Physical Sciences and Mathematics Commons^™

Methods For The Direct Simulation Of Nanoscale Film Breakup And Contact Angles, Kyle Mahady

Dissertations

This thesis investigates direct simulation of fluids with free surfaces and contact lines, with a focus on capturing nanoscale physics in a continuum based computational framework. Free surfaces and contact lines have long presented some of the most challenging problems in computational fluid dynamics. Extensive progress has been made in recent years, and a wide variety of different methods are currently employed for direct simulation in these contexts. The complexity of the full governing equations for such flows poses significant challenges in terms of analytical techniques, and leads to lengthy computational times for direct simulations. For these reasons, reduced models …

Thermochemistry And Kinetics: Hydrogen Atom Addition Reactions With Alkenes, Oxidation Of Cyclopentadienone, Trifluoroethene And Transport Properties, Suriyakit Yommee

Dissertations

Thermochemical and transport properties and reaction kinetic parameters are important to understand and to model atmospheric chemistry, combustion and other thermal systems. These processes are all important to the environment. Thermochemical properties kinetic parameters and models for several atmospheric and combustion related chemical systems are determined using computational chemistry coupled with fundamentals of thermodynamics and statistical mechanics. Transport properties of hydrocarbon and oxygenated hydrocarbons which are important to the calculation of fluid dynamics of gas phase flow reactions and mixing needed for evaluation in the combustion and thermal (flow) fluid dynamic modeling. Transport properties of radicals cannot be measured so …

Social Analytics For Health Integration, Intelligence, And Monitoring, Xiang Ji

Dissertations

Nowadays, patient-generated social health data are abundant and Healthcare is changing from the authoritative provider-centric model to collaborative and patient-oriented care. The aim of this dissertation is to provide a Social Health Analytics framework to utilize social data to solve the interdisciplinary research challenges of Big Data Science and Health Informatics. Specific research issues and objectives are described below.

The first objective is semantic integration of heterogeneous health data sources, which can vary from structured to unstructured and include patient-generated social data as well as authoritative data. An information seeker has to spend time selecting information from many websites and …

Investigation Of Infinite-Dimensional Dynamical System Models Applicable To Granular Flows, Hao Wu

Dissertations

Recently Blackmore, Samulyak and Rosato developed a class of infinite-dimensional dynamical systems in the form of integro-partial differential equations, which have been called the BSR models. The BSR models were originally derived to model granular flows, but they actually have many additional applications in a variety of fields. BSR models have already been proven to be completely integrable infinite-dimensional Hamiltonian dynamical systems for perfectly elastic interactions in the case of one space dimension, but the well-posedness question of these systems is at least partially answered for the first time here. In particular, dynamical systems of the BSR type are proven …

Continuous Monitoring Of Enterprise Risks: A Delphi Feasibility Study, Robert Baksa

Dissertations

A constantly evolving regulatory environment, increasing market pressure to improve operations, and rapidly changing business conditions are creating the need for ongoing assurance that organizational risks are continually and adequately mitigated. Enterprises are perpetually exposed to fraud, poor decision making and/or other inefficiencies that can lead to significant financial loss and/or increased levels of operating risk. Increasingly, Information Systems are being harnessed to reinvent the risk management process. One promising technology is Continuous Auditing, which seeks to transform the audit process from periodic reviews of a few transactions to a continuous review of all transactions. However, the highly integrated, rapidly …

Methods For Two-Sample Comparisons From Censored Time-To-Event Data, Nubyra Ahmed

Dissertations

In the analysis of censored survival data, it is frequently of interest to determine the efficacy of a treatment or new method over a control or existing method. For this purpose, one may report estimates of the two survival functions or, more specifically, their difference, accompanied by simultaneous confidence bands (SCBs). Alternatively, or in addition, one may conduct hypothesis testing for the difference of the two survival functions.

The first project exploits two bootstrap methods to develop new Wald-type SCBs for the difference of survival functions. The censored data bootstrap is employed to obtain nonparametric SCBs for the difference of …

Data Mining In Computational Proteomics And Genomics, Yang Song

Dissertations

This dissertation addresses data mining in bioinformatics by investigating two important problems, namely peak detection and structure matching. Peak detection is useful for biological pattern discovery while structure matching finds many applications in clustering and classification.

The first part of this dissertation focuses on elastic peak detection in 2D liquid chromatographic mass spectrometry (LC-MS) data used in proteomics research. These data can be modeled as a time series, in which the X-axis represents time points and the Y-axis represents intensity values. A peak occurs in a set of 2D LC-MS data when the sum of the intensity values in a …

Multiple Testing Procedures For Complex Structured Hypotheses And Directional Decisions, Anjana Grandhi

Dissertations

Several multiple testing procedures are developed based on the inherent structure of the tested hypotheses and specific needs of data analysis. Incorporating the inherent structure of the hypotheses results in development of more powerful and situation-specific multiple testing procedures than existing ones. The focus of this dissertation is on developing multiple testing procedures that utilize the information on this structure of the hypotheses and aims at answering research questions while controlling appropriate error rates.

In the first part of the thesis, a mixed directional false discovery rate (mdFDR) controlling procedure is developed in the context of uterine fibroid gene expression …

Designing Novel Abstraction Networks For Ontology Summarization And Quality Assurance, Christopher Ochs

Dissertations

Biomedical ontologies are complex knowledge representation systems. Biomedical ontologies support interdisciplinary research, interoperability of medical systems, and Electronic Healthcare Record (EHR) encoding. Ontologies represent knowledge using concepts (entities) linked by relationships. Ontologies may contain hundreds of thousands of concepts and millions of relationships. For users, the size and complexity of ontologies make it difficult to comprehend “the big picture” of an ontology's content. For ontology editors, size and complexity make it difficult to uncover errors and inconsistencies. Errors in an ontology will ultimately affect applications that utilize the ontology.

In prior studies abstraction networks (AbNs) were developed to provide a …

Information Filtering By Multiple Examples, Mingzhu Zhu

Dissertations

A key to successfully satisfy an information need lies in how users express it using keywords as queries. However, for many users, expressing their information needs using keywords is difficult, especially when the information need is complex. Search By Multiple Examples (SBME), a promising method for overcoming this problem, allows users to specify their information needs as a set of relevant documents rather than as a set of keywords.

Most of the studies on SBME adopt the Positive Unlabeled learning (PU learning) techniques by treating the user's provided examples (denoted as query examples) as positive set and the entire data …

Assessing Learning Outcomes And Social Capital Formation Resulting From The Use And Sharing Of Internet Knowledge Resources, Regina S. Collins

Dissertations

Today’s “digital natives” use the Internet to address most, if not all, their learning-related knowledge needs. This research evaluates the outcomes of formal learning activities requiring students to use, manage, share, and consolidate Internet knowledge resources (such as websites, videos, and blogs) to achieve both individual and group learning. This research takes an integrative approach to learning, capturing learner cognitive, interpersonal, and intrapersonal characteristics as well as the impact of the digital environment by evaluating the technological affordances of two different systems supporting such learning activities. This research also examines pedagogical modifications that would best integrate course assignments utilizing Internet …

Development Of Flexible Batteries Using Nano-Carbons And Polymers, Zhiqian Wang

Dissertations

Flexible electronics such as wearable equipment, displays, cell phones and smart cards require flexible power sources like batteries. In this thesis, the development of flexible batteries and supercapacitors are presented. Different types of flexible batteries including zinc carbon batteries, primary alkaline batteries, secondary alkaline batteries and zinc air cells are presented, These were designed, fabricated and improved using polymers and nano-carbons like carbon nanotubes (CNTs). CNTs are found to be effective as conductive additives compared to the traditional graphite. Purification is important to remove impurities that lead to side reactions/ corrosions. However, further treatment like carboxylation lead to higher electric …

Unsupervised Gene Regulatory Network Inference On Microarray Data, Nidhi Radia

Theses

Obtaining gene regulatory networks (GRNs) from expression data is a challenging and crucial task. Many computational methods and algorithms have been developed to infer gene networks for gene expression data, which are usually obtained from microarray experiments. A gene network is a method to depict the relation among clusters of genes. To infer gene networks, the unsupervised method is used in this study. The two types of data used are time-series data and steady-state data. The data is analyzed using various tools containing different algorithms and concepts. GRNs from time-series data tools are obtained using the Time-delayed Algorithm for the …

Exact Genome Alignment, Nandini Ghosh

Theses

The increase in the volume of genomic data due to the decrease in the cost of whole genome sequencing techniques has opened up new avenues of research in the field of Bioinformatics, like comparative genomics and evolutionary dynamics. The fundamental task in these studies is to align the genome sequences accurately. Sequence alignment helps to identify regions of similarity between the sequences to establish their functional, evolutionary and structural relationship. The thesis investigates the performance of two sequence alignment programs LASTZ, a hash table based faster method and SSEARCH, a slower but more rigorous Smith-Waterman based approach, on whole genome …

Identifying Modifier Genes In Sma Model Mice, Weiting Xu

Theses

Spinal Muscular Atrophy (SMA) involves the loss of nerve cells called motor neurons in the spinal cord and is classified as a motor neuron disease, it affects 1 in 5000-10000 newborns, one of the leading genetic causes of infant death in USA. Mutations in the SMN1, UBA1, DYNC1H1 and VAPB genes cause spinal muscular atrophy. Extra copies of the SMN2 gene modify the severity of spinal muscular atrophy. Mutations in SMN1 (Motor Neuron 1) mainly causes SMA (Autosomal recessive inheritance). SMN1 gene mutations lead to a shortage of the SMN protein and SMN protein forms SMN complex …

Characterizing Alma For Solar Observation, Yi Chai

Theses

ALMA (Atacama Large Millimeter/submillimeter Array) is an antenna array of 66 antennas located in northern Chile at 5000 meters altitude. It is the largest ground-based array operated at millimeter/submillimeter wavelengths. In this thesis, the advantages of using ALMA for solar observation are presented, together with the introduction of a campaign to commission ALMA for solar observations. Observation modes of the solar campaign are reviewed in Chapter 2. Methods for constructing images from single dish data as well as the procedure for processing interferometer data, including calibration and imaging, are given in Chapter 3. The CLEAN algorithm that is used for …

Mueller Matrix Spectroscopic Ellipsometry Of Multiferroics, Roman Basistyy

Dissertations

Multiferroics, materials which possess several ferroic orders, are the focus of research in recent years. Among these materials are oxide crystals, such as, for example, RMnO₃, RMn₂O₅, R₃Fe₅O₁₂, where R stands for rare earth ions. The most fascinating physics occurs when magnon-lattice coupling reveals itself in the far-IR spectra of multiferroics. The expected optical behavior puts multiferroics into a more general category of bi-anisotropic materials, the properties of which could be only described using anisotropic dielectric ε(ω), magnetic μ(ω), and …

Design And Analysis Of Algorithms For Similarity Search Based On Intrinsic Dimension, Xiguo Ma

Dissertations

One of the most fundamental operations employed in data mining tasks such as classification, cluster analysis, and anomaly detection, is that of similarity search. It has been used in numerous fields of application such as multimedia, information retrieval, recommender systems and pattern recognition. Specifically, a similarity query aims to retrieve from the database the most similar objects to a query object, where the underlying similarity measure is usually expressed as a distance function.

The cost of processing similarity queries has been typically assessed in terms of the representational dimension of the data involved, that is, the number of features used …

Local Selection Of Features And Its Applications To Image Search And Annotation, Jichao Sun

Dissertations

In multimedia applications, direct representations of data objects typically involve hundreds or thousands of features. Given a query object, the similarity between the query object and a database object can be computed as the distance between their feature vectors. The neighborhood of the query object consists of those database objects that are close to the query object. The semantic quality of the neighborhood, which can be measured as the proportion of neighboring objects that share the same class label as the query object, is crucial for many applications, such as content-based image retrieval and automated image annotation. However, due to …

Synthetic Approaches To The Understanding Of Dna Nucleobase Methylation, Jagruti Rana

Dissertations

DNA methylation is a major source of genetic variation and cancer. Methylation occurs when nucleophilic DNA bases react with methylating agent methyl methanesulfonate (MMS), dimethyl sulfate (DMS), N-methyl-N-nitrosourea (MNU), N-methyl-N-nitro-N-nitrosoguanidine (MNNG), etc. N7-methyl-2'-deoxyguanosine (N7-methyl-dG, or ^7MedG) adduct is the most abundant DNA methylation products for most methylating agents. DNA polymerase actions on ^7MedG are difficult to study due to its instability against ring- opening hydrolysis and deglycosyl ati on. Oligonucleotides containing a single chemical adduct of ^7MedG cannot be chemically synthesized. In addition, ^7MedG is unstable in vivo …

Location Reliability And Gamification Mechanisms For Mobile Crowd Sensing, Manoop Talasila

Dissertations

People-centric sensing with smart phones can be used for large scale sensing of the physical world by leveraging the sensors on the phones. This new type of sensing can be a scalable and cost-effective alternative to deploying static wireless sensor networks for dense sensing coverage across large areas. However, mobile people-centric sensing has two main issues: 1) Data reliability in sensed data and 2) Incentives for participants. To study these issues, this dissertation designs and develops McSense, a mobile crowd sensing system which provides monetary and social incentives to users.

This dissertation proposes and evaluates two protocols for location reliability …

Electronic, Thermoelectric And Optical Properties Of Vanadium Oxides: Vo2, V2o3 And V2o5, Chiranjivi Lamsal

Dissertations

Correlated electrons in vanadium oxides are responsible for their extreme sensitivity to external stimuli such as pressure, temperature or doping. As a result, several vanadium oxides undergo insulator-to-metal phase transition (IMT) accompanied by structural change. Unlike vanadium pentoxide (V₃O₃), vanadium dioxide (VO₃) and vanadium sesquioxide (V₃O₃) show I MT in their bulk phases. In this study, we have performed one electron Kohn-Sham electronic band-structure calculations of VO₃, V₃O₃ and V₂O₅ in both metallic and insulating phases, implementing a full ab-initio simulation package …

A Comprehensive Study Of Evolution Of Photospheric Magnetic Field And Flows Associated With Solar Eruptions, Shuo Wang

Dissertations

The rapid, irreversible change of the photospheric magnetic field has been recognized as an important element of the solar flare process. Recent theoretical work has shown that such a change would imply Lorentz force perturbations acting on both the outer solar atmosphere and the solar surface. This research uses vector magnetograms obtained with the Helioseismic and Magnetic Imager on board the Solar Dynamics Observatory to study a number of flares, which range from GOES-class C4 to X5 and occur in four active regions. In all the events, a permanent and rapid change of photospheric magnetic field closely associated with the …

Adaptive Global Optimization Algorithms, William Phillips

Dissertations

Global optimization is concerned with finding the minimum value of a function where many local minima may exist. The development of a global optimization algorithm may involve using information about the target function (e.g., differentiability) and functions based on statistical models to better the worst case time complexity and expected error of similar deterministic algorithms.

Recent algorithms are investigated, new ones proposed and their performance is analyzed. Minimum, maximum and average case error bounds for the algorithms presented are derived. Software architecture implemented with MATLAB and Java is presented and experimental results for the algorithms are displayed.

The graphical capabilities …

Enabling Virtualization Technologies For Enhanced Cloud Computing, Kashifuddin Qazi

Dissertations

Cloud Computing is a ubiquitous technology that offers various services for individual users, small businesses, as well as large scale organizations. Data-center owners maintain clusters of thousands of machines and lease out resources like CPU, memory, network bandwidth, and storage to clients. For organizations, cloud computing provides the means to offload server infrastructure and obtain resources on demand, which reduces setup costs as well as maintenance overheads. For individuals, cloud computing offers platforms, resources and services that would otherwise be unavailable to them.

At the core of cloud computing are various virtualization technologies and the resulting Virtual Machines (VMs). Virtualization …

Rice And Mouse Quantitative Phenotype Prediction In Genome-Wide Association Studies With Support Vector Regression, Abdulrhman Fahad M. Aljouie

Theses

Quantitative phenotypes prediction from genotype data is significant for pathogenesis, crop yields, and immunity tests. The scientific community conducted many studies to find unobserved quantitative phenotype high predictive ability models. Early genome-wide association studies (GWAS) focused on genetic variants that are associated with disease or phenotype, however, these variants manly covers small portion of the whole genetic variance, and therefore, the effectiveness of predictions obtained using this information may possibly be circumscribed [ 1 ].

Instead, this study shows prediction ability from whole genome single nucleotide polymorphisms (SNPs) data of 1940 genotyped stoke mouse with - 12k SNPs, and 413 …

Cancer Risk Prediction With Next Generation Sequencing Data Using Machine Learning, Nihir Patel

Theses

The use of computational biology for next generation sequencing (NGS) analysis is rapidly increasing in genomics research. However, the effectiveness of NGS data to predict disease abundance is yet unclear. This research investigates the problem in the whole exome NGS data of the chronic lymphocytic leukemia (CLL) available at dbGaP. Initially, raw reads from samples are aligned to the human reference genome using burrows wheeler aligner. From the samples, structural variants, namely, Single Nucleotide Polymorphism (SNP) and Insertion Deletion (INDEL) are identified and are filtered using SAMtools as well as with Genome Analyzer Tool Kit (GATK). Subsequently, the variants are …