Physical Sciences and Mathematics Commons^™

Using Delay-Differential Equations For Modeling Calcium Cycling In Cardiac Myocytes, Ryan Thompson

Theses

The cycling of calcium at the intracellular level of cardiac cells plays a key role in the excitation-contraction process. The interplay between ionic currents, buffering agents, and calcium release from the sarcoplasmic reticulum (SR) is a complex system that has been shown experimentally to exhibit complex dynamics including period-2 states (alternans) and higher-order rhythms. Many of the calcium cycling activities involve the sensing, binding, or diffusion of calcium between intracellular compartments; these are physical processes that take time and typically are modeled by “relaxation” equations where the steady-state value and time course of a particular variable are specified through an …

Stability And Entanglement In An Optomechanical System, Matthew Schumacher

Theses

Optomechanical systems are currently of great interest as they lie at the boundary between quantum and classical mechanics, promising fundamental insights as well as new technologies. The practical operation of an optomechanical system requires that it satisfy the criteria of mechanical stability. Further, for quantum applications, it is important to characterize the degree of nonclassical correlation present between the mechanical and optical subsystems. In this study, we analyze the stability and entanglement in an optomechanical system where couplings linear as well as quadratic in the mechanical displacement are present simultaneously. Such systems can be realized experimentally. Our analysis of the …

Group Selection And Key Management Strategies For Ciphertext-Policy Attribute-Based Encryption, Russell F. Martin

Theses

Ciphertext-Policy Attribute-Based Encryption (CPABE) was introduced by Bethencourt, Sahai, and Waters, as an improvement of Identity Based Encryption, allowing fine grained control of access to encrypted files by restricting access to only users whose attributes match that of the monotonic access tree of the encrypted file. Through these modifications, encrypted files can be placed securely on an unsecure server, without fear of malicious users being able to access the files, while allowing each user to have a unique key, reducing the vulnerabilites associated with sharing a key between multiple users.

However, due to the fact that CPABE was designed for …

Analysis Of Polarimetric Synthetic Aperture Radar And Passive Visible Light Polarimetric Imaging Data Fusion For Remote Sensing Applications, Sanjit Maitra

Theses

The recent launch of spaceborne (TerraSAR-X, RADARSAT-2, ALOS-PALSAR, RISAT) and airborne (SIRC, AIRSAR, UAVSAR, PISAR) polarimetric radar sensors, with capability of imaging through day and night in almost all weather conditions, has made polarimetric synthetic aperture radar (PolSAR) image interpretation and analysis an active area of research. PolSAR image classification is sensitive to object orientation and scattering properties. In recent years, significant work has been done in many areas including agriculture, forestry, oceanography, geology, terrain analysis. Visible light passive polarimetric imaging has also emerged as a powerful tool in remote sensing for enhanced information extraction. The intensity image provides information …

Quantum Dot Enhanced Epitaxial Lift-Off Solar Cells, Mitchell F. Bennett

Theses

Embedded nanostructures such as quantum dots (QDs) have been studied for many applications in solar cells including enhanced mini-band absorption in intermediate-band solar cells and current matching in multi junction cells. The major drawbacks of using such techniques to decrease intrinsic solar cell loss mechanisms are twofold: first, it is difficult to maintain partially populated states using QDs due to a quick thermal extraction of carriers; second, QDs have a weak absorption which necessitates a near-perfect control of QD growth mechanisms to carefully ensure a balance between dot size and density. One avenue for improving absorption into QDs is to …

Evaluating The Effectiveness Of Design For The Environment Tools To Help Meet Sustainability And Design Goals, Ana Maria Leal-Yepes

Theses

Environmental impacts of electronics are a growing concern because the amount and type of materials used in production of the devices, the impacts to the environment from discarded

electronics and the early retirement of products due to rapidly evolving devices, changing design trends, and perceived technological obsolescence. Design for the Environment is a sustainability strategy that aims to reduce the environmental impacts through techniques that enable sustainability solutions during the design decision-making process. In order to suit the diverse

needs of sustainable design practitioners, there has been a large number of tools for Design for the Environment (DfE) developed, confusing …

Rule-Based Conditional Trust With Openpgp., Andrew Jackson

Theses

This thesis describes a new trust model for OpenPGP encryption. This trust model uses conditional rule-based trust to establish key validity and trust. This thesis describes "Trust Rules" that may be used to sort and categorize keys automatically without user interaction. "Trust Rules" are also capable of integrating key revocation status into its calculations so it too is automated. This thesis presents that conditional trust established through "Trust Rules" can enforce stricter security while reducing the burden of use and automating the process of key validity, trust, and revocation.

Physics-Based Surface Energy Model Optimization For Water Bodies In Cold Climates Using Visible And Calibrated Thermal Infrared Imagery, May V. Casterline

Theses

When tasked with accurately modeling a water body in a cold climate environment, the complexity of the system being simulated and the numerous parameters affecting the observable outcome pose an arduous task for any modeling effort. The task is increasingly complicated when the body of water is serving as a cooling pond for a power plant and can become partially frozen. The introduction of a heat effluent into the water creates a highly dynamic system whose physical state is not only reactionary to the surrounding environmental conditions, but the industrial facility's operating parameters as well. Both calibrated thermal and visible …

A Forensic Comparison: Windows 7 And Windows 8, Peter J. Wilson

Theses

Whenever a new operating system or new version of an operating system is released, forensic investigators must re-examine the new operating system or new version. They do so to determine if there are significant differences that will impact and change the way they perform their investigations. With the release of Microsoft's latest operating system, Windows 8, and its update, Windows 8.1, understanding the similarities and differences between Windows 8 and previous operating systems such as Windows 7 is critical. This paper forensically examines Windows 7 and Windows 8 to determine those similarities and differences.

Solar Eclipse Observation On May 21, 2012 From Jvla, Shaheda Begum Shaik

Theses

The annular solar eclipse occurred on May 21, 2012 is studied using the radio data from the Jansky Very Large Array (JVLA), Sorrocco, Mexico. The eclipse is observed in the solar minimum activity period of solar cycle 24. The centimeter wavelength observation of the Sun's surface during the solar eclipse helps in determining the spatially well resolved features not obtained by the man made advanced technology. Even though, the activity on the Sun is observed to be low in the period of eclipse, the study provides a good opportunity to understand the quiet Sun features in the regions occulted by …

Segmentation And Model Generation For Large-Scale Cyber Attacks, Steven E. Strapp

Theses

Raw Cyber attack traffic can present more questions than answers to security analysts. Especially with large-scale observables it is difficult to identify which packets are relevant and what attack behaviors are present. Many existing works in Host or Flow Clustering attempt to group similar behaviors to expedite analysis; these works often phrase the problem directly as offline unsupervised machine learning. This work proposes online processing to simultaneously model coordinating actors and segment traffic that is relevant to a target of interest, all while it is being received. The goal is not just to aggregate similar attack behaviors, but to provide …

Understanding Effects Of Presentation On Concept Learning In Technology Supported Learning, Nivedita Singh

Theses

The world of technology has had a significant impact on learning and instructional domain. Today, a large number of devices and software are specifically designed to afford faster and effective learning and instruction. They have not only erased the physical boundaries to resources in education but have also helped create new interactions and engagements for learners and instructors. With this changed scenario, the content or instructional material also needs our attention to become usable and compatible with the changed learning styles and preferences of the learners today. Not only does the content need to seamlessly integrate with the delivery methodology …

Aquifer Characterization And Quantitative Assessment Of Over Exploitation Of The Shallow Aquifer In Al Maqam Al Saad Area, The Eastern Region, Abu Dhabi Emirate, Ismail Mohammed Hamad Ai Badi

Theses

Al Maqam-AI Saad area is located to the west of Al Ain city on Al Ain-Abu Dhabi Highway. This area was chosen to be studied because of the rapid decline of the water levels in the shallow aquifer as a result of continuous heavy withdrawal of the ground water. In 1990-1991, the area was recognized as one of the major ground water depressions in the Eastern Region where more than 40 meters of draw down were noted in the center of depression. The objective of this study is to determine the hydraulic status of the aquifer by means of characterization …

Genome Wide Search For Pseudo Knotted Non-Coding Rnas, Meghana S. Vasavada

Theses

Non-coding RNAs (ncRNAs) are the functional RNA molecules that are involved in many biological processes including gene regulation, chromosome replication and RNA modification. Searching genomes using computational methods has become an important asset for prediction and annotation of ncRNAs. To annotate an individual genome for a specific family of ncRNAs, a computational tool is interpreted to scan through the genome and align its sequence segments to some structure model for the ncRNA family. With the recent advances in detecting an ncRNA in the genome, heuristic techniques are designed to perform an accurate search and sequence-structure alignment. This study uses a …

Rna-Sequence Analysis Of Human Melanoma Cells, Jharna Miya

Theses

RNA-sequencing refers to the use of high throughput sequencing technologies that are used to sequence cDNA in order to get the complete information of a sample’s RNA content. The objective of this study is to analyze this data in different aspects and to characterize gene expression. Besides this characterization, the data was also used to investigate the effect of sequencing depth on gene expression measurements.

This research focuses on quantitative measurement of expression levels of genes and their transcripts. In this study, complementary DNA fragments of cultured human melanoma cells are sequenced and a total of 139,501,106 million 200-bp reads …

Performance Comparison Of Five Rna-Seq Alignment Tools, Yuanpeng Lu

Theses

Aligning millions of short reads to a reference genome is a critical task in high throughput sequencing. In recent years, a large number of mapping algorithms have been developed, all of which have in common that they align a vast number of reads to genomic or transcriptomic sequences. RNA-Seq data is discrete in nature, therefore with reasonable gene models and comparative metrics RNA-Seq data can be simulated to sufficient accuracy to enable meaningful benchmarking of alignment algorithms. To provide guidance in the choice of alignment algorithms, five different alignment tools for RNA-Seq data are evaluated. In order to compare the …

Polyaseeker: A Computational Framework For Identifying Polyadenylation Cleavage Site From Rna-Seq, Xiao Ling

Theses

Alternative polyadenylation (APA) of mRNA plays a crucial role for post-transcriptional gene regulation. Recently, advances in next generation sequencing technology have made it possible to efficiently characterize the transcriptome and identify the 3’end of polyadenylated RNAs. However, no comprehensive bioi nformatic pipelines have fulfilled this goal. The PolyASeeker, a computational framework for identifying polyadenylation cleavage sites from RNA-Seq data is proposed in this thesis. By using the simulated RNA-seq dataset, a novel method is developed to evaluate the performance of the proposed framework versus the traditional A-stretch approach, and compute accurate Precisions and Recalls that previous estimation could not get. …

Validation Of Solar Flare Forecasting & Evolution Of Magnetic Helicity Of Two Active Regions, Qin Li

Theses

This thesis includes two components: (1) Validation of the NJIT flare-forecasting model that was established in recent years is carried out based on the statistical correlation between solar magnetic parameters and flare productivity of active regions (ARs). 378 ARs are examined, comparing observation with prediction. It is found that the accuracy rate to some extent decreases with the level of flares. (2) The temporal evolution of the relative magnetic helicity of two ARs, AR 11072 and 11158 is investigated. The former is flare-quiet while the latter is flare-productive over the 5-day observation period. It is found that for both regions, …

A Gpu Program To Compute Snp-Snp Interactions In Genome-Wide Association Studies, Srividya Ramakrishnan

Theses

With the recent advances in the next generation sequencing technologies, short read sequences of human genome are made more accessible. Paired end sequencing of short reads is currently the most sensitive method for detecting somatic mutations that arise during tumor development. In this study, a novel approach to optimize the detection of structural variants using a new short read alignment program is presented.

Pairwise interaction effects of the Single Nucleotide Polymorphisms (SNPs) have proven to uncover the underlying complex disease traits. Computing the disease risk based on the interaction effects of SNPs on a case - control study is a …

New Economy : Assessment Of The Institutionalization Of An Emerging Paradigm And Academic Field Through Inquiry Into Prominent Boundary Organizations, Jeanine Cava Rodgers

Theses

It is increasingly acknowledged that in order to reach global and regional sustai nabi l ity goals, economic growth and consumption levels in wealthy developed nations will need to stabilize or reverse. Organizations and projects of a wide variety have emerged and expanded to take on this challenge, and shape the so-called, "new economy". The purpose of this research is to gain a clearer picture of the impacts of efforts to develop a shared new-economy knowledge framework on the broader sustai nabi l ity conversation, and to assess the intellectual institutionalization of same. This thesis focuses in on the influence …

Improving Usability: Evaluating The Effect Of Changing Environmental Factors On Cognitive Load, Robin J. Deegan

Theses

Mobile devices are now truly ubiquitous. Their pervasiveness in all facets of our lives brings many advantages. Principle to these advantages is the notion that mobile devices can be used “Anytime, Anywhere”. The size, portability, battery life and computational power of mobile devices mean that they can be used for a diverse range of uses in an equally diverse range of environments.

Usability is primarily concerned with “ease of use” and “learnability”. Mobile devices are challenging this notion of Usability as they are used in new ways. Firstly mobile devices arc used in complex distracting environments and these distractions interfere …

Evaluation, Adaptation And Validation Of A Model To Predict Grass Growth In Ireland, Christina Hurtado Uria

Theses

Budgeting grass supply allows producers to minimise the quantity of purchased feed required in the diet of grazing livestock. One tool for managing grass supply could be a mathematical model that can simulate grass growth. The development of such a model would allow better management around the variability of feed supply and help identify feed surpluses and deficits, and therefore increase the accuracy of management decisions. This would be a key feature of profitable milk and meat production systems in the future which will be hugely important as global food demand increases due to population growth. It is forecasted that …

Optical Emission Properties Of Band Structure Tailored Semiconductor Nanostructures, Nicola Pavarelli

Theses

In the past decades, with the development of low-dimensional semiconductor heterostructures, research has been focused on studying novel materials and proposing new solutions for the improvement and optimization of numerous optoelectronic applications. Examples of these applications include optical data storage, displays and medical diagnostics in the ultraviolet and visible spectral range, or telecommunication networks, solar cells, gas sensing and imaging systems in the near- and mid-infrared. In this thesis, the optical characterization of a number of promising semiconductor nanostructures for the realization of next-generation optoelectronic devices is reported. The optical emission properties of each structure, measured by means of power-dependent …

Investigation Of Wastewater Treatment Plant Sustainability Potential In Terms Of Resource Recovery Essentials, Aoife Moloney

Theses

This thesis aims to explore the sustainability potential which exists in Wastewater Treatment Plants (WWTP's); particularly focusing on nutrient, energy, and water recovery and reuse. The core of the research will focus on the establishment of a sustainable Resource Recovery Treatment Plant (RRTP) plan for Limerick Main Drainage (LMD) WWTP, and potentially utilising this as a case study plant which could act as a foundation example within the sector.

There is a genuine need to investigate more sustainable options in wastewater treatment (WWT); increasing energy and sludge management costs are a real issue for non-sustainable WWTP's given that thousands of …

Novel Liquid Chromatography - Fourier Transform Mass Spectrometry (Ms) And Triple Quadrupole Ms Methods For The Determination Of Diarrhetic Shellfish Poisoning (Dsp) Toxins., Bébhine Carey

Theses

Harmful algal blooms (HABs) appear to be on the rise globally, which not only has a negative impact on the shellfish industry but can also cause human and animal intoxications. In order to advance our knowledge of HABs, specific and sensitive analytical methods are required to aid in monitoring shellfish and algal samples for biotoxins, harmful to consumers.

Investigation Of Drinking Water/Beverage Contaminants Within The Beverage Industry, Elizabeth Hobbs

Theses

The impact of water resource quality has influenced the community worldwide. It is an on-going target for water suppliers to produce suitable drinking water and the beverage industry to provide suitable water for the production of beverages. This diligence will ensure the consumer is provided with a product safe for consumption. The research and analytical techniques explored in this thesis may be of benefit to the beverage industry for the monitoring of inorganic contaminants present in water and carbonated soft drinks. The occurrence of certain contaminants in drinking water has become a major issue in the water industry in recent …

Ultrafast Carrier Dynamics In Semiconductor Nanostructures, Jaroslaw Pulka

Theses

Rapid development of telecommunication systems forces a switch to all- optical data processing and transmission. To design such systems it is critical to understand the ultrafast processes which occur in the components of such systems, especially in Monolithic Modelocked Lasers. The purpose of this work was to identify the main physical processes influencing carrier dynamics in semiconductor nanostructures which show promise for future telecommunication systems. This study was carried out by means of ultrafast pump-probe spectroscopy, which allowed characterisation with a sub-picosecond resolution. The main part of the thesis concentrates on the analysis of the InAs/GaAs Quantum Dot (QD) system. …