Physical Sciences and Mathematics Commons^™

A New Algorithm For Protein-Protein Interaction Prediction, Yiwei Li

Electronic Thesis and Dissertation Repository

Protein-protein interactions (PPI) are vital processes in molecular biology. However, the current understanding of PPIs is far from satisfactory. Improved methods of pre- dicting PPIs are very much needed. Since experimental methods are labour and time consuming and lack accuracy, the improvement is expected to come from the area of computational methods. We designed and implemented a new algorithm based on protein primary structure to predict PPIs using C++ and OpenMP for parallel computing. We compared our method with four leading methods. Our results are better than the competition for most of the important values. Furthermore, it succeeds in surpassing …

New Algorithms For Structural Variation Detection By De Novo Genome Assembly, Ehsan Haghshenas

Electronic Thesis and Dissertation Repository

Structural variations (SVs) are changes in the human genome that are reported in several studies to be associated with some diseases. Therefore, designing methods to find these types of variations would help us for early detection of those diseases and utilizing new treatment methods such as personalized medicine. Currently computational methods are applied to find structural variations from short reads obtained by Next Generation Sequencing (NGS) platforms. Usually each method has more power in finding particular types or sizes of SVs and limitations in finding others. Thus, still new approaches and methods are on demand for SV discovery.

In this …

Color Separation For Image Segmentation, Meng Tang

Electronic Thesis and Dissertation Repository

Image segmentation is a fundamental problem in computer vision that has drawn intensive research attention during the past few decades, resulting in a variety of segmentation algorithms. Segmentation is often formulated as a Markov random field (MRF) and the solution corresponding to the maximum a posteriori probability (MAP) is found using energy minimiza- tion framework. Many standard segmentation techniques rely on foreground and background appearance models given a priori. In this case the corresponding energy can be efficiently op- timized globally. If the appearance models are not known, the energy becomes NP-hard, and many methods resort to iterative schemes that …

Pore Morphometrics And Thermal Evolution Of Organic-Matter Microporosity, Colorado Group, Western Canada Foreland Basin, Peng Jiang

Electronic Thesis and Dissertation Repository

Pores that develop within kerogen particles make a significant contribution to the network flow capacity and hydrocarbon storage of carbonaceous mudstone reservoirs. It has been suggested that development of Organic matter pores results from thermal degradation of kerogen. The range of thermal and subsidence histories of strata in the Western Canada Foreland Basin provide an excellent framework in which to evaluate the influence of thermal maturity on organic matter micropore morphometrics, and the opportunity to evaluate clay microfabric characteristics. Imaging and pore characterization of mudstone samples from the Upper Cretaceous (Cenomanian-Turonian) Colorado Group of the WCFB has been conducted using …

Disaster Data Management In Cloud Environments, Katarina Grolinger

Electronic Thesis and Dissertation Repository

Facilitating decision-making in a vital discipline such as disaster management requires information gathering, sharing, and integration on a global scale and across governments, industries, communities, and academia. A large quantity of immensely heterogeneous disaster-related data is available; however, current data management solutions offer few or no integration capabilities and limited potential for collaboration. Moreover, recent advances in cloud computing, Big Data, and NoSQL have opened the door for new solutions in disaster data management.

In this thesis, a Knowledge as a Service (KaaS) framework is proposed for disaster cloud data management (Disaster-CDM) with the objectives of 1) facilitating information gathering …

On The Interoperability Of Programming Languages Based On The Fork-Join Parallelism Model, Sushek Shekar

Electronic Thesis and Dissertation Repository

This thesis describes the implementation of MetaFork, a meta-language for concurrency platforms targeting multicore architectures. First of all, MetaFork is a multithreaded language based on the fork-join model of concurrency: it allows the programmer to express parallel algorithms assuming that tasks are dynamically scheduled at run-time. While MetaFork makes no assumption about the run-time system, it formally defines the serial C-elision of a MetaFork program. In addition, MetaFork is a suite of source-to-source compilers permitting the automatic translation of multithreaded programs between programming languages based on the fork-join model. Currently, this compilation framework supports the OpenMP and CilkPlus concurrency platforms. …

Missing Requirements Information And Its Impact On Software Architectures: A Case Study, Md Rounok Salehin

Electronic Thesis and Dissertation Repository

[Context & motivation] In the development of large, software-intensive systems, the system’s requirements are seldom, if ever, concluded upon prior to commencing with systems architecture. Research shows that, in order to manage development and domain complexities, instances of requirements engineering (RE) and systems architecting (SA) processes tend to inter-weave. [Question/problem] However, missing requirements information can cause one to create (or recreate) the needed information during different SA activities. While backtracking in the software development process is known to be costly, the costs associated with missing requirements in the SA process have not been investigated empirically. [Principal ideas/results] We …

Performance Comparison Of 3d Sinc Interpolation For Fmri Motion Correction By Language Of Implementation And Hardware Platform, Andrew B. Kope

Electronic Thesis and Dissertation Repository

Substantial effort is devoted to improving neuroimaging data processing; this effort however, is typically from the algorithmic perspective only. I demonstrate that substantive running time performance improvements to neuroscientific data processing algorithms can be realized by considering their implementation. Focusing specifically on 3D sinc interpolation, an algorithm used for processing functional magnetic resonance imaging (fMRI) data, I compare the performance of Python, C and OpenCL implementations of this algorithm across multiple hardware platforms. I also benchmark the performance of a novel implementation of 3D sinc interpolation on a field programmable gate array (FPGA). Together, these comparisons demonstrate that the performance …

Rheology Of Solutions Of Polyisophrene And Polyisoprene-Carbon Nanotube Composites, Ruiping Ge

Electronic Thesis and Dissertation Repository

The addition of a small amount of carbon nanotubes to a polymer matrix can result in large changes in its mechanical properties. In this work, we study the rheological behavior of solutions of polyisoprene (PI) in chloroform and suspensions of multi-walled carbon nanotubes (MWCNT) and single-walled carbon nanotubes (SWCNT) in these PI solutions using shear rheometry.

We perform rheological measurements to study the viscoelastic properties of solutions of trans-PI in chloroform for polymer concentrations ranging from 1.0 wt% to 10.0 wt%. Oscillatory strain sweep tests show a concentration-and-frequency independent critical strain of that defines the limit of the linear viscoelastic …

An Access Control Model For Nosql Databases, Motahera Shermin

Electronic Thesis and Dissertation Repository

Current development platforms are web scale, unlike recent platforms which were just network scale. There has been a rapid evolution in computing paradigm that has created the need for data storage as agile and scalable as the applications they support. Relational databases with their joins and locks influence performance in web scale systems negatively. Thus, various types of non-relational databases have emerged in recent years, commonly referred to as NoSQL databases. To fulfill the gaps created by their relational counter-part, they trade consistency and security for performance and scalability. With NoSQL databases being adopted by an increasing number of organizations, …

Progress Toward Synthesis Of Molecular Beacons Incorporating Dabcyl Analog Quenchers, Christie M. Ettles

Electronic Thesis and Dissertation Repository

Progress toward the synthesis of molecular beacons containing analogs of the universal quencher 4-(4'-dimethylaminophenylazo)benzoic acid (DABCYL) has been made. A synthetic methodology has been developed for the differential labeling of a PNA molecular beacon with quencher and fluorophore moieties. A DABCYL analog diarylazo compound and three small fluorescent molecules have been derivatized with terminal alkyne groups for incorporation into azide-decorated PNA oligomers by on-resin “click” chemistry. An optimized on-resin procedure was used to determine the viability of the fluorophores and quencher for incorporation into PNA.

The synthesis of a pyrrolocytidine phosphoramidite containing a diarylazo DABCYL analog moiety was undertaken with …

Multinuclear Solid-State Nuclear Magnetic Resonance Spectroscopy Of Microporous Materials, Jun Xu

Electronic Thesis and Dissertation Repository

Microporous materials have attracted tremendous attention since 18^th century due to their industrial importance. It is essential to understand the relationships between the properties of microporous materials and their structures. However, the structures of many microporous materials are determined from the more limited powder X-ray diffraction (XRD) data due to the lack of suitable single-crystals for XRD. In such cases, an unambiguous structure solution of microporous materials requires additional information from other techniques such as solid-state NMR (SSNMR) spectroscopy. This thesis is focused on the study of two types of microporous materials, metal–organic frameworks (MOFs) and titanosilicates, by multinuclear …

A Modular Approach To The Development Of Interactive Augmented Reality Applications., Nelson J. Andre

Electronic Thesis and Dissertation Repository

Augmented reality (AR) technologies are becoming increasingly popular as a result of the increase in the power of mobile computing devices. Emerging AR applications have the potential to have an enormous impact on industries such as education, healthcare, research, training and entertainment. There are currently a number of augmented reality toolkits and libraries available for the development of these applications; however, there is currently no standard tool for development. In this thesis we propose a modular approach to the organization and development of AR systems in order to enable the creation novel AR experiences. We also investigate the incorporation of …

Flexible Partially Linear Single Index Regression Models For Multivariate Survival Data, Na Lei

Electronic Thesis and Dissertation Repository

Survival regression models usually assume that covariate effects have a linear form. In many circumstances, however, the assumption of linearity may be violated. The present work addresses this limitation by adding nonlinear covariate effects to survival models. Nonlinear covariates are handled using a single index structure, which allows high-dimensional nonlinear effects to be reduced to a scalar term. The nonlinear single index approach is applied to modeling of survival data with multivariate responses, in three popular models: the proportional hazards (PH) model, the proportional odds (PO) model, and the generalized transformation model. Another extension of the PH and PO model …

Potential For Measurement Of Mesospheric Ozone Density From Overdense Meteor Trains With A Monostatic Meteor Radar, Reynold E. Sukara

Electronic Thesis and Dissertation Repository

Thermally ablating meteoroids, colliding with the Earth’s atmosphere, leave a high temperature trail containing extremely energetic metallic ions and electrons. A well recognized, but unresolved, anomaly associated with ambipolar diffusion of meteor trains, which is more dominant in overdense meteors, takes place in the initial post-adiabatic train expansion. In this work, a newly proposed mechanism explaining this anomaly involves hyperthermal chemical reactions is presented. Data from the SKiYMET meteor radar system, deployed at latitudinally dispersed locations, were used to determine ozone density in the upper atmosphere by analyzing diffusion of overdense meteor trains. The results obtained in this study are …

Mitigating Permafrost Degradation Due To Linear Disturbances In Sub-Arctic Peatlands, Aaron A. Mohammed

Electronic Thesis and Dissertation Repository

The presence or absence of permafrost significantly influences the hydrology and ecology of northern watersheds. Linear disturbances resulting from tree canopy removal have led to widespread permafrost degradation in northern peatlands. Seismic lines resulting from oil and gas exploration now account for large portions of the drainage density of sub-arctic basins, and affect the region’s water and energy balances. As these peatlands represent some of the most sensitive ecosystems to climate and human disturbances, the ability to simulate perturbations to natural systems in a controlled lab environment is particularly important. This study presents a method that is able to simulate …

Asymptotic Theory For Garch-In-Mean Models, Weiwei Liu

Electronic Thesis and Dissertation Repository

The GARCH-in-mean process is an important extension of the standard GARCH (generalized autoregressive conditional heteroscedastic) process and it has wide applications in economics and finance. The parameter estimation of GARCH type models usually involves the quasi-maximum likelihood (QML) technique as it produces consistent and asymptotically Gaussian distributed estimators under certain regularity conditions. For a pure GARCH model, such conditions were already found with asymptotic properties of its QML estimator well understood. However, when it comes to GARCH-in-mean models those properties are still largely unknown. The focus of this work is to establish a set of conditions under which the QML …

Detecting Multilingual Lines Of Text With Fusion Moves, Igor Milevskiy

Electronic Thesis and Dissertation Repository

This thesis proposes an optimization-based algorithm for detecting lines of text in images taken by hand-held cameras. The majority of existing methods for this problem assume alphabet-based texts (e.g. in Latin or Greek) and they use heuristics specific to such texts: proximity between letters within one line, larger distance between separate lines, etc. We are interested in a more challenging problem where images combine alphabet and logographic characters from multiple languages where typographic rules vary a lot (e.g. English, Korean, and Chinese). Significantly higher complexity of fitting multiple lines of text in different languages calls for an energy-based formulation combining …

Redesign Of Johar: A Framework For Developing Accessible Applications, Oladapo Oyebode

Electronic Thesis and Dissertation Repository

As the population of disabled people continues to grow, designing accessible applications is still a challenge, since most applications are incompatible with assistive technologies used by disabled people to interact with the computer. This accessibility issue is usually caused by the reluctance of software engineers or developers to include complete accessibility features in their applications, which in turn is often due to the extra cost and development effort required to dynamically adapt applications to a wide range of disabilities. Our aim to resolve accessibility issues led to the design and implementation of the "Johar" framework, which facilitates the development of …

Electrochemical And Surface Compositional Studies On Uranium Dioxide, Mayuri Razdan

Electronic Thesis and Dissertation Repository

This thesis describes electrochemical and surface compositional studies performed on a number of simulated nuclear fuel (SIMFUEL) materials under conditions relevant to permanent disposal of spent nuclear fuel in a geologic repository. This is important since a number of critical issues have been identified in the event of waste container failure. The research performed was mainly focused in three areas: (i) the influence of low pH on the surface chemistry of UO₂, since acidity could develop within corrosion product deposits and flaws in the fuel; (ii) the combined influence of dissolved H₂ and H₂O_{2 …}

Enhancing The Performance Of Organic Thin Film Transistors By Cross-Linking The Organic Gate Dielectric, Soheila Naderi Gohar

Electronic Thesis and Dissertation Repository

Amongst various surface modification techniques, hyperthermal hydrogen induced cross-linking (HHIC) has been used to modify the surface of polymeric samples. In this novel and innovative technique neutral hydrogen projectiles with appropriate kinetic energy are produced to generate carbon radicals on the impacted surface through the collision-induced C-H bond breaking. Subsequently, this phenomenon results in cross-linking hydrocarbon chains in the treated polymeric samples.

Verifying the validity of cross-linking process through experiments is the target of first part of presented dissertation. Spin-coated poly(methyl methacrylate) (PMMA) films on silicon wafer were exposed to hydrogen projectiles for different durations, while the other conditions related …

Characterization Of The Corrosion And Oxide Film Properties Of Alloy 600 And Alloy 800, Melissa Faichuk

Electronic Thesis and Dissertation Repository

The passive film properties of Alloy 600 and Alloy 800, both of which are used as steam generator tubing in CANDU reactors, have been studied using techniques such as polarization scans, electrochemical impedance spectroscopy and X-ray photoelectron and Auger spectroscopies. The composition of the oxides formed in a 0.1 M Na₂S₂O₃ solution have been characterized over a wide range of potentials from the pre-passive, through the passive to the transpassive regions. These changes have been correlated to the electrochemical behaviour. A second set of experiments was performed to determine the effectiveness of the surface mechanical …

Hydrogeological And Thermal Sustainability Of Geothermal Borehole Heat Exchangers, S. Emad Dehkordi

Electronic Thesis and Dissertation Repository

Assessment of the current approach taken by guidelines and design methods of vertical closed loop heat exchangers shows that often groundwater flow is either disregarded or is not methodically incorporated. The state of scientific research in this arena reveals that overlooking the groundwater flow in the design procedure may not always be a correct assumption. The significance of advective heat transport compared to conduction is defined by the groundwater flux or Darcy velocity which heavily depends on the hydraulic conductivity of the ground, followed by the hydraulic gradient which has a relatively limited range. A sensitivity analysis on ground and …

Crevice Corrosion Behavior Of Ni-Cr-Mo-W Alloys In Aggressive Environment, Ajit K. Mishra

Electronic Thesis and Dissertation Repository

Ni-Cr-Mo (W) alloys, having an optimum concentration of Cr. Mo and W, are highly corrosion resistant alloys which do not fail by uniform corrosion in aggressive environments. However, when creviced at high applied potential and high temperatures, these materials can be susceptible to crevice corrosion. This study focuses on a family of seven commercial Ni-Cr-Mo (W) alloys containing various amounts of Cr, Mo and W.

Different electrochemical techniques were used to determine the characteristic potentials and temperature which indicate susceptibility to crevice corrosion, and to investigate the individual and synergistic roles of major and minor alloying elements. The corroded alloys …

Representation, Recognition And Collaboration With Digital Ink, Rui Hu

Electronic Thesis and Dissertation Repository

Pen input for computing devices is now widespread, providing a promising interaction mechanism for many purposes. Nevertheless, the diverse nature of digital ink and varied application domains still present many challenges. First, the sampling rate and resolution of pen-based devices keep improving, making input data more costly to process and store. At the same time, existing applications typically record digital ink either in proprietary formats, which are restricted to single platforms and consequently lack portability, or simply as images, which lose important information. Moreover, in certain domains such as mathematics, current systems are now achieving good recognition rates on individual …

Symplectomorphism Groups Of Weighted Projective Spaces And Related Embedding Spaces, Martin L. Vanhoof

Electronic Thesis and Dissertation Repository

In this thesis, we study 4-dimensional weighted projective spaces and homotopy properties of their symplectomorphism groups. Using these computations, we also investigate some homotopy theoretic properties of a few associated embedding spaces. In the classical case of the complex projective plane, Gromov observed that its symplectomorphism group is homotopy equivalent to its subgroup of Kahler isometries. We find that in the case of one singularity, the symplectomorphism group is weakly homotopy equivalent to the Kahler isometry group of a certain Hirzebruch surface, which corresponds to the resolution of the singularity. In the case of multiple singularities, the symplectomorphism groups are …

Polynomially Adjusted Saddlepoint Density Approximations, Susan Zhe Sheng

Electronic Thesis and Dissertation Repository

This thesis aims at obtaining improved bona fide density estimates and approximants by means of adjustments applied to the widely used saddlepoint approximation. Said adjustments are determined by solving systems of equations resulting from a moment-matching argument. A hybrid density approximant that relies on the accuracy of the saddlepoint approximation in the distributional tails is introduced as well. A certain representation of noncentral indefinite quadratic forms leads to an initial approximation whose parameters are evaluated by simultaneously solving four equations involving the cumulants of the target distribution. A saddlepoint approximation to the distribution of quadratic forms is also discussed. By …

Hardware Acceleration Technologies In Computer Algebra: Challenges And Impact, Sardar Anisul Haque

Electronic Thesis and Dissertation Repository

The objective of high performance computing (HPC) is to ensure that the computational power of hardware resources is well utilized to solve a problem. Various techniques are usually employed to achieve this goal. Improvement of algorithm to reduce the number of arithmetic operations, modifications in accessing data or rearrangement of data in order to reduce memory traffic, code optimization at all levels, designing parallel algorithms to reduce span are some of the attractive areas that HPC researchers are working on. In this thesis, we investigate HPC techniques for the implementation of basic routines in computer algebra targeting hardware acceleration technologies. …

Development Of Biodegradable And Stimuli-Responsive Macromolescules And Their Assemblies, Ali Nazemi

Electronic Thesis and Dissertation Repository

Polymersomes are potentially multifunctional soft materials constructed by the self-assembly of amphiphilic block copolymers in aqueous medium. While much research has focused on controlling the assembly and encapsulation properties of polymersomes, their surface functionalization has been relatively unexplored. This is important because it plays a critical role in determining their properties such as toxicity and biodistribution behavior. The work described in this thesis involves the development of a biocompatible and biodegradable polymersome systems based on poly(ethylene oxide)-b-polycaprolactone (PEO-PCL) block copolymers with azide surface groups as a novel scaffold for various biomedical applications. The surface functionalization of these polymersomes …

Two Dimensional Angular Domain Optical Imaging In Biological Tissues, Eldon Ng

Electronic Thesis and Dissertation Repository

Optical imaging is a modality that can detect optical contrast within a biological sample that is not detectable with other conventional imaging techniques. Optical trans-illumination images of tissue samples are degraded by optical scatter. Angular Domain Imaging (ADI) is an optical imaging technique that filters scattered photons based on the trajectory of the photons. Previous angular filters were limited to one dimensional arrays, greatly limiting the imaging capability of the system.

We have developed a 2D Angular Filter Array (AFA) that is capable of acquiring two dimensional projection images of a sample. The AFA was constructed using rapid prototyping techniques. …