Physical Sciences and Mathematics Commons^™

Statistical Models For Gene And Transcripts Quantification And Identification Using Rna-Seq Technology, Han Wu

Open Access Dissertations

RNA-Seq has emerged as a powerful technique for transcriptome study. As much as the improved sensitivity and coverage, RNA-Seq also brings challenges for data analysis. The massive amount of sequence reads data, excessive variability, uncertainties, and bias and noises stemming from multiple sources all make the analysis of RAN-Seq data difficult. Despite much progress, RNA-Seq data analysis still has much room for improvement, especially on the quantification of gene and transcript expression levels. The quantification of gene expression level is a direct inference problem, whereas the quantification of the transcript expression level is an indirect problem, because the label of …

Biophysical Studies Of Cholesterol In Unsaturated Phospholipid Model Membranes, Justin Adam Williams

Open Access Dissertations

Cellular membranes contain a staggering diversity of lipids. The lipids are heterogeneously distributed to create regions, or domains, whose physical properties differ from the bulk membrane and play an essential role in modulating the function of resident proteins. Many basic questions pertaining to the formation of these lateral assemblies remain. This research employs model membranes of well-defined composition to focus on the potential role of polyunsaturated fatty acids (PUFAs) and their interaction with cholesterol (chol) in restructuring the membrane environment. Omega-3 (n-3) PUFAs are the main bioactive components of fish oil, whose consumption alleviates a variety of health problems by …

Predictive Duty Cycling Of Radios And Cameras Using Augmented Sensing In Wireless Camera Networks, Joonhwa Shin

Open Access Dissertations

Energy efficiency dominates practically every aspect of the design of wireless camera networks (WCNs), and duty cycling of radios and cameras is an important tool for achieving high energy efficiencies. However, duty cycling in WCNs is made complex by the camera nodes having to anticipate the arrival of the objects in their field-of-view. What adds to this complexity is the fact that radio duty cycling and camera duty cycling are tightly coupled notions in WCNs.

Abstract In this dissertation, we present a predictive framework to provide camera nodes with an ability to anticipate the arrival of an object in the …

Development Of Isotags For Nmr Based Metabolite Profiling And Applications, Fariba Tayyari

Open Access Dissertations

NMR spectroscopy is a powerful analytical tool for both qualitative and quantitative metabolite profiling analysis. However, accurate quantitative analysis of biological systems especially using one dimensional NMR has been challenging due to signal overlap. In contrast, the enhanced resolution and sensitivity offered by chemoselective isotope tags have enabled new and enhanced methods for detecting hundreds of quantifiable metabolites in biofluids using NMR spectroscopy or mass spectrometry. In this thesis we show improved sensitivity and resolution of NMR experiments imparted by 15N and 13C isotope tagging which enables the accurate analysis of plasma metabolites. To date, isotope tagging has been used …

Automated Failure Explanation Through Execution Comparison, William Nicholas Sumner

Open Access Dissertations

When fixing a bug in software, developers must build an understanding or explanation of the bug and how the bug flows through a program. The effort that developers must put into building this explanation is costly and laborious. Thus, developers need tools that can assist them in explaining the behavior of bugs. Dynamic slicing is one technique that can effectively show how a bug propagates through an execution up to the point where a program fails. However, dynamic slices are large because they do not just explain the bug itself; they include extra information that explains any observed behavior that …

Synthesis Of Novel Isoprenoid Diphosphate Analogs As Chemical Tools To Investigate Protein Geranylgeranylation, Kayla Jo Temple

Open Access Dissertations

Many proteins require prenylation in order to be biologically functional. Some such proteins include the small Ras and Rho GTPase superfamilies, nuclear lamins A and B, and the kinesin motor proteins CENP-E and F. Prenyltransferase (PTase) inhibition is currently being explored as a possible treatment not only for cancer but for a wide variety of other diseases.

Clinical studies revealed that the effectiveness of farnesyltransferase inhibitors (FTIs) to treat Ras-dependent tumors is determined by which isoform of Ras is overactive. Unfortunately the majority of Ras-dependent tumors have a mutation in either the N- or K-Ras isoforms; both of these isoforms …

Implementation Of A Research-Based Lab Module In A High School Chemistry Curriculum: A Study Of Classroom Dynamics, Matthew Pilarz

Open Access Dissertations

Pilarz, Matthew. Ph.D., Purdue University, December 2013. Implementation of a Research-Based Lab Module in a High School Chemistry Curriculum: A Study of Classroom Dynamics. Major Professor: Gabriela C. Weaver.

For this study, a research-based lab module was implemented in two high school chemistry classes for the purpose of examining classroom dynamics throughout the process of students completing the module. A research-based lab module developed for use in undergraduate laboratories by the Center for Authentic Science Practice in Education (CASPiE) was modified and implemented in two high school settings. This module consisted of four phases: Skill Building, Experimental Design, Independent Research, …

Quantifying Crop Yield, Bioenergy Production And Greenhouse Gas Emissions From Cropland And Marginal Land Using A Model-Data Fusion Approach, Zhangcai Qin

Open Access Dissertations

Bioenergy is becoming increasingly attractive to many countries, but has sparked an intensive debate regarding energy, economy, society and environment. Biofuels provide alternative energy to conventional fossil fuels. However, the environmental impact of producing and using biofuel is a major concern to our society. This study is dedicated to quantifying and evaluating biofuel production and potential climate change mitigation due to potential large-scale bioenergy expansion in the conterminous United States, using model-data fusion approaches.

Biofuel made from conventional (e.g., maize (Zea mays L.)) and cellulosic crops (e.g., switchgrass (Panicum virgatum L.) and Miscanthus (Miscanthus × giganteus)) …

Silica Colloidal Crystals As Emerging Materials For The High-Throughput Sizing Of Proteins By Packed Capillary Electrophoresis, Nadine K. Njoya

Open Access Dissertations

Protein heterogeneity is currently one of the leading problems in formulation of therapeutic proteins. The effectiveness of therapeutic proteins is diminished when they exhibit heterogeneity due to aggregates and degradation by-products. Furthermore, guidelines set forth by the FDA require therapeutic proteins to have high stability as well as high purity. With development time on the order of years and costs incurred in the millions, pharmaceutical companies are investing more time in finding fast and efficient ways to screen for protein heterogeneity. Current methods such as native polyacrylamide gel electrophoresis (PAGE), size-exclusion chromatography (SEC) and capillary electrophoresis (CE) are time consuming, …

Utilizing Electron Microscopy And Spectroscopy Methods To Understand Water Structure And Water Doping, Lior Miller

Open Access Dissertations

Water is the second most common element in the universe and the most studied material on earth. Most of the studies concerning water are from the fields of chemistry and biology. Hence, the structure of water molecules and short range order and interactions are well characterized and understood. However, the collective arrangement of water molecules and the long range order are still missing. Understanding of this long range order in water is needed, as it is the key to many water activities.

To fill this gap, this study utilizes a new direct method for characterization of water in the vapor …

Control-Theoretic Decision Support For Mitigation Of Modeled Software Project Cost Overruns, Scott David Miller

Open Access Dissertations

Despite sixty years of practice, the production of software remains an endeavor that is difficult to manage according to a schedule. Control theory studies the ability to influence the dynamical behavior of systems to achieve desired behaviors or eliminate undesired behaviors. In this work, the management problem of software project schedule adherence is re-cast as a problem in control theory.

Below, a modeling framework is proposed for capturing the constraints and dependencies found in the arbitrary organization specific work-flows underlying software production. Combined with proposed models for productivity, defect introduction, and defect detection, the framework completes a method for producing …

Energy Systems Analysis For A Solar Economy, Dharik Sanchan Mallapragada

Open Access Dissertations

The use of solar energy for human needs faces challenges owing to its relatively low energy intensity and intermittent availability, coupled with the constrained availability of renewable carbon and land resources. This study uses systems analysis tools to identify carbon and energy efficient transformations of solar energy for different purposes, including transportation fuels and grid-scale energy storage. These efforts have been complemented with a feasibility analysis of existing fossil-energy and other hybrid pathways.

In an era of limited fossil resources, liquid fuels from sustainably available (SA) biomass could meet the energy needs of the transportation sector. We present a method …

Spectroscopic Characterization Of The Water-Oxidation Intermediates In The Ru-Based Catalysts For Artificial Photosynthesis, Dooshaye Moonshiram

Open Access Dissertations

Utilization of sunlight requires solar capture, light-to-energy conversion and storage. One effective way to store energy is to convert it into chemical energy by fuel-forming reactions, such as water splitting into hydrogen and oxygen. Ruthenium complexes are among few molecular-defined catalysts capable of water splitting. Insight into the mechanism of their action will help to design future robust and economically feasible catalysts for light-to-energy conversion. Mechanistic insights about the design of such catalysts can be acquired through spectroscopic analysis of short-lived intermediates of catalytic water oxidation. Development of time-resolved approaches through stopped flow UV-Vis Spectroscopy to follow the catalysis of …

An Experimental Investigation Of Wind Turbine Aerodynamic Interaction, Brandon Lee Ennis

Open Access Dissertations

Wind turbines have become a viable component in the overall energy makeup of the United States due to improved economics where energy prices have risen and production costs dropped. For a fixed cost, the effectiveness of a wind turbine financially is highly related to its performance. Considering the size of current wind farms, a minor performance improvement will result in large additional sums of revenue. A problem that has received attention with wind farms is that while the fixed costs of the development do get spread out further to reduce the installed cost of each wind turbine, the wind turbines …

A Jackknife Empirical Likelihood Approach To Goodness Of Fit U-Statistic Testing With Side Information, Qun Lin

Open Access Dissertations

Motivated by applications to goodness of fit U-statistics testing, the jackknife empirical likelihood of Jing, et al. (2009) is justified with an alternative approach, and the Wilks theorem for vector U-statistics is proved. This generalizes Owen's empirical likelihood theorem for a vector mean to a vector U-statistics-based mean and includes the jackknife empirical likelihood of U-statistics with side information as a special case. The results are generalized to allow for the constraints to use estimated criteria functions and for the number of constraints to grow with the sample size. The latter is needed to handle naturally occurring nuisance parameters in …

Top-Down Interrogation And Characterization Of Biological Macromolecules, Yang Gao

Open Access Dissertations

Analytical mass spectrometry has been widely applied in the field of biomolecule identification and characterization. It provides fast, accurate and robust information relevant to the molecular mass, composition and structure of the target analytes.

This thesis is focused on the top-down analysis of various macrobiomolecules, nucleic acids and proteins, in the context of ion/ion reaction and gas-phase unimolecular dissociation. The first part of the thesis deals with gas phase fragmentation behavior of chemically modified oligonucleotides. Factors, such as the observation time-scale, the ion type and the energy deposition method, are explored using a quadrupole/time-of-flight mass spectrometer. Novel fragmentation pathway associated …

Methods For Increasing Domains Of Convergence In Iterative Linear System Solvers, David Michael Imberti

Open Access Dissertations

In this thesis, we introduce and improve various methods for increasing the domains of convergence for iterative linear system solvers. We rely on the following three approaches: making the iteration adaptive, or nesting an inner iteration inside of a previously determined outer iteration; using deflation and projections to manipulate the spectra inherent to the iteration; and/or focusing on reordering schemes. We will analyze a specific combination of these three strategies. In particular, we propose to examine the influence of nesting a Flexible Generalized Minimum Residual algorithm together with an inner Recursive Projection Method using a banded preconditioner resulting from the …

The Formation Of Distal Impact Ejecta, Brandon C. Johnson

Open Access Dissertations

Here we present two models for the dynamics of ejection and formation of distal impact ejecta. The first model focuses on the most highly shocked material that forms a massive expanding vapor plume or fireball. In this model molten droplets or spherules condense from the vapor. We model the expanding vapor plume using a one dimensional Lagrangian hydrocode. The condensation of droplets is treated by directly coupling the equations for homogeneous nucleation and growth with our hydrocode. The second model is focused on less energetic material ejected as part of the excavation flow. Using the iSALE hydrocode, we determine the …

Mass Spectrometric Studies On The Primary Products Of Fast Pyrolysis Of Carbohydrates And The Molecular Structures Of Asphaltenes, And The Development Of A Rastering Probe For Laser-Induced Acoustic Desorption Into An Atmospheric Pressure Chemical Ionization Source, Matthew Robert Hurt

Open Access Dissertations

Mass spectrometry (MS) has proven invaluable in the field of mixture analysis and structural elucidation. Tandem mass spectrometry (MS/MS) utilizing collision-activated dissociation (CAD) has become the technique of choice for structural elucidation of unknown analytes in mixtures. When coupled with gas chromatography (GC) or high performance liquid chromatography (HPLC), it allows for trace level analysis of mixture components. In spite of the utility of mass spectrometry in complex mixture analysis, it does have limitations. Traditional GC/MS methods used for the analysis of fast pyrolysis products cannot be used to analyze the primary products, thus limiting the knowledge that can be …

Structural Analysis Of Carbohydrates By Mass Spectrometry, Chiharu Konda

Open Access Dissertations

Protein glycosylation is a highly frequent post-translational modification. Glycosylation is actively involved in intermolecular and intercellular binding events that are important to a wide range of biological functions such as immunity and fertility. The unique functions of glycans are directly related to their structures. In order to fully characterize the structure of an unknown glycan, 5 levels of structural information is needed: sugar unit identity, anomeric configuration, linkage types, sequence, and branching location. One of the grand challenges limiting the advance of glycosciences is the lack of sensitive tools for detailed glycan structural analysis. Tandem mass spectrometry (MS/MS) is a …

Generation And Statistical Modeling Of Active Protein Chimeras: A Sequence Based Approach, Nicholas Fico

Open Access Dissertations

Generation of active protein chimeras is a valuable tool to probe the functional space of proteins. Statistical modeling is the next logical step, allowing us to build a model of gene fragment replaceability between species. In this thesis I begin to develop the statistical tools that are needed to systematically describe combinatorial protein libraries. I present three sets of diverse chimeric protein libraries developed using sequence information. The statistical model of the human N-Ras and human K-Ras-4B genes reveal a set previously unidetifed surface residues on the N-Ras G-Domain that may be involved in cellular localization. Statistical modeling of a …

Development Of A Field-Portable Miniature Mass Spectrometer Designed For In-Situ Analysis And Ion Trap Miniaturization, Paul Isaac Hendricks

Open Access Dissertations

Chemical analysis by mass spectrometry has become the gold standard due to the sensitivity, selectivity, and short analysis times that are afforded by the method. Advances in miniaturized vacuum systems, mass analyzers, electronics, and ionization sources have allowed for the development of field-portable mass spectrometers. The performance of portable instruments has received much attention for their utility in the detection of illicit drugs, explosives, environmental contaminants, therapeutic drugs, and more recently, biological tissues. Furthermore, detection of the aforementioned compounds can be completed at atmospheric pressures and in the presence of complex matrices and sample surfaces when used in conjunction with …

Ribbons: A Partially Shared Memory Programming Model, Kevin John Hoffman

Open Access Dissertations

The need for programs to execute subcomponents in isolation from each other or with lower privileges is prevalent among today's systems. While modern operating systems provide mechanisms for fine-grained isolation of OS resources, only course-grained mechanisms exist for efficient isolation of heap memory. This dissertation develops a new memory programming model known as ribbons to enable fine-grained isolation of heap memory. Ribbons is a shared memory programming model that allows for more implicit sharing of memory than multiprocessing yet is more restrictive than multithreading. The ribbons model hierarchically structures the heap into protection domains. Privileges between these protection domains are …

Cloud To Cloud Registration For 3d Point Data, Darion Shawn Grant

Open Access Dissertations

The vast potential of digital representation of objects by large collections of 3D points is being recognized on a global scale and has given rise to the popularity of point cloud data (PCD). 3D imaging sensors provide a means for quickly capturing dense and accurate geospatial information that represent the 3D geometry of objects in a digital environment. Due to spatial and temporal constraints, it is quite common that two or more sets of PCD are obtained to provide full 3D analysis. It is therefore quite essential that all the PCD are referenced to a homogeneous coordinate frame of reference. …

Fluorous- Phase Synthesis Of Heparan Sulfate Disaccharides & Low-Molecular Weight Additives For Enhancing The Performance Of Lithium-Ion Batteries., Matthew Daniel Casselman

Open Access Dissertations

Heparan sulfate is a complex cell-surface proteoglycan that serves many important roles in biology, such as growth and development, immune response and pathogenesis. Heparan sulfate is structurally heterogeneous due to the variable post- glycosylation modifications, particularly the generation of diverse sets of sulfate esters (sulfoforms) for any given disaccharide unit. In order to establish useful relationships between heparan sulfate structure and biological activity, a set of well-defined sulfoforms is necessary to support binding affinity screening. In this thesis, we describe the generation of diverse sulfoforms from heparan disaccharides using a fluorous tag to facilitate purification of highly charged intermediates, and …

Experimental Studies Of Lirb: Spectroscopy And Ultracold Molecule Formation By Photoassociation, Sourav Dutta

Open Access Dissertations

Heteronuclear polar molecules have recently attracted enormous attention owing to their ground state having a large electric dipole moment. The long range anisotropic dipole-dipole interaction in such systems is the basis for a variety of applications including quantum computing, precision measurements, ultracold chemistry and quantum simulations. Heteronuclear bi-alkali molecules, only a small subset of polar molecules, have received special attention mainly because the constituent alkali atoms are easy to laser cool and can be relatively easily associated to form molecules at ultracold temperatures. Our choice, the LiRb molecule, is motivated by the relatively high dipole moment (4.1 Debye) of the …

Observation-Based Algorithm Development For Subsurface Hydrology In Northern Temperate Wetlands, Chun-Mei Chiu

Open Access Dissertations

This study investigates wetland subsurface hydrology, as well as biogeochemistry - which is strongly influenced by water and temperature dynamics - as these interactions are expected to be highly significant, yet remain poorly represented in current ecosystem and climate models.

Northern wetlands have received widespread public attention due to steadily increasing summer mean global temperatures, extreme precipitation events and higher rates of natural greenhouse gas emissions, as well as the significant impacts on them due to human activities. The goal of my graduate research has been to improve quantification of the role of subsurface hydrology in northern wetlands by using …

Applicability Of Continuum Fracture Mechanics In Atomistic Systems, Shao-Huan Cheng

Open Access Dissertations

By quantitating the amplitude of the unbounded stress, the continuum fracture mechanics defines the stress intensity factor K to characterize the stress and displacement fields in the vicinity of the crack tip, thereby developing the relation between the stress singularity and surface energy (energy release rate G). This G-K relation, assigning physical meaning to the stress intensity factor, makes these two fracture parameters widely used in predicting the onset of crack propagation. However, due to the discrete nature of the atomistic structures without stress singularity, there might be discrepancy between the failure prediction and the reality of nanostructured materials. Defining …

Osmium Catalyzed Dihydroxylation And Oxidative Cleavage Of Vinyl Sulfone And Elucidation Of The Vinylsulfone Polypropionate Methodology For The Synthesis Of The C32 Des-Methyl C28-C34 Actin Binding Tail Of Aplyronine A, Thomas Paul Bobinski

Open Access Dissertations

A general methodology for the generation of dipropionate functionalities using cyclic 7-membered vinylsulfones has been devised for the purpose of synthesizing polyketide natural products such as aplyronine A. Final oxidative cleavage via ozonolysis has been shown to be difficult providing variable yields. Furthermore, elegant synthesis of the C28-C34 segment of the aplyronine A actin binding tail has proved elusive. Utilization of OsO4 and catalytic citric acid has led to a methodology whereby harsh ozonolysis procedures can be mostly avoided. A reengineering of the vinylsulfone polypropionate methodology in conjunction with osmylation has been found to provide the actin binding tail under …

An Analysis Of The Impact Of Storage Temperature, Moisture Content & Duration Upon The Chemical Components & Bioprocessing Of Lignocellulosic Biomass, Arun Athmanathan

Open Access Dissertations

The successful utilization of lignocellulosic biomass as a feedstock for fuels and chemicals necessitates storage for 2-6 months. It is correspondingly important to understand the impact of storage parameters - moisture concentration, temperature and duration - on biomass quality.

As aerobic storage is the most viable large-scale solution, aerobic storage experiments were carried out with three projected bioenergy feedstocks - sweet sorghum (Sorghum bicolor) bagasse, corn (Zea mays) stover and switchgrass (Panicum virgatum). Stored samples of each were examined for dry matter loss and composition change to develop a material balance around carbohydrates and lignin.

A mean dry matter loss …