used in developing the models. Copyright © 2007 by ASME.

The shape control of thin, flexible structures has been studied primarily for edge-supported thin-plates. For applications such as electromagnetic wave reflectors, corner-supported configurations may prove more applicable since they allow for greater flexibility and larger achievable deflections when compared to edge-supported geometries under similar actuation conditions. Models of such structures provide insight for effective, realizable designs, enable design optimization, and provide a means of active shape control. Models for small deformations of corner-supported, thin laminates actuated by integrated piezoelectric actuators have been developed. However, membrane deflections expected for nominal actuation exceed those stipulated by linear, small deflection theories. In addition, large deflection models have been developed for membranes; however these models are not formulated for shape control. This paper extends a previously-developed linear model for a corner-supported thin, rectangular laminate to a more general large deflection model for a clamped-corner laminate composed of moment actuators and an array of actuating electrodes. First, a nonlinear model determining the deflected shape of a laminate given a distribution of actuation voltages is derived. Second, a technique is employed to formulate the model as a map between input voltage and deflection alone, making it suitable for shape control. Finally, comparisons of simulated deflections with measured deflections of a fabricated active laminate are investigated.

Optical filters based on resonant gratings have spectral characteristics that are lithographically defined. Nanoimprint lithography is a relatively new method for producing large area gratings with sub-micron features. Computational modeling using rigorous coupled-wave analysis allows gratings to be designed to yield sharp reflectance maxima and minima. Combining these gratings with microfluidic channels and micromechanical actuators produced using micro electromechanical systems (MEMS) technology forms the basis for producing tunable filters and other wavelength selective elements. These devices achieve tunable optical characteristics by varying the index of refraction on the surface of the grating. Coating the grating surface with water creates a 33% change in the resonant wavelength whereas bringing a grating into contact with a quartz surface shifts the resonant wavelength from 558 nm to 879 nm, a fractional change of 58%. The reflectivity at a single wavelength can be varied by approximately a factor of three. Future applications of these devices may include tunable filters or optical modulators. © 2008 Society of Photo-Optical Instrumentation Engineers.

We describe a method of performing trilinear analysis on large data sets using a modification of the PARAFAC-ALS algorithm. Our method iteratively decomposes the data matrix into a core matrix and three loading matrices based on the Tuckerl model. The algorithm is particularly useful for data sets that are too large to upload into a computer's main memory. While the performance advantage in utilizing our algorithm is dependent on the number of data elements and dimensions of the data array, we have seen a significant performance improvement over operating PARAFAC-ALS on the full data set. In one case of data comprising hyperspectral images from a confocal microscope, our method of analysis was approximately 60 times faster than operating on the full data set, while obtaining essentially equivalent results. Published in 2008 by John Wiley & Sons, Ltd.

Chemical solution deposition has been used to fabricate continuous ultrathin lead lanthanum zirconate titanate (PLZT) films as thin as 20 nm. Further, multilayer capacitor structures with as many as 10 dielectric layers have been fabricated from these ultrathin PLZT films by alternating spin-coated dielectric layers with sputtered platinum electrodes. Integrating a photolithographically defined wet etch step to the fabrication process enabled the production of functional multilayer stacks with capacitance values exceeding 600 nF. Such ultrathin multilayer capacitors offer tremendous advantages for further miniaturization of integrated passive components.

Advances are reported in several aspects of clathrate hydrate desalination fundamentals necessary to develop an economical means to produce municipal quantities of potable water from seawater or brackish feedstock. These aspects include the following, (1) advances in defining the most promising systems design based on new types of hydrate guest molecules, (2) selection of optimal multi-phase reactors and separation arrangements, and, (3) applicability of an inert heat exchange fluid to moderate hydrate growth, control the morphology of the solid hydrate material formed, and facilitate separation of hydrate solids from concentrated brine. The rate of R141b hydrate formation was determined and found to depend only on the degree of supercooling. The rate of R141b hydrate formation in the presence of a heat exchange fluid depended on the degree of supercooling according to the same rate equation as pure R141b with secondary dependence on salinity. Experiments demonstrated that a perfluorocarbon heat exchange fluid assisted separation of R141b hydrates from brine. Preliminary experiments using the guest species, difluoromethane, showed that hydrate formation rates were substantial at temperatures up to at least 12 C and demonstrated partial separation of water from brine. We present a detailed molecular picture of the structure and dynamics of R141b guest molecules within water cages, obtained from ab initio calculations, molecular dynamics simulations, and Raman spectroscopy. Density functional theory calculations were used to provide an energetic and molecular orbital description of R141b stability in both large and small cages in a structure II hydrate. Additionally, the hydrate of an isomer, 1,2-dichloro-1-fluoroethane, does not form at ambient conditions because of extensive overlap of electron density between guest and host. Classical molecular dynamics simulations and laboratory trials support the results for the isomer hydrate. Molecular dynamics simulations show that R141b hydrate is stable at temperatures up to 265K, while the isomer hydrate is only stable up to 150K. Despite hydrogen bonding between guest and host, R141b molecules rotated freely within the water cage. The Raman spectrum of R141b in both the pure and hydrate phases was also compared with vibrational analysis from both computational methods. In particular, the frequency of the C-Cl stretch mode (585 cm{sup -1}) undergoes a shift to higher frequency in the hydrate phase. Raman spectra also indicate that this peak undergoes splitting and intensity variation as the temperature is decreased from 4 C to -4 C.

This work utilized advanced engineering in several fields to find solutions to the challenges presented by the integration of MEMS/NEMS with optoelectronics to realize a compact sensor system, comprised of a microfabricated sensor, VCSEL, and photodiode. By utilizing microfabrication techniques in the realization of the MEMS/NEMS component, the VCSEL and the photodiode, the system would be small in size and require less power than a macro-sized component. The work focused on two technologies, accelerometers and microphones, leveraged from other LDRD programs. The first technology was the nano-g accelerometer using a nanophotonic motion detection system (67023). This accelerometer had measured sensitivity of approximately 10 nano-g. The Integrated NEMS and optoelectronics LDRD supported the nano-g accelerometer LDRD by providing advanced designs for the accelerometers, packaging, and a detection scheme to encapsulate the accelerometer, furthering the testing capabilities beyond bench-top tests. A fully packaged and tested die was never realized, but significant packaging issues were addressed and many resolved. The second technology supported by this work was the ultrasensitive directional microphone arrays for military operations in urban terrain and future combat systems (93518). This application utilized a diffraction-based sensing technique with different optical component placement and a different detection scheme from the nano-g accelerometer. The Integrated NEMS LDRD supported the microphone array LDRD by providing custom designs, VCSELs, and measurement techniques to accelerometers that were fabricated from the same operational principles as the microphones, but contain proof masses for acceleration transduction. These devices were packaged at the end of the work.

We analyze and compare findings from identical national surveys of the US general public on nuclear security and terrorism administered by telephone and Internet in mid-2007. Key areas of investigation include assessments of threats to US security; valuations of US nuclear weapons and nuclear deterrence; perspectives on nuclear proliferation, including the specific cases of North Korea and Iran; and support for investments in nuclear weapons capabilities. Our analysis of public views on terrorism include assessments of the current threat, progress in the struggle against terrorism, preferences for responding to terrorist attacks at different levels of assumed casualties, and support for domestic policies intended to reduce the threat of terrorism. Also we report findings from an Internet survey conducted in mid 2007 that investigates public views of US energy security, to include: energy supplies and reliability; energy vulnerabilities and threats, and relationships among security, costs, energy dependence, alternative sources, and research and investment priorities. We analyze public assessments of nuclear energy risks and benefits, nuclear materials management issues, and preferences for the future of nuclear energy in the US. Additionally, we investigate environmental issues as they relate to energy security, to include expected implications of global climate change, and relationships among environmental issues and potential policy options.

We report Lithium-Ion batteries are being considered as a high-energy density replacement for Nickel Metal Hydride (NiMH) batteries in Hybrid Electric Vehicles (HEVs) and in the new Plug-In Hybrids (PHEVs). Although these cells can result in significant reduction in weight and volume, they have several safety related issues that still need to be addressed. We report here on the thermal response of Li-ion cells specifically assembled in our laboratory to test new materials, electrolytes and additives. Finally, improvements in the thermal abuse tolerance of cells are reported and discussed in terms of the need for overall battery system safety.

A previous LDRD studying radiation hardened optoelectronic components for space-based applications led to the result that increased neutron irradiation from a fast-burst reactor caused increased responsivity in GaAs photodiodes up to a total fluence of 4.4 x 10{sup 13} neutrons/cm{sup 2} (1 MeV Eq., Si). The silicon photodiodes experienced significant degradation. Scientific literature shows that neutrons can both cause defects as well as potentially remove defects in an annealing-like process in GaAs. Though there has been some modeling that suggests how fabrication and radiation-induced defects can migrate to surfaces and interfaces in GaAs and lead to an ordering effect, it is important to consider how these processes affect the performance of devices, such as the basic GaAs p-i-n photodiode. In this LDRD, we manufactured GaAs photodiodes at the MESA facility, irradiated them with electrons and neutrons at the White Sands Missile Range Linac and Fast Burst Reactor, and performed measurements to show the effect of irradiation on dark current, responsivity and high-speed bandwidth.

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An analytic model for electron flow in a system driving a fixed inductive load is described and evaluated with particle in cell simulations. The simple model allows determining the impedance profile for a magnetically insulated transmission line given the minimum gap desired, and the lumped inductance inside the transition to the minimum gap. The model allows specifying the relative electron flow along the power flow direction, including cases where the fractional electron flow decreases in the power flow direction. The electrons are able to return to the cathode because they gain energy from the temporally rising magnetic field. The simulations were done with small cell size to reduce numerical heating. An experiment to compare electron flow to the simulations was done. The measured electron flow is {approx}33% of the value from the simulations. The discrepancy is assumed to be due to a reversed electric field at the cathode because of the inductive load and falling electron drift velocity in the power flow direction. The simulations constrain the cathode electric field to zero, which gives the highest possible electron flow.

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Understanding and controlling friction in micromachine interfaces is critical to the reliability and operational efficiency of microelectromechanical systems (MEMS). The relatively high adhesion forces and friction forces encountered in these devices often present major obstacles to the design of reliable MEMS devices. Using surface micromachining, arrays of microstructures are being designed and tested to examine the adhesion characteristics, static friction behavior, and dynamic friction response. Emphasis is also being given to the control and actuation of the test structures and the modeling of the dynamic response and contact mechanics at the interface. Specifically, the purpose of the research is to fabricate and test MEMS devices in order to obtain insight into the effect of surface topography, material properties, surface chemical state, environmental conditions, and contact load on the static and dynamic characteristics of the contact interface.

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This paper presents an overview of algorithms for directing messages through networks of varying topology. These are commonly referred to as routing algorithms in the literature that is presented. In addition to providing background on networking terminology and router basics, the paper explains the issues of deadlock and livelock as they apply to routing. After this, there is a discussion of routing algorithms for both store-and-forward and wormhole-switched networks. The paper covers both algorithms that do and do not adapt to conditions in the network. Techniques targeting structured as well as irregular topologies are discussed. Following this, strategies for routing in the presence of faulty nodes and links in the network are described.

Emerging high-bandwidth, low-latency network technology has made network-based architectures both feasible and potentially desirable for use in satellite payload architectures. The selection of network topology is a critical component when developing these multi-node or multi-point architectures. This study examines network topologies and their effect on overall network performance. Numerous topologies were reviewed against a number of performance, reliability, and cost metrics. This document identifies a handful of good network topologies for satellite applications and the metrics used to justify them as such. Since often multiple topologies will meet the requirements of the satellite payload architecture under development, the choice of network topology is not easy, and in the end the choice of topology is influenced by both the design characteristics and requirements of the overall system and the experience of the developer.

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Peridynamics is a nonlocal formulation of continuum mechanics. The discrete peridynamic model has the same computational structure as a molecular dynamic model. This document details the implementation of a discrete peridynamic model within the LAMMPS molecular dynamic code. This document provides a brief overview of the peridynamic model of a continuum, then discusses how the peridynamic model is discretized, and overviews the LAMMPS implementation. A nontrivial example problem is also included.

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This report documents work done for a late-start LDRD project, which was carried out during the last quarter of FY07. The objective of this project was to experimentally explore the feasibility of converting vegetable (e.g., soybean) oils to biodiesel by employing slit-channel reactors and solid catalysts. We first designed and fabricated several slit-channel reactors with varying channel depths, and employed them to investigate the improved performance of slit-channel reactors over traditional batch reactors using a NaOH liquid catalyst. We then evaluated the effectiveness of several solid catalysts, including CaO, ZnO, MgO, ZrO{sub 2}, calcium gluconate, and heteropolyacid or HPA (Cs{sub 2.5}H{sub 0.5}PW{sub 12}O{sub 40}), for catalyzing the soybean oil-to-biodiesel transesterification reaction. We found that the slit-channel reactor performance improves as channel depth decreases, as expected; and the conversion efficiency of a slit-channel reactor is significantly higher when its channel is very shallow. We further confirmed CaO as having the highest catalytic activity among the solid catalysts tested, and we demonstrated for the first time calcium gluconate as a promising solid catalyst for converting soybean oil to biodiesel, based on our preliminary batch-mode conversion experiments.

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This LDRD began as a three year program to integrate through-wafer vias, micro-mirrors and control electronics with high-voltage capability to yield a 64 by 64 array of individually controllable micro-mirrors on 125 or 250 micron pitch with piston, tip and tilt movement. The effort was a mix of R&D and application. Care was taken to create SUMMiT{trademark} (Sandia's ultraplanar, multilevel MEMS technology) compatible via and mirror processes, and the ultimate goal was to mate this MEMS fabrication product to a complementary metal-oxide semiconductor (CMOS) electronics substrate. Significant progress was made on the via and mirror fabrication and design, the attach process development as well as the electronics high voltage (30 volt) and control designs. After approximately 22 months, the program was ready to proceed with fabrication and integration of the electronics, final mirror array, and through wafer vias to create a high resolution OMEMS array with individual mirror electronic control. At this point, however, mission alignment and budget constraints reduced the last year program funding and redirected the program to help support the through-silicon via work in the Hyper-Temporal Sensors (HTS) Grand Challenge (GC) LDRD. Several months of investigation and discussion with the HTS team resulted in a revised plan for the remaining 10 months of the program. We planned to build a capability in finer-pitched via fabrication on thinned substrates along with metallization schemes and bonding techniques for very large arrays of high density interconnects (up to 2000 x 2000 vias). Through this program, Sandia was able to build capability in several different conductive through wafer via processes using internal and external resources, MEMS mirror design and fabrication, various bonding techniques for arrayed substrates, and arrayed electronics control design with high voltage capability.

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Vapor Phase Lubrication (VPL) of silicon surfaces with pentanol has been demonstrated. Two potential show stoppers with respect to application of this approach to real MEMS devices have been investigated. Water vapor was found to reduce the effectiveness of VPL with alcohol for a given alcohol concentration, but the basic reaction mechanism observed in water-free environments is still active, and devices operated much longer in mixed alcohol and water vapor environments than with chemisorbed monolayer lubricants alone. Complex MEMS gear trains were successfully lubricated with alcohol vapors, resulting in a factor of 104 improvement in operating life without failure. Complex devices could be made to fail if operated at much higher frequencies than previously used, and there is some evidence that the observed failure is due to accumulation of reaction products at deeply buried interfaces. However, if hypothetical reaction mechanisms involving heated surfaces are valid, then the failures observed at high frequency may not be relevant to operation at normal frequencies. Therefore, this work demonstrates that VPL is a viable approach for complex MEMS devices in conventional packages. Further study of the VPL reaction mechanisms are recommended so that the vapor composition may be optimized for low friction and for different substrate materials with potential application to conventionally fabricated, metal alloy parts in weapons systems. Reaction kinetics should be studied to define effective lubrication regimes as a function of the partial pressure of the vapor phase constituent, interfacial shear rate, substrate composition, and temperature.

This document provides general guidance for the design and analysis of bolted joint connections. An overview of the current methods used to analyze bolted joint connections is given. Several methods for the design and analysis of bolted joint connections are presented. Guidance is provided for general bolted joint design, computation of preload uncertainty and preload loss, and the calculation of the bolted joint factor of safety. Axial loads, shear loads, thermal loads, and thread tear out are used in factor of safety calculations. Additionally, limited guidance is provided for fatigue considerations. An overview of an associated Mathcad{copyright} Worksheet containing all bolted joint design formulae presented is also provided.

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Synthetic Aperture Radar (SAR) performance testing and estimation is facilitated by observing the system response to known target scene elements. Trihedral corner reflectors and other canonical targets play an important role because their Radar Cross Section (RCS) can be calculated analytically. However, reflector orientation and the proximity of the ground and mounting structures can significantly impact the accuracy and precision with which measurements can be made. These issues are examined in this report.

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The annual program report provides detailed information about all aspects of the Sandia National Laboratories, California (SNL/CA) Environmental Planning and Ecology Program for a given calendar year. It functions as supporting documentation to the SNL/CA Environmental Management System Program Manual. The program report describes the activities undertaken during the past year, and activities planned in future years to implement the Planning and Ecology Program, one of six programs that supports environmental management at SNL/CA.

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