Physical Sciences and Mathematics Commons^™

Hybrid Stm/Htm For Nested Transactions In Java, Keith G. Chapman

Open Access Dissertations

Transactional memory (TM) has long been advocated as a promising pathway to more automated concurrency control for scaling concurrent programs running on parallel hardware. Software TM (STM) has the benefit of being able to run general transactional programs, but at the significant cost of overheads imposed to log memory accesses, mediate access conflicts, and maintain other transaction metadata. Recently, hardware manufacturers have begun to offer commodity hardware TM (HTM) support in their processors wherein the transaction metadata is maintained “for free” in hardware. However, HTM approaches are only best-effort: they cannot successfully run all transactional programs, whether because of hardware …

Visual Analytics Of Location-Based Social Networks For Decision Support, Junghoon Chae

Open Access Dissertations

Recent advances in technology have enabled people to add location information to social networks called Location-Based Social Networks (LBSNs) where people share their communication and whereabouts not only in their daily lives, but also during abnormal situations, such as crisis events. However, since the volume of the data exceeds the boundaries of human analytical capabilities, it is almost impossible to perform a straightforward qualitative analysis of the data. The emerging field of visual analytics has been introduced to tackle such challenges by integrating the approaches from statistical data analysis and human computer interaction into highly interactive visual environments. Based on …

Exploring The Potential Impacts Of Climate Change On North America's Laurentian Great Lakes Tourism Sector, Natalie Chin

Open Access Dissertations

Climate change is one of the major challenges facing the global hospitality and tourism sector in the coming century and, given the important role that weather and climate play in all aspects of the tourism experience, tourism businesses owners need to start thinking about and enacting climate change adaptation strategies now. This work has utilized a combination of social science and physical science methods to (1) understand how the Great Lakes tourism sector could be impacted by climate change and (2) provide some insights into how researchers can help business owners prepare for these potential impacts. Overall, the results of …

Combinatorial Algorithms For Perturbation Theory And Application On Quantum Computing, Yudong Cao

Open Access Dissertations

Quantum computing is an emerging area between computer science and physics. Numerous problems in quantum computing involve quantum many-body interactions. This dissertation concerns the problem of simulating arbitrary quantum many-body interactions using realistic two-body interactions. To address this issue, a general class of techniques called perturbative reductions (or perturbative gadgets) is adopted from quantum complexity theory and in this dissertation these techniques are improved for experimental considerations. The idea of perturbative reduction is based on the mathematical machinery of perturbation theory in quantum physics. A central theme of this dissertation is then to analyze the combinatorial structure of the perturbation …

Effective Memory Management For Mobile Environments, Ahmed Mohamed Abd-Elhaffiez Hussein

Open Access Dissertations

Smartphones, tablets, and other mobile devices exhibit vastly different constraints compared to regular or classic computing environments like desktops, laptops, or servers. Mobile devices run dozens of so-called “apps” hosted by independent virtual machines (VM). All these VMs run concurrently and each VM deploys purely local heuristics to organize resources like memory, performance, and power. Such a design causes conflicts across all layers of the software stack, calling for the evaluation of VMs and the optimization techniques specific for mobile frameworks.

In this dissertation, we study the design of managed runtime systems for mobile platforms. More specifically, we deepen the …

Hydrocode Modeling Of Oblique Impacts Into Terrestrial Planets, Jordan D. Kendall

Open Access Dissertations

The abundance of moderately siderophile elements (“iron-loving”; e.g., Co, Ni) in the Earth’s mantle is 10 to 100 times larger than predicted by chemical equilibrium between silicate melt and iron at low pressure, but it does match expectation for equilibrium at high pressure and temperature. Recent studies of differentiated planetesimal impacts assume that planetesimal cores survive the impact intact as concentrated masses that passively settle from a zero initial velocity and undergo turbulent entrainment in a global magma ocean; under these conditions, cores greater than 10 km in diameter do not fully mix without a sufficiently deep magma ocean. I …

Gravity-Assist Trajectories To Venus, Mars, And The Ice Giants: Mission Design With Human And Robotic Applications, Kyle M. Hughes

Open Access Dissertations

Gravity-assist trajectories to Uranus and Neptune are found (with the allowance of impulsive maneuvers using chemical propulsion) for launch dates ranging from 2024 to 2038 for Uranus and 2020 to 2070 for Neptune. Solutions are found using a patched conic model with analytical ephemeris via the Satellite Tour Design Program (STOUR), originally developed at the Jet Propulsion Laboratory (JPL). Delivered payload mass is computed for all solutions for select launch vehicles, and attractive solutions are identified as those that deliver a specified amount of payload mass into orbit at the target body in minimum time. The best cases for each …

Ambient Ionization - Mass Spectrometry: Advances Toward Intrasurgical Cancer Detection, Alan Keith Jarmusch

Open Access Dissertations

My dissertation research has focused on the development of ambient ionization – mass spectrometry (MS) for clinical measurements, specifically intrasurgical cancer detection. The molecular differences between normal and cancerous tissue were detected via direct tissue analysis in vitro by touch spray ionization (TS) or by analyzing sectioned or smeared tissue using desorption electrospray ionization (DESI). The physical form of the tissue, e.g. in vitro sampling, sectioned, or smeared, was inconsequential in differentiating normal from cancerous tissue; however, the spectra acquired by TS and DESI differed due to differences in ionization processes. We envision that TS-MS and DESI-MS could impact diagnostic …

A Framework For The Statistical Analysis Of Mass Spectrometry Imaging Experiments, Kyle Bemis

Open Access Dissertations

Mass spectrometry (MS) imaging is a powerful investigation technique for a wide range of biological applications such as molecular histology of tissue, whole body sections, and bacterial films , and biomedical applications such as cancer diagnosis. MS imaging visualizes the spatial distribution of molecular ions in a sample by repeatedly collecting mass spectra across its surface, resulting in complex, high-dimensional imaging datasets. Two of the primary goals of statistical analysis of MS imaging experiments are classification (for supervised experiments), i.e. assigning pixels to pre-defined classes based on their spectral profiles, and segmentation (for unsupervised experiments), i.e. assigning pixels to newly …

Plasmonic Devices Based On Transparent Conducting Oxides For Near Infrared Applications, Kim Jongbum

Open Access Dissertations

In the past decade, there have been many breakthroughs in the field of plasmonics and nanophotonics that have enabled optical devices with unprecedented functionalities. Even though remarkable demonstration of at photonic devices has been reported, constituent materials are limited to the noble metals such as gold (Au) and silver (Ag) due to their abundance of free electrons which enable the support of plasmon resonances in the visible range. With the strong demand for extension of the optical range of plasmonic applications, it is now a necessity to explore and develop alternative materials which can overcome intrinsic issues of noble metals …

Quantifying Terrestrial Ecosystem Carbon Dynamics With Mechanistically-Based Biogeochemistry Models And In Situ And Remotely Sensed Data, Shaoqing Liu

Open Access Dissertations

Terrestrial ecosystem plays a critical role in the global carbon cycle and climate system. Therefore, it is important to accurately quantify the carbon dynamics of terrestrial ecosystem under future climatic change condition. This dissertation evaluates the regional carbon dynamics by using upscaling approach, mechanistically-based biogeochemistry models and in situ and remotely sensed data.

The upscaling studies based on FLUXNET network has provided us the spatial and temporal pattern of the carbon fluxes but it fails to consider the atmospheric CO2 effect given its important physiological role in carbon assimilation. In the second chapter, we consider the effect of atmospheric CO2 …

Annual Forage Cropping-Systems For Midwestern Ruminant Livestock Production, John Ernest Mcmillan

Open Access Dissertations

Annual forage cropping systems are a vital aspect of livestock forage production. One area where this production system can be enhanced is the integration of novel annual forages into conventional cropping systems. Two separate projects were conducted to investigate alternative forage options in annual forage production. In the first discussed research trial, two sets of crops were sown following soft red winter wheat (Triticum aestivum L.) grain harvest, at two nitrogen application rates 56 and 112 kg ha-1 . The first set of crops were C4 summer annuals seeded within two weeks of wheat grain harvest and included, brown …

What Broke Where For Distributed And Parallel Applications — A Whodunit Story, Subrata Mitra

Open Access Dissertations

Detection, diagnosis and mitigation of performance problems in today's large-scale distributed and parallel systems is a difficult task. These large distributed and parallel systems are composed of various complex software and hardware components. When the system experiences some performance or correctness problem, developers struggle to understand the root cause of the problem and fix in a timely manner. In my thesis, I address these three components of the performance problems in computer systems. First, we focus on diagnosing performance problems in large-scale parallel applications running on supercomputers. We developed techniques to localize the performance problem for root-cause analysis. Parallel applications, …

Group Transformation And Identification With Kernel Methods And Big Data Mixed Logistic Regression, Chao Pan

Open Access Dissertations

Exploratory Data Analysis (EDA) is a crucial step in the life cycle of data analysis. Exploring data with effective methods would reveal main characteristics of data and provides guidance for model building. The goal of this thesis is to develop effective and efficient methods for data exploration in the regression setting.

First, we propose to use optimal group transformations as a general approach for exploring the relationship between predictor variables X and the response Y. This approach can be considered an automatic procedure to identify the best characteristic of P( Y|X) under which the relationship …

The Search For Dark Matter In Xenon: Innovative Calibration Strategies And Novel Search Channels, Shayne Edward Reichard

Open Access Dissertations

The direct detection dark matter experiment XENON1T became operational in early 2016, heralding the era of tonne-scale dark matter detectors. Direct detection experiments typically search for elastic scatters of dark matter particles off target nuclei. XENON1T's larger xenon target provides the advantage of stronger dark matter signals and lower background rates compared to its predecessors, XENON10 and XENON100; but, at the same time, calibration of the detector's response to backgrounds with traditional external sources becomes exceedingly more difficult.

A 220Rn source is deployed on the XENON100 dark matter detector in order to address the challenges in calibration of tonne-scale liquid …

Convicted By Memory: Automatically Recovering Spatial-Temporal Evidence From Memory Images, Brendan D. Saltaformaggio

Open Access Dissertations

Memory forensics can reveal “up to the minute” evidence of a device’s usage, often without requiring a suspect’s password to unlock the device, and it is oblivious to any persistent storage encryption schemes, e.g., whole disk encryption. Prior to my work, researchers and investigators alike considered data-structure recovery the ultimate goal of memory image forensics. This, however, was far from sufficient, as investigators were still largely unable to understand the content of the recovered evidence, and hence efficiently locating and accurately analyzing such evidence locked in memory images remained an open research challenge.

In this dissertation, I propose breaking from …

Characterizing The Effects Of Repetitive Head Trauma In Female Soccer Athletes For Prevention Of Mild Traumatic Brain Injury, Diana Otero Svaldi

Open Access Dissertations

As participation in women’s soccer continues to grow and the longevity of female athletes’ careers continues to increase, prevention of mTBI in women’s soccer has become a major concern for female athletes as the long-term risks associated with a history of mTBI are well documented. Among women’s sports, soccer exhibits the highest concussion rates, on par with those of men’s football at the collegiate level. Head impact monitoring technology has revealed that “concussive hits” occurring directly before symptomatic injury are not predictive of mTBI, suggesting that the cumulative effect of repetitive head impacts experienced by collision sport athletes should be …

Dynamic Holography In Semiconductors And Biomedical Optics, Hao Sun

Open Access Dissertations

Three-dimensional scanning and display are rapidly-advancing new technologies with important commercial drivers such as 3D printing and remote imaging for big data applications. Holography is a natural approach to recording and displaying three-dimensional information because it uses phase-sensitive interferometry to record interference patterns when a reference beam encounters coherent light arriving from an object. The 3D information is contained in the values of wave optics. Holography is a broad field that goes beyond recording and displaying. For instance, holographic optical elements, which take advantage of holographic imaging principles, perform the functions of lenses, gratings or mirrors. Holographic interferometry is also …

Efficient Processing Of Similarity Queries With Applications, Mingjie Tang

Open Access Dissertations

Today, a myriad of data sources, from the Internet to business operations to scientific instruments, produce large and different types of data. Many application scenarios, e.g., marketing analysis, sensor networks, and medical and biological applications, call for identifying and processing similarities in "big" data. As a result, it is imperative to develop new similarity query processing approaches and systems that scale from low dimensional data to high dimensional data, from single machine to clusters of hundreds of machines, and from disk-based to memory-based processing. This dissertation introduces and studies several similarity-aware query operators, analyzes and optimizes their performance.

The first …

Policy Design Tool For Managing Indoor Residential Water Demand In Water-Scarce Regions, Mujahed M. Thneibat

Open Access Dissertations

In view of population growth; climate change; and economic evolution, water resources in numerous parts of the world have reached their natural capacities. Consequently, the ability of many countries to grow; meet the basic needs of inhabitants; and protect the environment will be endangered like never before unless water resources are smartly handled and managed. ^ In the past few decades, many developed and developing countries have suffered from water scarcity, and more are certain to follow. The water security dilemma is much more challenging in developing countries. Water utilities have had to follow regulatory plans to manage demand on …

Preparative Mass Spectrometry Applications In Nanomaterials And Organic Synthesis, Michael Wleklinski

Open Access Dissertations

Preparative mass spectrometry was traditionally a vacuum based experiment where mass selected ion beams were deposited onto surfaces; however, recently ions have been manipulated in the open air to perform accelerated synthesis. The work of this dissertation focuses on the generation of charged ions from microdroplets and their use in organic synthesis and the preparation of atomically precise metal nanoclusters. First the mechanism for charging in the zero volt paper spray will be presented. This works builds a computational model based on the statistical fluctuation of positive and negative charges based on the theory of Dodd. It is found through …

Qos And Trust Prediction Framework For Composed Distributed Systems, Dimuthu Undupitiya Gamage

Open Access Dissertations

The objective of this dissertation is to propose a comprehensive framework to predict the QoS and trust (i.e, the degree of compliance of a service to its specification) values of composed distributed systems created out of existing quality-aware services. We improve the accuracy of the predictions by building context-aware models and validating them with real-life case studies. The context is the set of environmental factors that affect QoS attributes (such as response time and availability), and trust of a service or a composed system. The proposed framework uses available context-QoS dependency information of individual services and information about the interaction …

Synthesis And Performance Of Novel Supramolecular Tools For Single-Particle Cryogenic Electron Microscopy And Drug And Gene Delivery, Kyle J. Wright

Open Access Dissertations

High-resolution biomacromolecular structure elucidation is fundamentally important to structure-based drug design and basic research into complex biochemical processes. Cryo-EM is an emerging alternative to XRD and NMR that is complementary in many ways relative to XRD and NMR. Materials approaches to cryo-EM are anticipated to greatly facilitate the cryo-EM process, allowing progress toward a more high-throughput application of cryo-EM to address challenges in structural biology. ^ Various affinity-based approaches inspired by approaches previously introduced for 2D crystallization were developed for facilitation of cryo-EM. A library of affinity lipopolymer constructs were synthesized consisting of lipopolymers of various PEG molecular weights conjugated …

Computational Environment For Modeling And Analysing Network Traffic Behaviour Using The Divide And Recombine Framework, Ashrith Barthur

Open Access Dissertations

There are two essential goals of this research. The first goal is to design and construct a computational environment that is used for studying large and complex datasets in the cybersecurity domain. The second goal is to analyse the Spamhaus blacklist query dataset which includes uncovering the properties of blacklisted hosts and understanding the nature of blacklisted hosts over time.

The analytical environment enables deep analysis of very large and complex datasets by exploiting the divide and recombine framework. The capability to analyse data in depth enables one to go beyond just summary statistics in research. This deep analysis is …

Lagrangian Analysis Of Vector And Tensor Fields: Algorithmic Foundations And Applications In Medical Imaging And Computational Fluid Dynamics, Zi'ang Ding

Open Access Dissertations

Both vector and tensor fields are important mathematical tools used to describe the physics of many phenomena in science and engineering. Effective vector and tensor field visualization techniques are therefore needed to interpret and analyze the corresponding data and achieve new insight into the considered problem. This dissertation is concerned with the extraction of important structural properties from vector and tensor datasets. Specifically, we present a unified approach for the characterization of distinguished manifolds that form the skeleton of vector and tensor fields and play a key role in understanding their properties.

This dissertation makes several important contributions in this …

Low Rank Methods For Optimizing Clustering, Yangyang Hou

Open Access Dissertations

Complex optimization models and problems in machine learning often have the majority of information in a low rank subspace. By careful exploitation of these low rank structures in clustering problems, we find new optimization approaches that reduce the memory and computational cost.

We discuss two cases where this arises. First, we consider the NEO-K-Means (Non-Exhaustive, Overlapping K-Means) objective as a way to address overlapping and outliers in an integrated fashion. Optimizing this discrete objective is NP-hard, and even though there is a convex relaxation of the objective, straightforward convex optimization approaches are too expensive for large datasets. We utilize low …

In-Column Polymer Modifications: Advancing Polymer Bonded Phases, Alexis G. Huckabee

Open Access Dissertations

Glycosylation is the most common post-translational modification affecting protein activities, including delivery to cell surface, binding affinity, and mediating different physiological effects. Separations of glycoproteins and their glycoforms are essential for drug discovery and development, identification of potential disease biomarkers and quality control. The efficiency of glycoprotein separations is limited by the bonded phases, requiring advances in chromatographic materials. Such advances would improve resolution, allowing for more species to be isolated from a mixture and studied.

Our group found that submicrometer nonporous silica stationary phases with tethered polymer chains (acrylamide) give excellent hydrophilic liquid chromatography (HILIC), a common method used …

Wave Propagation And Imaging In Structured Optical Media, Zun Huang

Open Access Dissertations

Structured optical media, usually characterized by periodic patterns of inhomogeneities in bulk materials, provide a new approach to ultimate control of wave propagation with possible practical applications: from distributed feedback lasers by diffraction gratings, to highly nonlinear performance for super-continuum generation, to fiber-optic telecommunications by microstructured photonic crystal fibers, to invisibility cloaking, to super-resolution imaging with metamaterials etc.

In particular, structured optical media allow to manipulate the wave propagation and dispersion. In this thesis, we focus on engineering the propagation phase dispersion by modulating the compositions and dimensions of the periodic elements. By tailoring the dispersion in momentum space, we …

Gonadal Intersex In Teleosts: Mechanisms, Molecular Biomarkers And Diagnostic Assays, Ahmed M.E. Abdel-Moneim Mohamed

Open Access Dissertations

Natural and synthetic estrogenic and androgenic compounds are continuously released into aquatic ecosystems. Exposure of teleost fishes to these contaminants can negatively impact sex differentiation and reproductive output. Specifically, development of gonadal intersex in gonochoristic (fixed sex) fish species has been studied extensively in relation to exposure to this class of compounds. The main objectives of this dissertation were to: 1) conduct field and laboratory studies to investigate the molecular signaling pathways behind the development of gonadal intersex; and 2) establish molecular biomarkers and assays for testing the ability of environmental pollutants to develop this condition using a battery of …

Securing Cloud-Based Data Analytics: A Practical Approach, Julian James Stephen

Open Access Dissertations

The ubiquitous nature of computers is driving a massive increase in the amount of data generated by humans and machines. The shift to cloud technologies is a paradigm change that offers considerable financial and administrative gains in the effort to analyze these data. However, governmental and business institutions wanting to tap into these gains are concerned with security issues. The cloud presents new vulnerabilities and is dominated by new kinds of applications, which calls for new security solutions. In the direction of analyzing massive amounts of data, tools like MapReduce, Apache Storm, Dryad and higher-level scripting languages like Pig Latin …