Publications

Relatively small motion measurement errors manifest themselves principally as a phase error in Synthetic Aperture Radar (SAR) complex data samples, and if large enough become observable as a smearing, blurring, or other degradation in the image. The phase error function can be measured and then deconvolved from the original data to compensate for the presumed motion error, ultimately resulting in a well-focused image. Techniques that do this are termed 'autofocus' algorithms. A very popular autofocus algorithm is the Phase Gradient Autofocus (PGA) algorithm. The nearly universal, and typically reasonable, assumption is that the motion errors are less than the range resolution of the radar, allowing solely a phase correction to suffice. Very large relative motion measurement errors manifest themselves as an unexpected additional shifting or migration of target locations beyond any deterministic migration during the course of the synthetic aperture. Degradation in images from data exhibiting errors of this magnitude are substantial, often rendering the image completely useless. When residual range migration due to either real or apparent motion errors exceeds the range resolution, conventional autofocus algorithms fail. Excessive residual migration is increasingly encountered as resolutions become finer, less expensive inertial sensors are used, and operating ranges become longer (due to atmospheric phenomena). A new migration-correction autofocus algorithm has been developed that estimates the excessive residual migration and applies phase and frequency corrections to properly focus the image. This overcomes the conventional constraint that motion errors not exceed the SAR range resolution.

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This report describes an integrated approach for designing communication, sensing, and control systems for mobile distributed systems. Graph theoretic methods are used to analyze the input/output reachability and structural controllability and observability of a decentralized system. Embedded in each network node, this analysis will automatically reconfigure an ad hoc communication network for the sensing and control task at hand. The graph analysis can also be used to create the optimal communication flow control based upon the spatial distribution of the network nodes. Edge coloring algorithms tell us that the minimum number of time slots in a planar network is equal to either the maximum number of adjacent nodes (or degree) of the undirected graph plus some small number. Therefore, the more spread out that the nodes are, the fewer number of time slots are needed for communication, and the smaller the latency between nodes. In a coupled system, this results in a more responsive sensor network and control system. Network protocols are developed to propagate this information, and distributed algorithms are developed to automatically adjust the number of time slots available for communication. These protocols and algorithms must be extremely efficient and only updated as network nodes move. In addition, queuing theory is used to analyze the delay characteristics of Carrier Sense Multiple Access (CSMA) networks. This report documents the analysis, simulation, and implementation of these algorithms performed under this Laboratory Directed Research and Development (LDRD) effort.

The control volume finite element method (CVFEM) was developed to combine the local numerical conservation property of control volume methods with the unstructured grid and generality of finite element methods (FEMs). Most implementations of CVFEM include mass-lumping and upwinding techniques typical of control volume schemes. In this work we compare, via numerical error analysis, CVFEM and FEM utilizing consistent and lumped mass implementations, and stabilized Petrov-Galerkin streamline upwind schemes in the context of advection-diffusion processes. For this type of problem, we find no apparent advantage to the local numerical conservation aspect of CVFEM as compared to FEM. The stabilized schemes improve accuracy and degree of positivity on coarse grids, and also reduce iteration counts for advection-dominated problems.

Electrical contact resistance testing was performed by hot-switching a simulated gold-platinum metal microelectromechanical systems contact. The experimental objective was to determine the sensitivity of the contact resistance degradation to current level and environment. The contact resistance increased sharply after 100 hot-switched cycles in air. Hot-switching at a reduced current and in nitrogen atmosphere curtailed contact resistance degradation by several orders of magnitude. The mechanism responsible for the resistance degradation was found to be arc-induced decomposition of adsorbed surface contaminants.

Intra-molecular cross-linking has been suggested as a method of obtaining distance constraints that would be useful in developing structural models of proteins. Recent work published on intra-molecular cross-linking for protein structural studies has employed commercially available primary amine selective reagents that can cross-link lysine residues to other lysine residues or the amino terminus. Previous work using these cross-linkers has shown that for several proteins of known structure, the number of cross-links that can be obtained experimentally may be small compared to what would be expected from the known structure, due to the relative reactivity, distribution, and solvent accessibility of the lysines in the protein sequence. To overcome these limitations we have investigated the use of cross-linking reagents that can react with other reactive sidechains in proteins. We used 1-Ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride (EDC) to activate the carboxylic acid containing residues, aspartic acid (D), glutamic acid (E), and the carboxy terminus (O), for cross-linking reactions. Once activated, the DEO sidechains can react to form 'zero-length' cross-links with nearby primary amine containing resides, lysines (K) and the amino terminus (X), via the formation of a new amide bond. We also show that the EDC-activated DEO sidechains can be cross-linked to each other using dihydrazides, two hydrazide moieties connected by an alkyl cross-linker ann of variable length. Using these reagents, we have found three new 'zero-length' cross-links in ubiquitin consistent with its known structure (M1-E16, M1-E18, and K63-E64). Using the dihydrazide cross-linkers, we have identified 2 new cross-links (D21-D32 and E24-D32) unambiguously. Using a library of dihydrazide cross-linkers with varying arm length, we have shown that there is a minimum arm length required for the DEO-DEO cross-links of 5.8 angstroms. These results show that additional structural information can be obtained by exploiting new cross-linker chemistry, increasing the probability that the protein target of choice will yield sufficient distance constraints to develop a structural model.

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 16 and K325, requires backbone motion to bring the reactive atoms into sufficient proximity for cross-linking. Evidence from other studies suggests that residues around K325 for a region of high backbone mobility. These findings show that cross-linking studies can provide insight into the structural dynamics of membrane proteins in their native environment.

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 activity.

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 kill ranges equal to detection range. Moreover, at glider speeds greater than the speed of the threat, swarm performance becomes a weak function of speed. At these speeds swarm performance is dominated by detection range. Therefore, to future enhance swarm performance or to reduce the number of gliders required for a given performance, detection range must be increased. Communications latency is also examined. It was found that relatively large communication delays did little to change swarm performance. Thus gliders may come to the surface and use SATCOMS to effectively communicate in this application.

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Economists, systems analysts, engineers, regulatory specialists, and other experts were assembled from academia, the national laboratories, and the energy industry to discuss present restoration practices (many have already been defined to the level of operational protocols) in the sectors of the energy infrastructure as well as other infrastructures, to identify whether economics, a discipline concerned with the allocation of scarce resources, is explicitly or implicitly a part of restoration strategies, and if there are novel economic techniques and solution methods that could be used help encourage the restoration of energy services more quickly than present practices or to restore service more efficiently from an economic perspective. AcknowledgementsDevelopment of this work into a coherent product with a useful message has occurred thanks to the thoughtful support of several individuals:Kenneth Friedman, Department of Energy, Office of Energy Assurance, provided the impetus for the work, as well as several suggestions and reminders of direction along the way. Funding from DOE/OEA was critical to the completion of this effort.Arnold Baker, Chief Economist, Sandia National Laboratories, and James Peerenboom, Director, Infrastructure Assurance Center, Argonne National Laboratory, provided valuable contacts that helped to populate the authoring team with the proper mix of economists, engineers, and systems and regulatory specialists to meet the objectives of the work.Several individuals provided valuable review of the document at various stages of completion, and provided suggestions that were valuable to the editing process. This list of reviewers includes Jeffrey Roark, Economist, Tennessee Valley Authority; James R. Dalrymple, Manager of Transmission System Services and Transmission/Power Supply, Tennessee Valley Authority; William Mampre, Vice President, EN Engineering; Kevin Degenstein, EN Engineering; and Patrick Wilgang, Department of Energy, Office of Energy Assurance.With many authors, creating a document with a single voice is a difficult task. Louise Maffitt, Senior Research Associate, Institute for Engineering Research and Applications at New Mexico Institute of Mining & Technology (on contract to Sandia National Laboratories) served a vital role in the development of this document by taking the unedited material (in structured format) and refining the basic language so as to make the flow of the document as close to a single voice as one could hope for. Louise's work made the job of reducing the content to a readable length an easier process. Additional editorial suggestions from the authors themselves, particularly from Sam Flaim, Steve Folga, and Doug Gotham, expedited this process.

Visualization in scientific computing refers to the process of transforming data produced by a simulation into graphical representations that help scientific users interpret the results. While the back-end rendering phase of this work can be performed efficiently in graphics card hardware, the front-end 'post processing' portion of visualization is currently performed entirely in software. Field-Programmable Gate Arrays (FPGAs) are an attractive option for accelerating post-processing operations because they enable users to offload computations into reconfigurable hardware. A key challenge in utilizing FPGAs for this work is developing an infrastructure that allows FPGAs to be integrated into a distributed visualization system. We propose a networked approach, where each post-processing FPGA is equipped with specialized network interface (NI) hardware that is capable of transporting graphics commands across the network to existing rendering resources. In this paper we discuss a NI for FPGAs that is comprised of a Chromium OpenGL interface, a TCP Offload Engine, and a Gigabit Ethernet module. A prototype system has been tested for a distributed isosurfacing application.

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The Sandia Z accelerator has become a unique platform to study matter at extreme conditions. The large currents (20 MA, 200-300 ns rise time) and magnetic fields (several MG) produced by Z generate magnetic compression in the multi-Mbar regime, enabling quasi-isentropic compression experiments (ICE) to several Mbar stresses. Thus, the Z platform is useful in determining high stress material isentropes, performing phase transition studies (including rapid solidification), obtaining constitutive property information, and estimating material strength at high stress. Furthermore, the magnetic pressure can also accelerate macroscopic flyer plates to velocities in excess of 30 km/s. Thus, impact experiments can be performed to ultra-high pressures. Furthermore, the adiabatic release response of materials can be investigated through shock and release experiments, allowing hot, dense liquid states to be probed. The Z platform allows a large expanse of the equation of state surface to be explored enabling new and exciting material dynamics experiments. Specific examples from each of the areas mentioned above will be discussed.

Concerns about acts of terrorism against critical infrastructures have been on the rise for several years. Critical infrastructures are those physical structures and information systems (including cyber) essential to the minimum operations of the economy and government. The President's Commission on Critical Infrastructure Protection (PCCIP) probed the security of the nation's critical infrastructures. The PCCIP determined the water infrastructure is highly vulnerable to a range of potential attacks. In October 1997, the PCCIP proposed a public/private partnership between the federal government and private industry to improve the protection of the nation's critical infrastructures. In early 2000, the EPA partnered with the Awwa Research Foundation (AwwaRF) and Sandia National Laboratories to create the Risk Assessment Methodology for Water Utilities (RAM-W{trademark}). Soon thereafter, they initiated an effort to create a template and minimum requirements for water utility Emergency Response Plans (ERP). All public water utilities in the US serving populations greater than 3,300 are required to undertaken both a vulnerability assessment and the development of an emergency response plan. This paper explains the initial steps of RAM-W{trademark} and then demonstrates how the security risk assessment is fundamental to the ERP. During the development of RAM-W{trademark}, Sandia performed several security risk assessments at large metropolitan water utilities. As part of the scope of that effort, ERPs at each utility were reviewed to determine how well they addressed significant vulnerabilities uncovered during the risk assessment. The ERP will contain responses to other events as well (e.g. natural disasters) but should address all major findings in the security risk assessment.

This report summarizes progress from the Laboratory Directed Research and Development (LDRD) program during fiscal year 2004. In addition to a programmatic and financial overview, the report includes progress reports from 352 individual R and D projects in 15 categories. The 15 categories are: (1) Advanced Concepts; (2) Advanced Manufacturing; (3) Biotechnology; (4) Chemical and Earth Sciences; (5) Computational and Information Sciences; (6) Differentiating Technologies; (7) Electronics and Photonics; (8) Emerging Threats; (9) Energy and Critical Infrastructures; (10) Engineering Sciences; (11) Grand Challenges; (12) Materials Science and Technology; (13) Nonproliferation and Materials Control; (14) Pulsed Power and High Energy Density Sciences; and (15) Corporate Objectives.

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