Publications

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Wireless computer networks are increasing exponentially around the world. They are being implemented in both the unlicensed radio frequency (RF) spectrum (IEEE 802.11a/b/g) and the licensed spectrum (e.g., Firetide [1] and Motorola Canopy [2]). Wireless networks operating in the unlicensed spectrum are by far the most popular wireless computer networks in existence. The open (i.e., proprietary) nature of the IEEE 802.11 protocols and the availability of ''free'' RF spectrum have encouraged many producers of enterprise and common off-the-shelf (COTS) computer networking equipment to jump into the wireless arena. Competition between these companies has driven down the price of 802.11 wireless networking equipment and has improved user experiences with such equipment. The end result has been an increased adoption of the equipment by businesses and consumers, the establishment of the Wi-Fi Alliance [3], and widespread use of the Alliance's ''Wi-Fi'' moniker to describe these networks. Consumers use 802.11 equipment at home to reduce the burden of running wires in existing construction, facilitate the sharing of broadband Internet services with roommates or neighbors, and increase their range of ''connectedness''. Private businesses and government entities (at all levels) are deploying wireless networks to reduce wiring costs, increase employee mobility, enable non-employees to access the Internet, and create an added revenue stream to their existing business models (coffee houses, airports, hotels, etc.). Municipalities (Philadelphia; San Francisco; Grand Haven, MI) are deploying wireless networks so they can bring broadband Internet access to places lacking such access; offer limited-speed broadband access to impoverished communities; offer broadband in places, such as marinas and state parks, that are passed over by traditional broadband providers; and provide themselves with higher quality, more complete network coverage for use by emergency responders and other municipal agencies. In short, these Wi-Fi networks are being deployed everywhere. Much thought has been and is being put into evaluating cost-benefit analyses of wired vs. wireless networks and issues such as how to effectively cover an office building or municipality, how to efficiently manage a large network of wireless access points (APs), and how to save money by replacing an Internet service provider (ISP) with 802.11 technology. In comparison, very little thought and money are being focused on wireless security and monitoring for security purposes.

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Traditional polar format image formation for Synthetic Aperture Radar (SAR) requires a large amount of processing power and memory in order to accomplish in real-time. These requirements can thus eliminate the possible usage of interpreted language environments such as MATLAB. However, with trapezoidal aperture phase history collection and changes to the traditional polar format algorithm, certain optimizations make MATLAB a possible tool for image formation. Thus, this document's purpose is two-fold. The first outlines a change to the existing Polar Format MATLAB implementation utilizing the Chirp Z-Transform that improves performance and memory usage achieving near realtime results for smaller apertures. The second is the addition of two new possible image formation options that perform a more traditional interpolation style image formation. These options allow the continued exploration of possible interpolation methods for image formation and some preliminary results comparing image quality are given.

This SAND report provides the technical progress through April 2005 of the Sandia-led project, ''Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling'', funded by the DOE Office of Science GenomicsGTL Program. Understanding, predicting, and perhaps manipulating carbon fixation in the oceans has long been a major focus of biological oceanography and has more recently been of interest to a broader audience of scientists and policy makers. It is clear that the oceanic sinks and sources of CO{sub 2} are important terms in the global environmental response to anthropogenic atmospheric inputs of CO{sub 2} and that oceanic microorganisms play a key role in this response. However, the relationship between this global phenomenon and the biochemical mechanisms of carbon fixation in these microorganisms is poorly understood. In this project, we will investigate the carbon sequestration behavior of Synechococcus Sp., an abundant marine cyanobacteria known to be important to environmental responses to carbon dioxide levels, through experimental and computational methods. This project is a combined experimental and computational effort with emphasis on developing and applying new computational tools and methods. Our experimental effort will provide the biology and data to drive the computational efforts and include significant investment in developing new experimental methods for uncovering protein partners, characterizing protein complexes, identifying new binding domains. We will also develop and apply new data measurement and statistical methods for analyzing microamy experiments. Computational tools will be essential to our efforts to discover and characterize the function of the molecular machines of Synechococcus. To this end, molecular simulation methods will be coupled with knowledge discovery from diverse biological data sets for high-throughput discovery and characterization of protein-protein complexes. In addition, we will develop a set of novel capabilities for inference of regulatory pathways in microbial genomes across multiple sources of information through the integration of computational and experimental technologies. These capabilities will be applied to Synechococcus regulatory pathways to characterize their interaction map and identify component proteins in these pathways. We will also investigate methods for combining experimental and computational results with visualization and natural language tools to accelerate discovery of regulatory pathways. The ultimate goal of this effort is develop and apply new experimental and computational methods needed to generate a new level of understanding of how the Synechococcus genome affects carbon fixation at the global scale. Anticipated experimental and computational methods will provide ever-increasing insight about the individual elements and steps in the carbon fixation process, however relating an organism's genome to its cellular response in the presence of varying environments will require systems biology approaches. Thus a primary goal for this effort is to integrate the genomic data generated from experiments and lower level simulations with data from the existing body of literature into a whole cell model. We plan to accomplish this by developing and applying a set of tools for capturing the carbon fixation behavior of complex of Synechococcus at different levels of resolution. Finally, the explosion of data being produced by high-throughput experiments requires data analysis and models which are more computationally complex, more heterogeneous, and require coupling to ever increasing amounts of experimentally obtained data in varying formats. These challenges are unprecedented in high performance scientific computing and necessitate the development of a companion computational infrastructure to support this effort.

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