Engineering Commons^™

Review Of Tools: A Tool-By-Tool Guide To Choosing And Using 150 Home Essentials, John Stephen Brantley

Faculty & Staff Research & Creative Activity

No abstract provided.

Cognitive Engineering Research Methodology: A Proposed Study Of Visualization Analysis Techniques, Cristin M. Hall, Sonya A.H. Mcmullen, David L. Hall

Publications

The rapid development of new sensors and wide-band communications provides the capability to collect enormous amounts of data. An increasing challenge involves how to understand and interpret the data to yield knowledge about evolving situations or threats (e.g., of military situations, state of complex systems, etc.). New visualization tools and techniques are becoming available to support advanced visualization including three-dimensional, full immersion display environments and tools to support novel visualizations. Examples include network system display tools and evolving multi-sensory situation environments. Despite the emergence of such tools, there has been limited systematic test and evaluations to determine the efficacy of …

A Comprehensive Analysis Of The Effect Of Microarray Data, Monika Ray, Johannes Freudenberg, Weixiong Zhang

All Computer Science and Engineering Research

Background: Microarray data preprocessing, such as differentially expressed (DE) genes selection, is performed prior to higher level statistical analysis in order to account for technical variability. Preprocessing for the Affymetrix GeneChip includes background correction, normalisation and summarisation. Numerous preprocessing methods have been proposed with little consensus as to which is the most suitable. Furthermore, due to poor concordance among results from cross-platform analyses, protocols are being developed to enable cross-platform reproducibility. However, the effect of data analysis on a single platform is still unknown. The objective of our study is two-fold: first to determine whether there is consistency in the …

The Meta-Theory Of Q_0 In The Calculus Of Inductive Constructions, Master's Thesis, May 2006, Li-Yang Tan

All Computer Science and Engineering Research

The notion of a proof is central to all of mathematics. In the language of formal logic, a proof is a finite sequence of inferences from a set of axioms, and any statement one yields from such a finitistic procedure is called a theorem. For better or for worse, this is far from the form a traditional mathematical proof takes. Mathematicians write proofs that omit routine logical steps, and details deemed tangential to the central result are often elided. These proofs are fuzzy and human-centric, and a great amount of context is assumed on the part of the reader. While …

The Remote-Clique Problem Revisited, Benjamin E. Birnbaum

All Computer Science and Engineering Research

Given a positive integer k and a complete graph with non-negative edge weights that satisfy the triangle inequality, the remote-clique problem is to find a subset of k vertices having a maximum-weight induced subgraph. A greedy algorithm for the problem has been shown to have an approximation ratio of 4, but this analysis was not shown to be tight. In this thesis, we present an algorithm called d-Greedy Augment that generalizes this greedy algorithm (they are equivalent when d = 1). We use the technique of factor-revealing linear programs to prove that d-Greedy Augment, which has a running time of …

Acceleration Of Profile-Hmm Search For Protein Sequences In Reconfigurable Hardware - Master's Thesis, May 2006 , Rahul Pratap Maddimsetty

All Computer Science and Engineering Research

Profile Hidden Markov models are highly expressive representations of functional units, or motifs, conserved across protein sequences. Profile-HMM search is a powerful computational technique that is used to annotate new sequences by identifying occurrences of known motifs in them. With the exponential growth of protein databases, there is an increasing demand for acceleration of such techniques. We describe an accelerator for the Viterbi algorithm using a two-stage pipelined design in which the first stage is implemented in parallel reconfigurable hardware for greater speedup. To this end, we identify algorithmic modifications that expose a high level of parallelism and characterize their …

Preserving Performance Of Byzantine Fault Tolerant Replica Groups In The Presence Of Malicious Clients, Sajeeva L. Pallemulle, Haraldur D. Thorvaldsson, Kenneth J. Goldman

All Computer Science and Engineering Research

The Castro and Liskov Byzantine Fault Tolerance protocol for replicated state machines (CLBFT) provides a practical means of tolerating arbitrary replica failures in replicated passive data servers. For better performance, CLBFT uses Message Authentication Codes (MAC) instead of public Key cryptography to authenticate messages and preserves replica consistency even in the presence of malicious clients. However, CLBFT is susceptible to potential attacks by malicious clients using corrupted MACs to force replica groups into expensive configuration changes repeatedly. While not affecting correctness, this vulnerability can seriously impair the performance of the replica group. We propose modifications to CLBFT that address this …

Mixed-Integer Linear Programming Solution To Multi-Robot Task Allocation Problem, Nuzhet Atay, Burchan Bayazit

All Computer Science and Engineering Research

Multi-robot systems require efficient and accurate planning in order to perform mission-critical tasks. This paper introduces a mixed-integer linear programming solution to coordinate multiple heterogenenous robots for detecting and controlling multiple regions of interest in an unknown environment. The objective function contains four basic requirements of a multi-robot system serving this purpose: control regions of interest, provide communication between robots, control maximum area and detect regions of interest. Our solution defines optimum locations of robots in order to maximize the objective function while efficiently satisfying some constraints such as avoiding obstacles and staying within the speed capabilities of the robots. …

Smooth Surface Reconstruction Using Charts For Medical Data, Cindy Grimm, Tao Ju

All Computer Science and Engineering Research

We present a surface reconstruction technique that constructs a smooth analytic surface from scattered data. The technique is robust to noise and both poorly and non-uniformly sampled data, making it well-suited for use in medical applications. In addition, the surface can be parameterized in multiple ways, making it possible to represent additional data, such as electromagnetic potential, in a different (but related) coordinate system to the geometric one. The parameterization technique also supports consistent parameterizations of multiple data sets.

The Design, Modeling, And Implementation Of Group Scheduling For Isolation Of Computations From Adversarial Interference, Terry Tidwell, Noah Watkins, Venkita Subramonian, Douglas Niehaus, Armando Gill, Migliaccio

All Computer Science and Engineering Research

To isolate computations from denial of service (DoS) attacks and other forms of adversarial interference, it is necessary to constrain the effects of interactions among computations. This paper makes four contributions to research on isolation of computations from adversarial interference: (1) it describes the design and implementation of a kernel level scheduling policy to control the effects of adversarial attacks on computations’ execution; (2) it presents formal models of the system components that are involved in a representative DoS attack scenario; (3) it shows how model checking can be used to analyze that example scenario, under default Linux scheduling semantics …

Smooth Key-Framing Using The Image Plane, Leon Barrett, Cindy Grimm

All Computer Science and Engineering Research

This paper demonstrates the use of image-space constraints for key frame interpolation. Interpolating in image-space results in sequences with predictable and controlable image trajectories and projected size for selected objects, particularly in cases where the desired center of rotation is not fixed or when the key frames contain perspective distortion changes. Additionally, we provide the user with direct image-space control over {\em how} the key frames are interpolated by allowing them to directly edit the object's projected size and trajectory. Image-space key frame interpolation requires solving the inverse camera problem over a sequence of point constraints. This is a variation …

Use Of Gene Expression Profiling And Machine Learning To Understand And Predict Primary Graft Dysfunction, Monika Ray, Sekhar Dharmarajan, Johannes Freudenberg, Weixiong Zhang, Alexander G. Patterson

All Computer Science and Engineering Research

No abstract provided.

Design Of Routers For Diversified Networks, Jonathan Turner

All Computer Science and Engineering Research

No abstract provided.

Extending Byzantine Fault Tolerance To Replicated Clients, Ian Wehrman, Sajeeva L. Pallemulle, Kenneth J. Goldman

All Computer Science and Engineering Research

Byzantine agreement protocols for replicated deterministic state machines guarantee that externally requested operations continue to execute correctly even if a bounded number of replicas fail in arbitrary ways. The state machines are passive, with clients responsible for any active ongoing application behavior. However, the clients are unreplicated and outside the fault-tolerance boundary. Consequently, agreement protocols for replicated state machines do not guarantee continued correct execution of long-running client applications. Building on the Castro and Liskov Byzantine Fault Tolerance protocol for unreplicated clients (CLBFT), we present a practical algorithm for Byzantine fault-tolerant execution of long-running distributed applications in which replicated deterministic …

Design And Analysis Of An Accelerated Seed Generation Stage For Blastp On The Mercury System - Master's Thesis, August 2006, Arpith Jacob

All Computer Science and Engineering Research

NCBI BLASTP is a popular sequence analysis tool used to study the evolutionary relationship between two protein sequences. Protein databases continue to grow exponentially as entire genomes of organisms are sequenced, making sequence analysis a computationally demanding task. For example, a search of the E. coli. k12 proteome against the GenBank Non-Redundant database takes 36 hours on a standard workstation. In this thesis, we look to address the problem by accelerating protein searching using Field Programmable Gate Arrays. We focus our attention on the BLASTP heuristic, building on work done earlier to accelerate DNA searching on the Mercury platform. We …

Design Of A Diversified Network Substrate, Jonathan Turner

All Computer Science and Engineering Research

A diversified network substrate enables multiple end-to-end metanetworks to co-exist within a shared physical infrastructure. Metanetworks are implemented by metarouters, hosted by substrate routers, and metarouters are connected by metalinks. The substrate allocates resources (both link bandwidth and processing resources) to metarouters based on advance reservations received from metanetwork planning systems. It also enables dynamic creation of access metalinks, connecting end systems to metarouters, and supports mobility of end systems under the control of their metanetworks. This report defines a model for a diversified internet and presents a detailed design of the substrate that enables metanetworks to co-exist. The design …

Discovering Functional Modules By Clustering Gene Co-Expression Networks, Jianhua Ruan, Weixiong Zhang

All Computer Science and Engineering Research

Identification of groups of functionally related genes from high throughput gene expression data is an important step towards elucidating gene functions at a global scale. Most existing approaches treat gene expression data as points in a metric space, and apply conventional clustering algorithms to identify sets of genes that are close to each other in the metric space. However, they usually ignore the topology of the underlying biological networks. In this paper, we propose a network-based clustering method that is biologically more realistic. Given a gene expression data set, we apply a rank-based transformation to obtain a sparse co-expression network, …

Fast Packet Classification Using Bloom Filters, Sarang Dharmapurikar, Haoyu Song, Jonathan Turner, John Lockwood

All Computer Science and Engineering Research

While the problem of general packet classification has received a great deal of attention from researchers over the last ten years, there is still no really satisfactory solution. Ternary Content Addressable Memory (TCAM), although widely used in practice, is both expensive and consumes a lot of power. Algorithmic solutions, which rely on commodity memory chips, are relatively inexpensive and power-efficient, but have not been able to match the generality and performance of TCAMs. In this paper we propose a new approach to packet classification, which combines architectural and algorithmic techniques. Our starting point is the well-known crossproducting algorithm, which is …

Acceleration Of Gapped Alignment In Blastp Using The Mercury System, Brandon B. Harris

All Computer Science and Engineering Research

Protein databases have grown exponentially over the last decade. This exponential growth has made extracting valuable information from these databases increasingly time consuming. This project presents a new method of accelerating a commonly used program for performing similarity searching on protein databases, BLASTP. This project describes the design and implementation of Mercury BLASTP, a customized hardware accelerated variant of BLASTP. This project focuses on the gapped alignment stage of Mercury BLASTP and provides design details and implementation results.

A Unified Architecture For Flexible Radio Power Management In Wireless Sensor Networks, Kevin Klues, Guoliang Xing, Chenyang Lu

All Computer Science and Engineering Research

A challenge for many wireless sensor networks is to remain operational for long periods of time on a very limited power supply. While many power management protocols have been proposed, a solution does not yet exist that allows them to be seamlessly integrated into the existing systems. In this paper we study the architectural support required to resolve this issue. We propose a framework that separates sleep scheduling from the basic MAC layer functionality and provide a set of unified interfaces between them. This framework enables different sleep scheduling policies to be easily implemented on top of multiple MAC layers. …

Flexible Maximum Urgency First Scheduling For Distributed Real-Time Systems, Yingming Chen, Chenyang Lu

All Computer Science and Engineering Research

No abstract provided.

A Thesis On Sketch-Based Techniques For Mesh Deformation And Editing, Raquel Bujans

All Computer Science and Engineering Research

The goal of this research is to develop new and more intuitive ways for editing a mesh from a static camera angle. I present two ways to edit a mesh via a simple sketching system. The first method is a gray-scale editor which allows the user to specify a fall off function for the region being deformed. The second method is a profile editor in which the user can re-sketch a mesh’s profile. Lastly, the types of edits possible will be discussed and our results will be presented.

Performance Evaluation Of The Permanent New Jersey Safety Shape Barrier – Update To Nchrp 350 Test No. 4-12 (2214nj-2), Karla A. Polivka, Ronald K. Faller, Dean L. Sicking, John R. Rohde, Robert W. Bielenberg, John D. Reid, Brian A. Coon

Mid-America Transportation Center: Final Reports and Technical Briefs

Based on the proposed changes to the National Cooperative Highway Research Program (NCHRP) Report No. 350 guidelines, NCHRP Project 22-14(2) researchers deemed it appropriate to evaluate permanent safety shape barrier systems prior to finalizing the new crash testing procedures and guidelines. For this effort, the permanent New Jersey Safety Shape barrier was selected for evaluation. One full-scale vehicle crash test was performed on the longitudinal barrier system in accordance with the Test Level 4 (TL-4) requirements presented in the Update to NCHRP Report No. 350. For the permanent barrier testing program, a 10000S single unit truck was used.

The permanent …

Nanobiomagnetics, Diandra Leslie-Pelecky, V. Labhasetwar, R. H. Kraus Jr.

Materials Research Science and Engineering Center: Faculty Publications

The application of nanomagnetic materials to biological systems has produced significant advances in research, diagnosis, and treatment of numerous pathologies. This chapter summarizes the major applications of magnetic materials: magnetic targeting, drug and gene delivery, magnetic separation, the use of magnetic beads in manipulating single molecules, as contrast agents in magnetic resonance imaging, and for hyperthermia. Biocompatibility requirements for magnetic materials used in these applications are reviewed.

“Nanobiomagnetism” is the intersection of nanomagnetism and medicine that focuses on biological systems and/or processes. Magnetism is an inherent facet of life, from iron in blood to the ability of magnetotactic bacteria, birds, …

Understanding And Control Of Lateral Contraction In Stamping Lithography, Zheng Li, Li Tan, Gang-Yu Liu

Materials Research Science and Engineering Center: Faculty Publications

Thin film contraction under external mechanical stress can be used to miniaturize size and increase density of patterned features on top. Nonlinear Finite Element Analysis is used to provide guidance on this contraction process. It was found that the substrate contraction causes stress accumulation along interfaces between protruded features and substrate. These stress accumulation complexes the control of profile changes on patterned features and suggest a design of patterned features arranged beyond a critical distance to avoid cross-interference.

Magnetic Aging, Ralph Skomski, Jian Zhou, Roger D. Kirby, David J. Sellmyer

Materials Research Science and Engineering Center: Faculty Publications

Thermally activated magnetization reversal is of great importance in areas such as permanent magnetism and magnetic recording. In spite of many decades of scientific research, the phenomenon of slow magnetization dynamics has remained partially controversial. It is now well-established that the main mechanism is thermally activated magnetization reversal, as contrasted to eddy currents and structural aging, but the identification of the involved energy barriers remains a challenge for many systems. Thermally activated slow magnetization processes proceed over energy barriers whose structure is determined by the micromagnetic free energy. This restricts the range of physically meaningful energy barriers. An analysis of …

Effects Of Ion-Beam Irradiation On The L10 Phase Transformation And Their Magnetic Properties Of Fept And Ptmn Films (Invited), Chih-Huang Lai, Sheng-Huang Huang, Cheng-Han Yang, C.C. Chiang, Sy_Hwang Liou, David J. Sellmyer, M. L. Yan, L. Yuan, T. Yokata

Materials Research Science and Engineering Center: Faculty Publications

In this paper, we illustrate how to modify the structure and magnetic properties of L1₀ FePt and PtMn films using ion-beam irradiation. Highly ordered L1₀ FePt and PtMn phases were achieved directly by using 2 MeV He-ion irradiation without conventional post-annealing. A high ion-beam current density (~μA/cm² ) was used to achieve direct beam heating on samples. This irradiation-induced heating process provides efficient microscopic energy transfer and creates excess point defects, which significantly enhances the diffusion and promotes the formation of the ordered L1₀ phase. In-plane coercivity of FePt films greater than 5700 Oe could be …

Surface Segregation In Multicomponent Clusters, Peter A. Dowben, Ning Wu, Natalie Palina, H. Modrow, R. Müller, J. Hormes, Yaroslav B. Losovyj

Materials Research Science and Engineering Center: Faculty Publications

Nanostructured materials are not immune from surface segregation, as can be shown for solid samples made from nanosized BaFe_12-2xCo_xTi_xO₁₉ barium ferrite particles and a variety of free clusters. Both theory and experiment provide ample demonstration that very limited dimensions of very small clusters does not necessarily impart stability against surface and grain boundary segregation. In fact, with the larger surface to volume ratio in small clusters and lower average atomic coordination, we anticipate that compositional instabilities in small clusters will readily occur.

Force Protection Using Composite Sandwich Structures, R. L. Sierakowski, M. L. Hughes

United States Air Force: Publications

In the recent past, advances have been made in the attempt to utilize composite materials as components in protective structures such as those employed by the Air Force to secure critical military assets. In such applications, where lightweight materials that exhibit large levels of energy absorption and high strength/stiffness characteristics are desirable, composite sandwich constructions offer an attractive solution.

In an attempt to evaluate the suitability of certain sandwich structures for use in force protection applications, several sandwich constructions with somewhat novel core materials were identified. A group of thermoplastic core materials have been developed that possess features of both …

United States Air Force Posture Statement 2006, U.S. Air Force

United States Air Force: Publications

Over a century ago, America crossed the threshold of powered flight and gave wings to the world. Soon military leaders realized the implications of this development, and warfare was changed forever. America was fortunate to have "Great Captains" with the vision to imagine the possibilities of air and space power - Airmen like Billy Mitchell, Frank Andrews, Hap Arnold, Ira Eaker, Jimmy Doolittle, Bennie Schriever. They have given us a proud heritage of courage, excellence and innovation. In so doing, they also give us a sense of perspective and a way to understand the Air Force's future.