Physical Sciences and Mathematics Commons^™

Fabrication Of Multilayered Structure For Coherent Random Lasing, John Rauchenstein, Young L. Kim

The Summer Undergraduate Research Fellowship (SURF) Symposium

High powered lasers have many applications, including medical treatment and surgery. However, these lasers are extremely expensive and are therefore not widely available. The aim of this study was to demonstrate a method to create such a laser with significantly decreased overall cost and increased efficiency. In order to do this, we explored a phenomenon called random lasing which is a light amplification process. To start with, a low-cost pumping laser is directed at normal incidence toward a multi-layered sample with two alternating layers. At first pearl, a naturally found material that has many organic nano-scale layers (similar to the …

Environmental Tradeoffs In Bioenergy Production And Agricultural Practices, Alicia Lynn English

Open Access Dissertations

The focus of this dissertation is the environmental tradeoffs of stover removal within the Corn Belt. The environmental tradeoffs considered are mainly concerned with managing soil erosion and soil quality. The analysis layers soil characteristics, management strategies and per acre costs using an integrated RUSLE2/WEPS model and an economic optimization model to illuminate a lower bound supply response. Different assumptions were tested in regards to sustainability, prices, and market integration for five states and 18,760 soil types throughout the Corn Belt. Sustainability was defined to limit soil erosion from wind and water to 5 tons/acre/year and the soil organic matter …

Reasoning Across Language And Vision In Machines And Humans, Andrei Barbu

Open Access Dissertations

Humans not only outperform AI and computer-vision systems, but use an unknown computational mechanism to perform tasks for which no suitable approaches exist. I present work investigating both novel tasks and how humans approach them in the context of computer vision and linguistics. I demonstrate a system which, like children, acquires high-level linguistic knowledge about the world. Robots learn to play physically-instantiated board games and use that knowledge to engage in physical play. To further integrate language and vision I develop an approach which produces rich sentential descriptions of events depicted in videos. I then show how to simultaneously detect …

The Role Of Resource Predictability In The Metapopulation Dynamics Of Insects, Byju Nambidiyattil Govindan

Open Access Dissertations

The metapopulation paradigm has emerged as an important tool to understand the dynamics of species living in fragmented landscapes. In this dissertation, I investigate the unpredictable nature of resource availability for species living in human-dominated heterogeneous and dynamic landscapes in the context of its consequences for long-term regional persistence of species. In particular, I test theoretical advancements in metapopulation ecology following a two-pronged approach - via experiments in the lab and observations in the field - using insects. In chapter 1, I introduce the concept of metapopulation ecology in the context of its relevance for dynamics of species living in …

Influence Of Cholesterol And Bilayer Asymmetry On Membrane Protein Distribution In Polymer-Tethered Raft-Mimicking Lipid Membranes, Noor Fueza Hussain

Open Access Dissertations

It is now widely recognized that lipid rafts, which are membrane domains enriched in cholesterol (CHOL) and sphingolipids (SL), play a significant functional role in the plasma membrane. Raft domains particularly affect membrane functionality by causing sequestering of membrane proteins. Underlying mechanisms of raft-associated membrane protein sequestration remain elusive, due to the complexity, transient nature, and small size of raft domains in cellular membranes. To address these challenges, this dissertation unveils the relationship between lipid raft composition and membrane protein sequestration and function using raft-mimicking model membrane mixtures comprised of coexisting liquid-ordered (lo) and liquid-disordered (ld) domains with reconstituted membrane …

Long-Term Disturbance Histories Of Managed And Natural Mixed-Hardwood Forests Of Central Indiana, Robert Charles Morrissey

Open Access Dissertations

Over the course of the last century, we have observed changes in forest composition and structure related to changes in disturbance regimes. Reduced frequency and severity of disturbance events has allowed for the ingrowth of shade-tolerant, mesophytic species into forest understories; the result is shifting species compositions and changes in forest structure. In some cases, the loss of masting species, such as oak (Quercus spp.) and hickory (Carya spp.), may also accompany a shift in forest function and further accommodate other species shifts among mammal, insect, and bird populations. Management efforts have been suggested as a possible means …

Design, Synthesis, And Evaluation Of Molecular Inhibitors For Biologically Relevant Enzymes, Sarah Emma St. John

Open Access Dissertations

The work in this thesis details the design, synthesis, and biological evaluation of molecular inhibitors for the inhibition of biologically relevant enzymes. The first three chapters of this thesis concern the polyphenol resveratrol and its inhibition of the quinone reductase 2 (QR2) enzyme. The work on this subject resulted in the complete design, synthesis, biological and structural evaluation of a second generation library of resveratrol analogues. From this work we identified a novel resveratrol analogue that inhibits QR2 in a previously unknown binding orientation. The fourth chapter of this thesis details the de novo design of molecules for the inhibition …

Gas-Phase Covalent And Non-Covalent Ion/Ion Chemistry Of Biological Macromolecules, John Robert Stutzman

Open Access Dissertations

Gas-phase ion/ion chemistry involves the interaction of oppositely charged ions inside of the mass spectrometer. During this gas-phase chemistry, particle transfer (i.e., proton and electron) or synthesis can occur at rapid reaction rates. Particle transfer represents a mature area of ion/ion chemistry, while selective covalent modification represents a fairly new area of gas-phase chemistry. Gas-phase covalent chemistry is based on traditional solution phase organic chemistry.

The work demonstrated in this dissertation greatly involves gas-phase covalent and non-covalent Schiff base chemistry on peptide and protein ions. The reagent dianion, 4-formyl 1,3-benzene disulfonic acid, has been used to covalently modify unprotonated primary …

Estimation Of Variation For High-Throughput Molecular Biological Experiments With Small Sample Size, Danni Yu

Open Access Dissertations

Motivation: In the quantification of molecular components, a large variation can affect and even potentially mislead the biological conclusions. Meanwhile, the high-throughput experiments often involve a small number of samples due to the limitation of cost and time. In such cases, the stochastic information may dominate the outcome of an experiment because there may not be enough samples to present the true biological information. It is challenging to distinguish the changes in phenotype from the stochastic variation.

Methods: Since the biological molecules have been quantified with different technologies, different statistical methods are required. Focusing on three types of important high-throughput …

The City In Mind: Environmental Literacy And Adaptation In Nineteenth-Century British Literature, Adam Edward Watkins

Open Access Dissertations

This dissertation argues that a new paradigm of selfhood emerged in nineteenth-century British literature, one that recognized the individual will and environmental influence not as antithetical but as dialectical forces in the formation of the self. The concept of an externally negotiated subject challenges both the inward and socially determined conceptions of self that have dominated the relevant criticism. Informed by empiricist, associationist, and evolutionary theories of the mind, the portrayals of subject-formation in this study highlight the radical changes occurring in the human environment in nineteenth-century, which catalyzed the conception of a malleable yet self-forming subject. Along with the …

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 …

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 …

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 …

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)) …

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 …

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 …

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 …

Agriculture In A Water Scarce World, Allison Roberts, Amjad Assi, Bassel Daher, Men Li

Student Papers in Public Policy

According to the McKinsey report (2009), the world is facing a water scarcity challenge where agriculture is its predominant consumer. It accounts for approximately 3100 billion m³, or 71 percent of global water withdrawals today, and is expected to increase to 4500 billion m³ by 2030. This increase is due to a number of factors: growing population and the ever growing necessity to cater for its food needs, economic growth, the variability of precipitation trends and increase in global temperatures. In addition to the increase in water scarcity, the agricultural sector faces an enormous challenge of producing …

Fate Of 17Α-Estradiol, 17Β-Estradiol, And Estrone In Agricultural Soils And Sediments, Michael L. Mashtare Jr

Open Access Dissertations

The shift to concentrated animal production facilities and increasing rural-urban migration has increased the localized land application of nearly 1 billion tons of manure and biosolids annually. Although these applications provide nutrients and contribute to soil tilth, they also serve as a source for an estimated 49 tons of the natural manure-borne estrogens, 17α-estradiol (17α-E2), 17β-estradiol (17β-E2), and estrone (E1). While these estrogens are critical to endocrine systems, the low concentrations observed in the environment can disrupt endocrine function in non-target organisms, e.g., altering secondary sex characteristics which can lead to changes in wildlife communities.

Research presented here focuses on …

The Palm-Tree Index: Indexing With The Crowd, Aamer Mahmood, Walid G. Aref, Eduard Dragut, Saleh Basalamah

Cyber Center Publications

Crowdsourcing services allow employing human intelligence in tasks that are difficult to accomplish with computers such as image tagging and data collection. At a relatively low monetary cost and through web interfaces such as Amazon’s Mechanical Turk (AMT), humans can act as a computational operator in large systems. Recent work has been conducted to build database management systems that can harness the crowd power in database operators, such as sort, join, count, etc. The fundamental problem of indexing within crowdsourced databases has not been studied. In this paper, we study the problem of tree-based indexing within crowd-nabled databases. We investigate …

Developing White Ash With Resistance To The Emerald Ash Borer, Kaitlin Joy Palla

Open Access Theses

Hypocotyls isolated from mature embryos germinated on Murashige and Skoog (MS) medium supplemented with 22.2 µM 6-benzyladenine (BA) and 0.5 µM thidiazuron (TDZ) were transformed using Agrobacterium tumefaciens strain EHA105 harboring the pBI121-8D2 vector containing the neomycin phosphotransferase (nptII) gene and a full length, codon-optimized Bacillus thuringiensis Cry8Da protoxin gene (cry8D2). Explants were transformed in a bacterial suspension with 100 µM acetosyringone using 90 s sonication and 10 min vacuum-infiltration. Four independent lines of transformed shoots were selectively regenerated on MS medium with 22.2 µM BA, 0.5 µM TDZ, 50 mg L^-1 adenine sulfate, 10% …

Specific Salt Effects On The Formation And Thermal Transitions Among Β-Lactoglobulin And Pectin Electrostatic Complexes, Stacey Ann Hirt

Open Access Theses

Factors of ion specificity and ionic strength (I~0-100) were studied in the electrostatic complex formation and protein particle formation by thermal treatment for a β-lactoglobulin and pectin system. ζ-potential showed β-lactoglobulin and pectin began to interact near pH 5.50 and interactions were strengthened with decrease in pH. Visible light turbidimetry and light scattering at 90° revealed a trend in critical pH transitions for electrostatic complex formation based on both the ionic strength and the anion of the salt species, while effects of the monovalent cation was insignificant. Critical pH values for complex formation and separation (pHc and pHΦ) decreased with …

Habitat Restoration Of A Constructed Ohio River Embayment, Caleb Michael Rennaker

Open Access Theses

Backwater habitats of large rivers provide habitat for aquatic biota and influence important predator-prey interactions in fishes and other aquatic organisms. However, these areas often exhibit turbid conditions and lack habitat complexity. Restoration of lentic habitats through direct habitat manipulations has shown success in prior efforts, but these methods have not been tested in backwater habitats of large rivers. I attempted to create habitat in an Ohio River embayment by establishing founder colonies of aquatic macrophytes coupled with the placement of underwater gravel beds. I also evaluated the effects of total suspended solids (TSS) on overwintering structures of American Pondweed …

Pickering Stabilization Of Oil-Water Interfaces By Heated B-Lactoglobulin/Pectin Particles, Laura Kathryn Zimmerer

Open Access Theses

The use of natural biopolymer particles as Pickering stabilizers for oil-in-water emulsions was investigated. B-lactoglobulin microgels and B-lactoglobulin/pectin complexes were created by heating appropriate biopolymer solutions at pH 5.8 and 4.75, respectively. Resultant particles exhibited spherical morphology with diameters of 100-300 nm and possessed significant negative surface charge. Particles were first homogenized with 1% corn oil at 0.05%, 0.1% or 0.25% (wt/ wt) particle concentrations. All emulsions appeared stable over seven days with only a thin, creamed ring forming after several hours. Corn oil emulsions were most stable with 0.25% heated complexes, with volume-weighted mean droplet diameter remaining around 480 …

Improving Model Performance For Invasive Plant Species Distribution Using Global-Scale Presence-Only Data: Parameterization And Data Quality, Feng Yu

Open Access Theses

Invasive species have significant ecological and economic impacts. To control species' invasion, risk assessment provides the most essential information for identification and evaluation of the potential risk of the invasive species, especially in their early invasion stages. Species distribution models (SDMs) is the foundation for risk assessment, in terms of both the practical and theoretical interest in our understanding of species invasion process. SDMs contribute to the proactive invasion management and the test of ecological or biogeographical hypotheses about species distributions in relation to their environment.

However, modeling of invasive species at large spatial scale (i.e., cross-continental) is rarely discussed. …

Swat Model Simulation Of Bioenergy Crop Impacts In A Tile-Drained Watershed, Chelsie Marie Werling Boles

Open Access Theses

Tile drains are an important component of agricultural production in the Midwest, and their inclusion in modeling studies is important in watersheds where they are a principal hydrologic pathway. The new tile drainage simulation method in the Soil Water Assessment Tool (SWAT) was parameterized and tile flow results were compared with reviewed literature. Streamflow, sediment, and nutrient outputs were compared to measured values and simulated crop yields were examined with respect to average county yields. Plant growth stressors were examined to account for differences between simulated and published yields. The bioenergy crop switchgrass (Panicum virgatum) was applied over …

Slurry Seeding Cover Crops, Edwin Alexander Suarez

Open Access Theses

Cover crops improve soil quality through increased organic matter, biological activity, aggregate stability, water infiltration, and nutrient cycling. Slurry seeding, the co-application of cover crop seed and swine (Sus domesticus) manure, is a new practice that saves fuel, time and labor. High salinity and/or ammonia, among other components in swine manure, may reduce cover crop seed germination and limit the use of slurry seeding. Ten cover crop species were evaluated to compare the effects of swine manure components on cover crop seed germination. Seed germination percentages and rates were affected by swine manure but not by equivalent salinity levels established …

A Spatially Explicit Watershed Scale Optimization Of Cellulosic Biofuels Production, Jingyu Song

Open Access Theses

Producing biofuels from energy crops is one such alternative. They can result in relatively lower greenhouse gas emissions compared to traditional energy sources. Up to now, corn grain is the most researched energy crop. Cellulosic perennial crops such as switchgrass, miscanthus and fast growing trees are also promising energy crops and are expected to help with the energy supply. The 2007 Renewable Fuel Standard requires 16 billion gallons of a total of 36 billion gallons of renewable fuels to be cellulosic biofuels by 2022. Many studies are being done to evaluate costs and feasibility of different potential feedstocks and the …