Publications

Real time protein binding interactions between biotinylated bovine serum albumen (BSA) and streptavidin (SA) are detected using chemoreceptive neuron MOS (CvMOS) transistors with extended floating gate structures. This enables protein interaction events to be monitored by a sensing gate area that is only capacitively coupled to the sensing circuits and far removed from the active area, reducing the invasiveness without loss of sensitivity. The use of both sensing and control gates to control the floating gate potential eliminates the need of an analyte reference electrode. © 2007 IEEE.

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Abstract not provided.

The U.S. Department of Energy (DOE) has a rich history of significant contributions to geospatial science spanning the past four decades. In the early years, work focused on basic research, such as development of algorithms for processing geographic data and early use of LANDSAT imagery. The emphasis shifted in the mid-1970s to development of geographic information system (GIS) applications to support programs such as the National Uranium Resource Evaluation (NURE), and later to issue-oriented GIS applications supporting programs such as environmental restoration and management (mid-1980s through present). Throughout this period, the DOE national laboratories represented a strong chorus of voices advocating the importance of geospatial science and technology in the decades to come. The establishment of a Geospatial Science Program by the DOE Office of the Chief Information Officer in 2005 reflects the continued potential of geospatial science to enhance DOE's science, projects, and operations, as is well demonstrated by historical analysis. © 2007 The Haworth Press, Inc. All rights reserved.

When a system design approach is applied to wind turbine blades, manufacturing and structural requirements are included along with aerodynamic considerations in the design optimization. The resulting system-driven design includes several innovative structural features such as flat-back airfoils, a constant thickness carbon spar-cap, and a thin, large diameter root. Subscale blades were manufactured to evaluate the as-built integrated performance. The design resulted in a 22% reduction in mass, but withstood over 300% of its design load during testing. Compressive strains of nearly 0.9% were measured in the carbon spar-cap. The test results from this and an earlier design are compared, as are finite element models of each design. Included in the analysis is a review of the acoustic emission events that were detected through the use of surface mounted microphones.

The US Strategic Petroleum Reserve (SPR) stores oil in large underground salt caverns. This oil has compositional and thermal gradients induced by geothermal heating from both the bottom surface and side walls. Temperature layering has been recorded in SPR oil caverns, which is hypothesized to be predominantly due to double-diffusive layering that occurs when a stable compositional gradient is heated from below. Initial results of a laboratory experimental program aimed at studying dynamics of such double-diffusive layers in the context of SPR are described in this paper. Of particular interest are the thickness of converting layers, layer evolution (migration/merging) and conditions for the formation/non-formation of double-diffusive layers. Copyright © 2007 by ASME.

When measuring the structural dynamic response of test objects, the desired data is sometimes combined with some type of undesired periodic data. This can occur due to N-per-revolution excitation in systems with rotating components or when dither excitation is used. The response due to these (typically unmeasured) periodic excitations causes spikes in system frequency response functions (FRFs) and poor coherence. This paper describes a technique to remove these periodic components from the measured data. The data must be measured as a continuous time history which is initially processed as a single, long record. Given an initial guess for the periodic signal's fundamental frequency, an automated search will identify the actual fundamental frequency to very high accuracy. Then the fundamental and a user-specified number of harmonics are removed from the acquired data to create new time histories. These resulting time histories can then be processed using standard signal processing techniques. An example of this technique will be presented from a test where a vehicle is dithered with a fixed-frequency, sinusoidal force to linearize the behavior of the shock absorbers, while measuring the acceleration responses due to a random force applied elsewhere on the vehicle.

We present an LES-type variational multiscale theory of turbulence. Our approach derives completely from the incompressible Navier-Stokes equations and does not employ any ad hoc devices, such as eddy viscosities. We tested the formulation on forced homogeneous isotropic turbulence and turbulent channel flows. In the calculations, we employed linear, quadratic and cubic NURBS. A dispersion analysis of simple model problems revealed NURBS elements to be superior to classical finite elements in approximating advective and diffusive processes, which play a significant role in turbulence computations. The numerical results are very good and confirm the viability of the theoretical framework. © 2007 Elsevier B.V. All rights reserved.

A small-scale 3×3 pipe network was simulated to evaluate the validity of complete-mixing and incomplete-mixing models for water distribution systems under different flow rates and boundary conditions. CFD simulations showed that accurate predictions of spatially variable tracer concentrations throughout the network could be attained when compared to experimental data. In contrast, an EPANET model that assumed complete mixing within the junctions yielded uniform concentrations throughout the network, which was significantly different than the spatially variable concentrations observed in the experimental network. The EPANET model was also modified to include mixing correlations derived from previous single-joint experiments. The results from the modified model correctly reflected the incomplete mixing at the pipe junctions and matched the trend in the experimental data. Additional CFD simulations showed that networks comprised of T-junctions separated by at least several pipe diameters could be adequately modeled with complete-mixing models. © 2007 ASCE.

Partitioned global address space (PGAS) programming models have been identified as one of the few viable approaches for dealing with emerging many-core systems. These models tend to generate many small messages, which requires specific support from the network interface hardware to enable efficient execution. In the past, Cray included E-registers on the Cray T3E to support the SHMEM API; however, with the advent of multi-core processors, the balance of computation to communication capabilities has shifted toward computation. This paper explores the message rates that are achievable with multi-core processors and simplified PGAS support on a more conventional network interface. For message rate tests, we find that simple network interface hardware is more than sufficient. We also find that even typical data distributions, such as cyclic or block-cyclic, do not need specialized hardware support. Finally, we assess the impact of such support on the well known RandomAccess benchmark. (c) 2007 ACM.

Implicit large eddy simulation (ILES) has provided many computer simulations with an efficient and effective model for turbulence. The capacity for ILES has been shown to arise from a broad class of numerical methods with specific properties producing nonoscillatory solutions using limiters that provide these methods with nonlinear stability. The use of modified equation has allowed us to understand the mechanisms behind the efficacy of ILES as a model. Much of the understanding of the ILES modeling has proceeded in the realm of incompressible flows. Here, we extend this analysis to compressible flows. While the general conclusions are consistent with our previous findings, the compressible case has several important distinctions. Like the incompressible analysis, the ILES of compressible flow is dominated by an effective self-similarity model (Bardina, J., Ferziger, J. H., and Reynolds, W. C., 1980, quot;Improved Subgrid Scale Models for Large Eddy Simulations, quot; AIAA Paper No. 80-1357; Borue, V., and Orszag, S. A., 1998, quot;Local Energy Flux and Subgrid-Scale Statistics in Three Dimensional Turbulence,quot; J. Fluid Mech., 366, pp. 1-31; Meneveau, C., and Katz, J., 2000, quot;Scale-Invariance and Turbulence Models for Large-Eddy Simulations,quot; Annu. Rev. Fluid. Mech., 32, pp. 1-32). Here, we focus on one of these issues, the form of the effective subgrid model for the conservation of mass equations. In the mass equation, the leading order model is a self-similarity model acting on the joint gradients of density and velocity. The dissipative ILES model results from the limiter and upwind differencing resulting in effects proportional to the acoustic modes in the flow as well as the convective effects. We examine the model in several limits including the incompressible limit. This equation differs from the standard form found in the classical Navier-Stokes equations, but generally follows the form suggested by Brenner (2005, quot;Navier-Stokes Revisited,quot; Physica A, 349(1-2), pp. 60-133) in a modification of Navier-Stokes necessary to successfully reproduce some experimentally measured phenomena. The implications of these developments are discussed in relation to the usual turbulence modeling approaches. Copyright ©2007 by ASME.

In this paper, we present an optimal method for calculating turning maneuvers for an unmanned aerial vehicle (UAV) developed for ecological research. The algorithm calculates several possible solutions using vectors represented in complex notation, and selects the shortest turning path given constraints determined by the aircraft. This algorithm considers the UAV's turning capabilities, generating a two-dimensional path that is feasible for the UAV to fly. We generate a test flight path and show that the UAV is capable of following the turn maneuvers.

The goal of this study is to model the electrical response of gold plated copper electrical contacts exposed to a mixed flowing gas stream consisting of air containing 10 ppb H2S at 30 °C and a relative humidity of 70%. This environment accelerates the attack normally observed in a light industrial environment (essentially a simplified version of the Battelle class 2 environment). Corrosion rates were quantified by measuring the corrosion site density, size distribution, and the macroscopic electrical resistance of the aged surface as a function of exposure time. A pore corrosion numerical model was used to predict both the growth of copper sulfide corrosion product which blooms through defects in the gold layer and the resulting electrical contact resistance of the aged surface. Assumptions about the distribution of defects in the noble metal plating and the mechanism for how corrosion blooms affect electrical contact resistance were needed to close the numerical model. Comparisons are made to the experimentally observed number density of corrosion sites, the size distribution of corrosion product blooms, and the cumulative probability distribution of the electrical contact resistance. Experimentally, the bloom site density increases as a function of time, whereas the bloom size distribution remains relatively independent of time. These two effects are included in the numerical model by adding a corrosion initiation probability proportional to the surface area along with a probability for bloom-growth extinction proportional to the corrosion product bloom volume. The cumulative probability distribution of electrical resistance becomes skewed as exposure time increases. While the electrical contact resistance increases as a function of time for a fraction of the bloom population, the median value remains relatively unchanged. In order to model this behavior, the resistance calculated for large blooms has been weighted more heavily. © 2007 IEEE.

Parallel adaptive mesh refinement methods potentially lead to realistic modeling of complex three-dimensional physical phenomena. However, they also present significant challenges in data partitioning and load balancing. As the mesh adapts to the solution, the partitioning requirements change. By explicitly considering these dynamic conditions, the scalability for large, realistic simulations could possibly be significantly improved. Our hypothesis is that adaptive partitioning, meaning dynamic and automatic switching of partitioning techniques, based on the current run-time state, can be beneficial for these simulations. However, switching partitioners can be expensive due to differences in the algorithms' native mapping of data onto processors. We suggest forcing a uniform starting point for all included partitioners. We present a penalty-based method for determining whether switching is beneficial. We study the effects on data migration, as well as on overall cost, of using the uniform starting point and the switching-penalties to select the best partitioning algorithm, among a set of graph-based and geometric partitioning algorithms, for each adaptive time-step for four different adaptive scientific applications. The results show that data migration can be significantly reduced and that adaptive partitioning indeed can be effective for unstructured adaptive applications.

This paper describes the electromagnetic analysis that has been completed using the OPERA-3d product to characterize the folces on the ITER shield modules as part of the conceptual design. These forces exist due to the interaction of the eddy currents induced in the shield modules and the large magnetic fields present in the tokamak. ©2007 IEEE.

Isentropic compression of a solid to 100's of GPa by a ramped, planar compression wave allows measurement of material properties at high strain and at modest temperature. Introduction of a measurement plane disturbs the flow, requiring special analysis techniques. If the measurement interface is windowed, the unsteady nature of the wave in the window requires special treatment. When the flow is hyperbolic the equations of motion can be integrated backward in space in the sample to a region undisturbed by the interface interactions, fully accounting for the untoward interactions. For more complex materials like hysteretic elastic/plastic solids or phase changing material, hybrid analysis techniques are required. © 2007 American Institute of Physics.

At Sandia National Laboratories, we have coined the term "microenergetics" to describe sub-millimeter energetic material studies aimed at gaining knowledge of combustion and detonation behavior at the mesoscale. Our approach is to apply technologies developed by the microelectronics industry to fabricate test samples with well-defined geometries. Substrates have been fabricated from materials such as silicon and ceramics, with channels to contain the energetic material. Energetic materials have been loaded into the channels, either as powders, femtosecond laser-micromachined pellets, or as vapor-deposited films. Ignition of the samples has been achieved by simple hotwires, integrated semiconductor bridges, and also by lasers. Additionally, grain-scale patterning has been performed on explosive films using both oxygen plasma etching and femtosecond laser micromachining. We have demonstrated simple work functions in microenergetic devices, such as piston motion, which is also a relevant diagnostic to examine combustion properties. Detonation has been achieved in deposited explosive films, recorded by high-speed photography. © 2007 American Institute of Physics.

Requirements Engineering viewpoints are converging more between the Software Engineering Community and the Systems Engineering Community, but there remains driving viewpoints that linger and constrain our complete understanding of a problem and of requirements for a solution. These driving ideas need to be reassessed in order to represent and assess the problem or opportunity as well as the requirements for systems that are introduced. In particular, in order to perform the modeling and acquire understanding of an Enterprise it is crucial that we reevaluate these driving viewpoints. © 2007 by R.M. Griego.

An accurate method for controlling strain rates in dynamic compressions studies involves using the non-linear elastic property of fused silica to transform an initial shock into a ramp wave of known amplitude and duration. Fused silica when placed between a dry Indiana limestone specimen and a projectile produces strain rates in the range of 104/s. Ramp-loading strain rates are higher than what can be produced on Hopkinson bars and lower than what shock experiments attain. The strength determined at the elastic limit under ramp loading compared to Hopkinson bar measurements shows a significant strength increase with increasing strain rate. © 2007 American Institute of Physics.

Optically powered devices are typically irradiated by high intensity lasers and rely on the temperature excursion generated by the laser for operation. While numerical modeling can estimate the temperature profile of the irradiated devices, only direct measurements can determine the actual device temperatures. Available surface thermometry techniques, such as infrared imaging, scanning thermal microscopy and thermoreflectance are generally incompatible with an optical powering scheme, the micron-scale layer thicknesses of microsystem devices, or both. In this paper we discuss the use of micro-Raman thermometry to obtain the first spatiallyresolved temperature measurements of various polycrystalline silicon (polysilicon) surfaces heated with an 808 nm continuous wave (CW) laser at a 60° angle of incidence. The micron-scale resolution of the micro-Raman technique permitted mapping of the surface temperature in the vicinity of the heating laser spot and throughout the device. In addition to discussing the requirements for accurate data collection, the implications of optical interference on the heated structures are also considered. Copyright © 2007 by ASME.

Potential events involving biological or chemical contamination of buildings are of major concern in the area of homeland security. Tools are needed to provide rapid, onsite predictions of contaminant levels given only approximate measurements in limited locations throughout a building. In principal, such tools could use calculations based on physical process models to provide accurate predictions. In practice, however, physical process models are too complex and computationally costly to be used in a real-time scenario. In this paper, we investigate the feasibility of using machine learning to provide easily computed but approximate models that would be applicable in the field. We develop a machine learning method based on Support Vector Machine regression and classification. We apply our method to problems of estimating contamination levels and contaminant source location. © 2007 IEEE.

In this paper, we introduce EXACT, the EXperimental Algorithmics Computational Toolkit. EXACT is a software framework for describing, controlling, and analyzing computer experiments. It provides the experimentalist with convenient software tools to ease and organize the entire experimental process, including the description of factors and levels, the design of experiments, the control of experimental runs, the archiving of results, and analysis of results. As a case study for EXACT, we describe its interaction with FAST, the Sandia Framework for Agile Software Testing. EXACT and FAST now manage the nightly testing of several large software projects at Sandia. We also discuss EXACT's advanced features, which include a driver module that controls complex experiments such as comparisons of parallel algorithms. Copyright 2007 ACM.

Recently, extensive focus has been placed on determining the optimal locations of sensors within a distribution system to minimize the impact on public health from intentional intrusion events. Modified versions of these tools may have additional benefits for determining monitoring locations for other more common objectives associated with distribution systems. A modified Sensor Placement Optimization Tool (SPOT) is presented that can be used for satisfying more generic location problems such as determining monitoring locations for tracer tests or disinfectant byproduct sampling. The utility for the modified SPOT algorithm is discussed with respect to implementing a distribution system field-scale tracer study. © 2007 ASCE.

Since the first vector supercomputers in the mid-1970's, the largest scale applications have traditionally been floating point oriented numerical codes, which can be broadly characterized as the simulation of physics on a computer. Supercomputer architectures have evolved to meet the needs of those applications. Specifically, the computational work of the application tends to be floating point oriented, and the decomposition of the problem two or three dimensional. Today, an emerging class of critical applications may change those assumptions: they are combinatorial in nature, integer oriented, and irregular. The performance of both classes of applications is dominated by the performance of the memory system. This paper compares the memory performance sensitivity of both traditional and emerging HPC applications, and shows that the new codes are significantly more sensitive to memory latency and bandwidth than their traditional counterparts. Additionally, these codes exhibit lower base-line performance, which only exacerbates the problem. As a result, the construction of future supercomputer architectures to support these applications will most likely be different from those used to support traditional codes. Quantitatively understanding the difference between the two workloads will form the basis for future design choices. ©2007 IEEE.

An S-band image reject downconversion mixer with high intercept point and fully integrated single-ended ports, including a UHF output, is demonstrated using GaAs pHEMT technology. The image rejection is better than 20 dB across a wide IF bandwidth ranging from 400 MHz to beyond 1 GHz with a high input IP3 of 20 dBm. On-chip passive baluns are used to provide the single-ended to differential conversion in the RF and IF paths necessary for the resistive FET mixer core. A polyphase filter is used to generate the quadrature local oscillator (LO) components, while an integrated UHF lumped element quadrature hybrid combines the intermediate frequency (IF) components to achieve image rejection fully on-chip without the need for external components. © 2007 IEEE.