Physical Sciences and Mathematics Commons^™

Efficient Algorithms For Prokaryotic Whole Genome Assembly And Finishing, Abhishek Biswas

Computer Science Theses & Dissertations

De-novo genome assembly from DNA fragments is primarily based on sequence overlap information. In addition, mate-pair reads or paired-end reads provide linking information for joining gaps and bridging repeat regions. Genome assemblers in general assemble long contiguous sequences (contigs) using both overlapping reads and linked reads until the assembly runs into an ambiguous repeat region. These contigs are further bridged into scaffolds using linked read information. However, errors can be made in both phases of assembly due to high error threshold of overlap acceptance and linking based on too few mate reads. Identical as well as similar repeat regions can …

Using Eye And Head Movements As A Control Mechanism For Tele-Operating A Ground-Based Robot And Its Payload, Kathryn C. Hicks

Computational Modeling & Simulation Engineering Theses & Dissertations

To date, eye and head tracking has been used to indicate users' attention patterns while performing a task or as an aid for disabled persons, to allow hands-free interaction with a computer. The increasing accuracy and the reduced cost of eye- and head-tracking equipment make utilizing this technology feasible for explicit control tasks, especially in cases where there is confluence between the visual task and control.

The goal of this research was to investigate the use of eye-tracking as a more natural interface for the control of a camera-equipped, remotely operated robot in tasks that require the operator to simultaneously …

Mobile Cloud Computing Based Non Rigid Registration For Image Guided Surgery, Arun Brahmavar Vishwanatha

Computer Science Theses & Dissertations

In this thesis we present the design and implementation of a Mobile Cloud computing platform for non-rigid registration required in Image Guided Surgery (MCIGS). MCIGS contributes in flexible, portable and accurate alignment of pre-operative brain data with intra-operative MRI, for image guided diagnosis and therapy and endoscopic skull base surgery. Improved precision of image guided therapy and specifically neurosurgery procedures is known to result in the improved prognosis for brain tumor patients. MCI GS system is tested with Physics Based Non-Rigid Registration method form ITK. Our preliminary results for brain images indicate that the proposed system over Wi-Fi can be …

Parallel Two-Dimensional Unstructured Anisotropic Delaunay Mesh Generation For Aerospace Applications, Juliette Kelly Pardue

Computer Science Theses & Dissertations

A bottom-up approach to parallel anisotropic mesh generation is presented by building a mesh generator from the principles of point-insertion, triangulation, and Delaunay refinement. Applications focusing on high-lift design or dynamic stall, or numerical methods and modeling test cases focus on two-dimensional domains. This push-button parallel mesh generation approach can generate high-fidelity unstructured meshes with anisotropic boundary layers for use in the computational fluid dynamics field.

Meta-Raps Hybridization With Machine Learning Algorithms, Fatemah Al-Duoli

Engineering Management & Systems Engineering Theses & Dissertations

This dissertation focuses on advancing the Metaheuristic for Randomized Priority Search algorithm, known as Meta-RaPS, by integrating it with machine learning algorithms. Introducing a new metaheuristic algorithm starts with demonstrating its performance. This is accomplished by using the new algorithm to solve various combinatorial optimization problems in their basic form. The next stage focuses on advancing the new algorithm by strengthening its relatively weaker characteristics. In the third traditional stage, the algorithms are exercised in solving more complex optimization problems. In the case of effective algorithms, the second and third stages can occur in parallel as researchers are eager to …

Detecting, Modeling, And Predicting User Temporal Intention, Hany M. Salaheldeen

Computer Science Theses & Dissertations

The content of social media has grown exponentially in the recent years and its role has evolved from narrating life events to actually shaping them. Unfortunately, content posted and shared in social networks is vulnerable and prone to loss or change, rendering the context associated with it (a tweet, post, status, or others) meaningless. There is an inherent value in maintaining the consistency of such social records as in some cases they take over the task of being the first draft of history as collections of these social posts narrate the pulse of the street during historic events, protest, riots, …

Energy Harvesting-Aware Design For Wireless Nanonetworks, Shahram Mohrehkesh

Computer Science Theses & Dissertations

Nanotechnology advancement promises to enable a new era of computing and communication devices by shifting micro scale chip design to nano scale chip design. Nanonetworks are envisioned as artifacts of nanotechnology in the domain of networking and communication. These networks will consist of nodes of nanometer to micrometer in size, with a communication range up to 1 meter. These nodes could be used in various biomedical, industrial, and environmental monitoring applications, where a nanoscale level of sensing, monitoring, control and communication is required. The special characteristics of nanonetworks require the revisiting of network design. More specifically, nanoscale limitations, new paradigms …

High Performance Large Graph Analytics By Enhancing Locality, Naga Shailaja Dasari

Computer Science Theses & Dissertations

Graphs are widely used in a variety of domains for representing entities and their relationship to each other. Graph analytics helps to understand, detect, extract and visualize insightful relationships between different entities. Graph analytics has a wide range of applications in various domains including computational biology, commerce, intelligence, health care and transportation. The breadth of problems that require large graph analytics is growing rapidly resulting in a need for fast and efficient graph processing.

One of the major challenges in graph processing is poor locality of reference. Locality of reference refers to the phenomenon of frequently accessing the same memory …

Accuracy Comparison Of Numerical Integration Algorithms For Real-Time Hybrid Simulations, Ganesh Anant Reddy

Civil & Environmental Engineering Theses & Dissertations

The use of accurate numerical integration algorithms is one of the key factors for a successful real-time hybrid simulation (RTHS). In RTHSs, explicit integration algorithms are preferred more than implicit methods since all calculations need to be completed within a given time step during simulation. Explicit methods require the use of effective stiffness and damping for experimental substructures, which are incorporated into the calculation of the integration parameters. In general, those values that are greater than the expected stiffness and damping of the experimental substructure are used to ensure the stability of simulation. If a rate-dependent and nonlinear experimental substructure …

Avoiding Spoilers On Mediawiki Fan Sites Using Memento, Shawn M. Jones

Computer Science Theses & Dissertations

A variety of fan-based wikis about episodic fiction (e.g., television shows, novels, movies) exist on the World Wide Web. These wikis provide a wealth of information about complex stories, but if readers are behind in their viewing they run the risk of encountering spoilers" -- information that gives away key plot points before the intended time of the show's writers. Enterprising readers might browse the wiki in a web archive so as to view the page prior to a specific episode date and thereby avoid spoilers. Unfortunately, due to how web archives choose the "best" page, it is still possible …

Proclivity Or Popularity? Exploring Agent Heterogeneity In Network Formation, Xiaotian Wang

Computational Modeling & Simulation Engineering Theses & Dissertations

The Barabasi-Albert model (BA model) is the standard algorithm used to describe the emergent mechanism of a scale-free network. This dissertation argues that the BA model, and its variants, rarely take agent heterogeneity into account in the analysis of network formation. In social networks, however, people's decisions to connect are strongly affected by the extent of similarity. In this dissertation, the author applies an agent-based modeling (ABM) approach to reassess the Barabasi-Albert model. This study proposes that, in forming social networks, agents are constantly balancing between instrumental and intrinsic preferences. After systematic simulation and subsequent analysis, this study finds that …

Toward A Theory Of Multi-Method Modeling And Simulation Approach, Mariusz A. Balaban

Computational Modeling & Simulation Engineering Theses & Dissertations

The representation via simulation models can easily lead to simulation models too simple for their intended purpose, or with too much detail, making them hard to understand. This problem is related to limitations of the modeling and simulation methods. A multi-method Modeling and Simulation (M&S) approach has the potential for improved representation by taking advantage of methods' strengths and mitigating their weaknesses. Despite a high appeal for using multiple M&S methods, several related problems should be addressed first. The current level of theoretical, methodological, and pragmatic knowledge related to a multi-method M&S approach is limited. It is problematic that there …

Computational Development For Secondary Structure Detection From Three-Dimensional Images Of Cryo-Electron Microscopy, Dong Si

Computer Science Theses & Dissertations

Electron cryo-microscopy (cryo-EM) as a cutting edge technology has carved a niche for itself in the study of large-scale protein complex. Although the protein backbone of complexes cannot be derived directly from the medium resolution (5-10 Å) of amino acids from three-dimensional (3D) density images, secondary structure elements (SSEs) such as alpha-helices and beta-sheets can still be detected. The accuracy of SSE detection from the volumetric protein density images is critical for ab initio backbone structure derivation in cryo-EM. So far it is challenging to detect the SSEs automatically and accurately from the density images at these resolutions. This dissertation …

Java Animated Software For Teaching The Frank-Wolfe Algorithm For Static Traffic Network Equilibrium, Zhi Li

Computational Modeling & Simulation Engineering Theses & Dissertations

The popular Frank-Wolfe (FW) algorithm for solving the network equilibrium problems plays an important role in transportation simulation. Not only has the basic Frank Wolfe algorithm been studied, but also other variations of the FW algorithm (such as Conjugate Frank Wolfe and Bi-Conjugate Frank Wolfe algorithms) have been extensively studied by the research communities.

In this work, the basic Frank Wolfe algorithm is re-visited for the purpose of developing a useful, user-friendly, and appealing Java computer animation for enhancing the teaching effectiveness of this fundamental transportation static network equilibrium algorithm. Since the shortest path (SP) algorithms (such as the well-known …

Wireless Networking For Vehicle To Infrastructure Communication And Automatic Incident Detection, Sarwar Aziz Sha-Mohammad

Computer Science Theses & Dissertations

Vehicular wireless communication has recently generated wide interest in the area of wireless network research. Automatic Incident Detection (AID), which is the recent focus of research direction in Intelligent Transportation System (ITS), aims to increase road safety. These advances in technology enable traffic systems to use data collected from vehicles on the road to detect incidents. We develop an automatic incident detection method that has a significant active road safety application for alerting drivers about incidents and congestion. Our method for detecting traffic incidents in a highway scenario is based on the use of distance and time for changing lanes …

Multi-Surface Simplex Spine Segmentation For Spine Surgery Simulation And Planning, Rabia Haq

Computational Modeling & Simulation Engineering Theses & Dissertations

This research proposes to develop a knowledge-based multi-surface simplex deformable model for segmentation of healthy as well as pathological lumbar spine data. It aims to provide a more accurate and robust segmentation scheme for identification of intervertebral disc pathologies to assist with spine surgery planning. A robust technique that combines multi-surface and shape statistics-aware variants of the deformable simplex model is presented. Statistical shape variation within the dataset has been captured by application of principal component analysis and incorporated during the segmentation process to refine results. In the case where shape statistics hinder detection of the pathological region, user-assistance is …

De Novo Protein Structure Modeling And Energy Function Design, Lin Chen

Computer Science Theses & Dissertations

The two major challenges in protein structure prediction problems are (1) the lack of an accurate energy function and (2) the lack of an efficient search algorithm. A protein energy function accurately describing the interaction between residues is able to supervise the optimization of a protein conformation, as well as select native or native-like structures from numerous possible conformations. An efficient search algorithm must be able to reduce a conformational space to a reasonable size without missing the native conformation. My PhD research studies focused on these two directions.

A protein energy function—the distance and orientation dependent energy function of …