Physical Sciences and Mathematics Commons^™

Generalized Techniques For Using System Execution Traces To Support Software Performance Analysis, Thelge Manjula Peiris

Open Access Dissertations

This dissertation proposes generalized techniques to support software performance analysis using system execution traces in the absence of software development artifacts such as source code. The proposed techniques do not require modifications to the source code, or to the software binaries, for the purpose of software analysis (non-intrusive). The proposed techniques are also not tightly coupled to the architecture specific details of the system being analyzed. This dissertation extends the current techniques of using system execution traces to evaluate software performance properties, such as response times, service times. The dissertation also proposes a novel technique to auto-construct a dataflow model …

Estimating The Water Quality Condition Of River And Lake Water In The Midwestern United States From Its Spectral Characteristics, Jing Tan

Open Access Dissertations

This study focuses on developing/calibrating remote sensing algorithms for water quality retrieval in Midwestern rivers and lakes. In the first part of this study, the spectral measurements collected using a hand-held spectrometer as well as water quality observations for the Wabash River and its tributary the Tippecanoe River in Indiana were used to develop empirical models for the retrieval of chlorophyll (chl) and total suspended solids (TSS). A method for removing sky and sun glint from field spectra for turbid inland waters was developed and tested. Empirical models were then developed using a subset of the field measurements with the …

Optimal "Big Data" Aggregation Systems - From Theory To Practical Application, William J. Culhane Iv

Open Access Dissertations

The integration of computers into many facets of our lives has made the collection and storage of staggering amounts of data feasible. However, the data on its own is not so useful to us as the analysis and manipulation which allows manageable descriptive information to be extracted. New tools to extract this information from ever growing repositories of data are required.

Some of these analyses can take the form of a two phase problem which is easily distributed to take advantage of available computing power. The first phase involves computing some descriptive partial result from some subset of the original …

Partition Density Functional Theory, Jonathan R. Nafziger

Open Access Dissertations

Partition density functional theory (PDFT) is a method for dividing a molecular electronic structure calculation into fragment calculations. The molecular density and energy corresponding to Kohn Sham density-functional theory (KS-DFT) may be exactly recovered from these fragments. Each fragment acts as an isolated system except for the influence of a global one-body 'partition' potential which deforms the fragment densities. In this work, the developments of PDFT are put into the context of other fragment-based density functional methods. We developed three numerical implementations of PDFT: One within the NWChem computational chemistry package using basis sets, and the other two developed from …

The Effect Of Macromolecular Crowding On The Structure Of The Protein Complex Superoxide Dismutase, Ajith Rathnaweera Rajapaksha Mudalige

Open Access Dissertations

Biological environments contain between 7 - 40% macromolecules by volume. This reduces the available volume for macromolecules and elevates the osmotic pressure relative to pure water. Consequently, biological macromolecules in their native environments tend to adopt more compact and dehydrated conformations than those in vitro. This effect is referred to as macromolecular crowding and constitutes an important physical difference between native biological environments and the simple solutions in which biomolecules are usually studied.^ We used small angle scattering (SAS) to measure the effects of macromolecular crowding on the size of a protein complex, superoxide dismutase (SOD). Crowding was induced using …

Overcoming Uncertainty For Within-Network Relational Machine Learning, Joseph J. Pfeiffer

Open Access Dissertations

People increasingly communicate through email and social networks to maintain friendships and conduct business, as well as share online content such as pictures, videos and products. Relational machine learning (RML) utilizes a set of observed attributes and network structure to predict corresponding labels for items; for example, to predict individuals engaged in securities fraud, we can utilize phone calls and workplace information to make joint predictions over the individuals. However, in large scale and partially observed network domains, missing labels and edges can significantly impact standard relational machine learning methods by introducing bias into the learning and inference processes. In …

Ergodic Properties Of Countable Extensions, Samuel Joshua Roth

Open Access Dissertations

First, we study countably piecewise continuous, piecewise monotone interval maps. We establish a necessary and sufficient criterion for the existence of a non-decreasing semiconjugacy to an interval map of constant slope in terms of the existence of an eigenvector of an operator acting on a space of measures. Then we give examples, both Markov and non-Markov, for which the criterion is violated. ^ Next, we establish a criterion for the existence of a constant slope map on the extended real line conjugate to a given countably piecewise monotone interval map. We require the given interval map to be continuous, Markov, …

Architectural Techniques To Extend Multi-Core Performance Scaling, Hamza Bin Sohail

Open Access Dissertations

Multi-cores have successfully delivered performance improvements over the past decade; however, they now face problems on two fronts: power and off-chip memory bandwidth. Dennard's scaling is effectively coming to an end which has lead to a gradual increase in chip power dissipation. In addition, sustaining off-chip memory bandwidth has become harder due to the limited space for pins on the die and greater current needed to drive the increasing load . My thesis focuses on techniques to address the power and off-chip memory bandwidth challenges in order to avoid the premature end of the multi-core era. ^ In the first …

Stability Of Machine Learning Algorithms, Wei Sun

Open Access Dissertations

In the literature, the predictive accuracy is often the primary criterion for evaluating a learning algorithm. In this thesis, I will introduce novel concepts of stability into the machine learning community. A learning algorithm is said to be stable if it produces consistent predictions with respect to small perturbation of training samples. Stability is an important aspect of a learning procedure because unstable predictions can potentially reduce users' trust in the system and also harm the reproducibility of scientific conclusions. As a prototypical example, stability of the classification procedure will be discussed extensively. In particular, I will present two new …

Privacy-Preserving Social Network Analysis, Christine Marie Task

Open Access Dissertations

Data privacy in social networks is a growing concern that threatens to limit access to important information contained in these data structures. Analysis of the graph structure of social networks can provide valuable information for revenue generation and social science research, but unfortunately, ensuring this analysis does not violate individual privacy is difficult. Simply removing obvious identifiers from graphs or even releasing only aggregate results of analysis may not provide sufficient protection. Differential privacy is an alternative privacy model, popular in data-mining over tabular data, that uses noise to obscure individuals' contributions to aggregate results and offers a strong mathematical …

Mass Spectrometric Characterization Of Peptide Radical Ions And Implication For Radical Chemistry, Lei Tan

Open Access Dissertations

Gas-phase radical ion chemistry has attracted increasing research interest from the mass spectrometry (MS) society because it provides new capabilities in bio-analysis which often complements traditional MS methods developed from even-electron ions. Fundamental studies of biomolecule related radical species are essential to broadening the scope of radical chemistry and pushing the frontiers of its analytical applications. This dissertation mainly discusses the gas-phase chemistry of peptide sulfinyl radicals (-SO·), which has been rarely studied before. In order to establish an effective research approach, a method that can generate site-specific peptide sulfinyl radical ion has been developed. This method is based on …

Heat Trace And Heat Content Asymptotics For Schrodinger Operators Of Stable Processes/Fractional Laplacians, Luis Guillermo Acuna Valverde

Open Access Dissertations

Let V be a bounded and integrable potential over R^d and 0 < α ≤ 2. We show the existence of an asymptotic expansion by means of Fourier Transform techniques and probabilistic methods for the following quantities [special characters omitted] and [special characters omitted] as t ↓ 0. These quantities are called the heat trace and heat content in R^d with respect to V, respectively. Here, p((α)/ t)(x, y) and p( ^H_V/t)(x, y) denote, respectively, the heat kernels of the heat semigroups with infinitesimal generators given by (-Δ)(α/2) and H_V = (-Δ)(α/2) + V. The former operator is known as the fractional Laplacian whereas the latter one is known as the fractional Schrödinger Operator. ^ The study …

Learning Compact Hashing Codes With Complex Objectives From Multiple Sources For Large Scale Similarity Search, Qifan Wang

Open Access Dissertations

Similarity search is a key problem in many real world applications including image and text retrieval, content reuse detection and collaborative filtering. The purpose of similarity search is to identify similar data examples given a query example. Due to the explosive growth of the Internet, a huge amount of data such as texts, images and videos has been generated, which indicates that efficient large scale similarity search becomes more important.^ Hashing methods have become popular for large scale similarity search due to their computational and memory efficiency. These hashing methods design compact binary codes to represent data examples so that …

Orderability And Rigidity In Contact Geometry, Peter Weigel

Open Access Dissertations

We study the existence of positive loops of contactomorphisms on a Liouville-fillable contact manifold (&Sgr;, ξ = ker(α)). Previous results (see [1]) show that a large class of Liouville-fillable contact manifolds admit contractible positive loops. In contrast, we show that for any Liouville-fillable (&Sgr;, α) with dim(&Sgr;) ≥ 7, there exists a Liouville-fillable contact structure ξ' on &Sgr; which admits no positive loop at all. Further, ξ' can be chosen to agree with ξ' on the complement of a Darboux ball. We then define a relative version of orderability for a Legendrian submanifold, and discuss the relationship between the two …

Effect Of Maleic Acid On The Selectivity Of Glucose And Fructose Dehydration And Degradation, Ximing Zhang

Open Access Dissertations

5-Hydroxymethyfurfural (HMF), a platform chemical can upgrade to a variety of fuels and polymers, can be manufactured from lignocellulose. This study focuses on the Lewis and Brønsted acid effect on hexose dehydration for HMF production. We report the positive effect of maleic acid, a dicarboxylic acid used as Brønsted acid, on the selectivity of hexose dehydration to 5-hydroxymethyfurfural (HMF), and subsequent hydrolysis to levulinic and formic acids. We also describe the kinetic analysis of a Lewis acid (AlCl ₃) alone and in combination with HCl or maleic acid to catalyze the isomerization of glucose to fructose, dehydration of fructose …

Permutohedra, Configuration Spaces And Spineless Cacti, Yongheng Zhang

Open Access Dissertations

It has been known that the configuration space F(R², n) of n distinct ordered points in R² deformation retracts to a regular CW complex with n!permutohedra P_n as the top dimensional cells. In this paper, we show that there exists a similar but different permutohedral structure of the spaceCact(n) of spineless cacti with n lobes. Based on these structures, direct homotopy equivalences between F (R², n) and Cact(n) are then given. It is well known that the little 2-discs space D₂(n) is homotopy equivalent toF(R², n). …

Modular Approach To Spintronics, Kerem Yunus Camsari

Open Access Dissertations

There has been enormous progress in the last two decades, effectively combining spintronics and magnetics into a powerful force that is shaping the field of memory devices. New materials and phenomena continue to be discovered at an impressive rate, providing an ever-increasing set of building blocks that could be exploited in designing transistor-like functional devices of the future. The objective of this thesis is to provide a quantitative foundation for this building block approach, so that new discoveries can be integrated into functional device concepts, quickly analyzed and critically evaluated. Through careful benchmarking against available theory and experiments we establish …

Consequences Of Short-Term Water Temperature Variability To Fish: Current And Future Climate Change Impacts, David P. Coulter

Open Access Dissertations

Water temperature has a profound influence on aquatic ectotherms by affecting all aspects of biological organization; from chemical and molecular functioning to whole-organism and population-level impacts. Natural processes and anthropogenic activities can create conditions where temperatures vary greatly through space and time. While exposure to temperature changes lasting ≥ 24 hours have been examined in some species, it is unclear how more rapid (< 24 hours; sub-daily) thermal fluctuations affect aquatic ectotherms. I used a combination of field observations, laboratory experiments, and modeling simulations to understand: 1) how habitat quality of aquatic ectotherms is affected in thermally dynamic environments; 2) the role of sub-daily temperature fluctuations on growth, survival, and stress responses in juvenile and adult fish; 3) how fish early life stages are affected by sub-daily temperature fluctuations; and 4) what impact thermally dynamic environments have on a model species at a population-level. A model quantifying habitat quality around power plant thermal discharges indicated that elevated and variable discharge temperatures affected habitat quality over a relatively small spatial area for aquatic ectotherms. Models examining elevated temperatures representing climate warming showed that the effects of industrial discharges and climate warming could have an interactive effect on habitat quality by increasing the spatial area and duration over which industrial thermal effluents impact aquatic ectotherms. Laboratory experiments indicated that closely related fishes can respond differently to the same sub-daily temperature fluctuations. Yellow perch (Perca flavescens) had higher consumption and growth under sub-daily temperature fluctuations but developed skin lesions; an indication of thermal stress. In contrast, these same fluctuations reduced growth in physiologically similar walleye (Sander vitreus) …

Studies Of Arctic Halogen Chemistry From The Snowpack To The Gas Phase, Kyle D Custard

Open Access Dissertations

The temporary depletion of both tropospheric ozone and gaseous mercury during the Arctic springtime has been a focus of active research over the past several decades. Both of these phenomena have been linked to chemical reactions with halogen radicals. In particular, bromine atoms have been shown to act as the primary driver for these chemical depletions, although both chlorine and iodine atoms also contribute. Molecular bromine, along with its oxidation products, have been well studied in the Arctic, yet chlorine has not. Chlorine is known to impact the local oxidation capacity via its high reactivity with volatile organic compounds. Despite …

Visibility Computation Through Image Generalization, Jian Cui

Open Access Dissertations

This dissertation introduces the image generalization paradigm for computing visibility. The paradigm is based on the observation that an image is a powerful tool for computing visibility. An image can be rendered efficiently with the support of graphics hardware and each of the millions of pixels in the image reports a visible geometric primitive. However, the visibility solution computed by a conventional image is far from complete. A conventional image has a uniform sampling rate which can miss visible geometric primitives with a small screen footprint. A conventional image can only find geometric primitives to which there is direct line …

Novel Methods For Manipulating Ion Types In The Solution And Gas Phases For The Structural Analysis Of Biomolecules Using Mass Spectrometry, Christine M Fisher

Open Access Dissertations

Mass Spectrometry has become a valuable tool for the analysis of a variety of molecules, making it applicable to many fields. The advent of nanoelectrospray ionization (nESI) as a soft/low energy ionization technique has enabled the analysis of large, intact biomolecules. Most mass spectrometry experiments consist of three main steps: ionization, probe step(s), and mass analysis. The present work focuses on a variety of methods for altering ion types at various stages of the mass spectrometry experiment to affect ion fragmentation. Ion types can be manipulated in the solution/droplet phases using novel nESI emitters, generated from borosilicate theta capillaries. These …

Public Understanding Of Chemistry Research In Print News, Michael D. Hands

Open Access Dissertations

Despite numerous calls for improving scientific literacy, many American adults show a lack of understanding of experiments, scientific study, and scientific inquiry. News media is one important avenue for science learning, but previous research investigating health and/or environmental science news has shown that it is inconsistent in the presentation of scientific research limitations, potentially impacting reader understanding. In the first phase of this dissertation, seventeen news articles reporting on a single chemistry research article, along with associated press releases and research articles, were analyzed using move analysis to determine the structure of each type of text. It was found that …

Uncertainty Quantification And Calibration Of Physical Models, Xian He

Open Access Dissertations

An ecosystem model is a representation of a real complex ecological system, and is usually described by sophisticated mathematical models. Terrestrial Ecosystem Model (TEM) is one of the ecosystem models, that describes the dynamics of car- bon, nitrogen, water and other vegetation related variables. There are uncertainties in the TEM which are attributed to inaccurate input data, insufficient knowledge of the parameters, inherent randomness and simplification of the physical model. Quantification of uncertainty of such an ecosystem model is computationally very heavy. Bayesian calibration method has been used as an efficient way to calibrate and quantify uncertainties of the computer …

Experimental Constraints On Exotic Spin-Dependent Interactions Using Specialized Materials, Rakshya Khatiwada

Open Access Dissertations

Various theories predict the possible existence of symmetry violating forces with mesoscopic range interactions from mm-m [1]. These forces can arise from the coupling of a spin 0 boson to spin 1/2 fermions through scalar (gs) and pseudoscalar (gp) couplings. We discuss two experiments that can investigate these interactions using nucleon rich, impressively low magnetic susceptibility (5-100 times lower than pure water) test masses and electron-spin rich, polarized test masses (spin density: 10^20 h/cm3 ). The first experiment looks for a P-odd, T-odd interaction potential proportional to (S.r) where S is the spin of one particle and r is the …

Polarization-Dependent Nonlinear Optical Microscopy Methods For The Analysis Of Crystals And Biological Tissues, Emma L. Kerian

Open Access Dissertations

The ability to solve a high-resolution protein structure is largely dependent on the successful generation and identification of protein crystals prior to X-ray diffraction (XRD). For novel protein targets, high-throughput crystallography often involves generation of multiple targets and thousands of crystallization trials per target to generate diffraction-quality crystals. Second harmonic generation (SHG) imaging has been developed as a fast, non-destructive and sensitive method for the selective identification of protein crystals, even in highly scattering environments. Polarization-dependent SHG microscopy methods were developed to assess the presence of multidomain crystals to provide a handle on crystal quality. In addition, polarization-dependent two-photon excited …

Transport Studies In Graphene-Based Materials And Structures, Jiuning Hu

Open Access Dissertations

Graphene, a single atomic layer of graphite, has emerged as one of the most attractive materials in recent years for its many unique and excellent properties, inviting a broad area of fundamental studies and applications. In this thesis, we present some theoretical/experimental studies about the thermal, electronic and thermoelectric transport properties in graphene-based systems. We employ the molecular dynamic simulations to study the thermal transport in graphene nanoribbons (GNRs) exhibiting various properties, including chirality dependent thermal conductivity, thermal rectification in asymmetric GNRs, defects and isotopic engineering of the thermal conductivity and negative differential thermal conductance (NDTC) at large temperature biases. …

Parallel Symmetric Eigenvalue Problem Solvers, Alicia Marie Klinvex

Open Access Dissertations

Sparse symmetric eigenvalue problems arise in many computational science and engineering applications: in structural mechanics, nanoelectronics, and spectral reordering, for example. Often, the large size of these problems requires the development of eigensolvers that scale well on parallel computing platforms. In this dissertation, we describe two such eigensolvers, TraceMin and TraceMin-Davidson. These methods are different from many other eigensolvers in that they do not require accurate linear solves to be performed at each iteration in order to find the smallest eigenvalues and their associated eigenvectors. After introducing these closely related eigensolvers, we discuss alternative methods for solving the saddle point …

A Hydroclimatic Assessment Of The U.S. Corn Belt Across Spatial And Temporal Scales, Olivia B. Kellner

Open Access Dissertations

The term hydroclimate is used to describe the climate of a given location as determined by the incident radiant energy (temperature) and the existence of water in its various forms on Earth. Two types of climate comprise the science of hydroclimatology: the climate as established by general global circulation patterns at specific locations on Earth (large-scale climate) and the climate established at Earth's surface resulting from the daily fluxes of radiant energy and water in its various forms between the atmosphere, Earth's surface, and the subsurface (local-scale climate) (Shelton 2009). This dissertation investigates different spatial and temporal scales of the …

Computational Optical Imaging: Applications In Synthetic Aperture Imaging, Phase Retrieval, And Digital Holography, Dennis Joseph Lee

Open Access Dissertations

Computational imaging has become an important field, as a merger of both algorithms and physical experiments. In the realm of microscopy and optical imaging, an important application is the problem of improving resolution, which is bounded by wavelength and numerical aperture according to the classic diffraction limit. We will investigate the resolution enhancement of phase objects such as transparent biological cells. One key challenge is how to measure phase experimentally. Standard interferometric techniques have the drawback of being sensitive to environmental vibrations and temperature fluctuations, and they use a reference arm which requires more space and cost. Non-holographic methods provide …

Quantitative Mrna Detection With Advanced Nonlinear Microscopy, Jing Liu

Open Access Dissertations

Cell-specific information on quantity and localization of key mRNA transcripts in single-cell level are critical to the assessment of cancer risk, therapy efficacy, and effective prevention strategies. While current techniques are not capable to visualize single mRNA transcript beyond the diffraction limit. In this thesis, two nonlinear technologies, second harmonic super-resolution microscopy (SHaSM) and transient absorption microscopy (TAM), are developed to detect and quantify single Human edimer receptor 2 (Her2) mRNA transcripts. The SHaSM is used to detect single mRNA transcript beyond the diffraction limit, while the TAM is employed to detect mRNA without the interference of fluorescence background. The …