Physical Sciences and Mathematics Commons^™

Mechanisms Of Nutrient Limitation And Nutrient Acquisition In Managed And Unmanaged Forest Ecosystems, Matthew A. Vadeboncoeur

Doctoral Dissertations

Understanding the interactions between global change, human and natural disturbances, and other factors on biogeochemical processes in forests is necessary to ensure the sustainability of forest management. Here I report the results of several investigations into nutrient acquisition processes in the forests of New Hampshire. I begin with a meta-analysis of fertilization studies showing that phosphorus (P) and calcium (Ca) as well as nitrogen (N) may limit primary production in deciduous forests of the region. Because these limiting nutrients are all removed from the ecosystem when trees are harvested, I compared nutrient budgets under a range of harvesting scenarios with …

New Applications Of Boron Dihalides And Organotrifluoroborates In Organic Synthesis, Kelly Elizabeth Hall

Doctoral Dissertations

This dissertation summarizes research focused on the use of boron dihalides and organotrifluoroborates in organic synthesis. The boron dihalide mediated aryl propargyl ether cleavage reactions to generate the corresponding aryl alcohols were investigated to explain the mechanistic pathway of using boron trihalides and boron dihalides in propargyl ether cleavage reactions. The results of this study strongly support that the mechanistic pathway for these reactions follows the pathway shown in this dissertation. In addition, the use of polymer-supported organotrifluoroborates for radiolabeling reactions was also investigated. The results of these studies support the use of polymer supported organotrifluoroborates in radiolabeling reactions as …

Geographic And Temporal Epidemiology Of Campylobacteriosis, Jennifer Weisent

Doctoral Dissertations

Campylobacteriosis is a leading cause of gastroenteritis in the United States. The focus of this research was to (i) analyze and predict spatial and temporal patterns and associations for campylobacteriosis risk and (ii) compare the utility of advanced modeling methods. Laboratory-confirmed Campylobacter case data, obtained from the Foodborne Diseases Active Surveillance Network were used in all investigations.

We compared the accuracy of forecasting techniques for campylobacteriosis risk in Minnesota, Oregon and Georgia and found that time series regression, decomposition, and Box-Jenkins Autoregressive Integrated Moving Averages reliably predict monthly risk of infection for campylobacteriosis. Decomposition provided the fastest, most accurate, user-friendly …

1,2,4-Triazine-Accelerated Azide-Alkyne Cycloaddition And Synthesis Of Metalloenzyme Inhibitors, Belinda Shea Lady

Doctoral Dissertations

The work of this dissertation describes the design and synthesis of 1,2,4-triazine ligands and other N-containing heterocycles and their use in the copper-catalyzed azide-alkyne cycloaddition (CuAAC). A variety of ligands were synthesized to probe the steric and electronic demands required for use in the CuAAC reaction. Substituents on the 1,2,4-triazine were systematically altered and the core 1,2,4-triazine modified to determine the most active ligand. Additional experiments explored the variability in the reaction conditions, such as solvent choice, use of reducing agents, and optimal stoichiometry. Under optimum conditions 5,6-diphenyl-3-(2-pyridyl)-1,2,4-triazine and copper (II) tetrafluoroborate in the presence of triethylamine was found to …

Application Of Computational Molecular Biophysics To Problems In Bacterial Chemotaxis, Davi Ortega

Doctoral Dissertations

The combination of physics, biology, chemistry, and computer science constitutes the promising field of computational molecular biophysics. This field studies the molecular properties of DNA, protein lipids and biomolecules using computational methods. For this dissertation, I approached four problems involving the chemotaxis pathway, the set of proteins that function as the navigation system of bacteria and lower eukaryotes.

In the first chapter, I used a special-purpose machine for molecular dynamics simulations, Anton, to simulate the signaling domain of the chemoreceptor in different signaling states for a total of 6 microseconds. Among other findings, this study provides enough evidence to propose …

Novel Bimetallic Plasmonic Nanomaterials, Ritesh Sachan

Doctoral Dissertations

Plasmonic nanomaterials have attracted a lot of attention recently due to their application in various fields such as chemical and biological sensing, catalysis, energy harvesting and optical devices. However, there is a need to address several outstanding issues with these materials, including cost-effective synthesis, tunability in plasmonic characteristics, and long term stability. In this thesis, we have focused on bimetallic nanoparticles (NPs) of Ag and Co due to their immiscibility as well as their individual properties. First, a pulsed laser induced dewetting route was used to synthesize Ag-Co bimetallic plasmonic NPs. An synthesis parameter space was derived to show the …

Effects Of Traffic Noise On The Social Behavior Of Tufted Titmice (Baeolophus Bicolor)., Jessica Lynn Owens

Doctoral Dissertations

The presence of traffic noise and its potential effects on wildlife is a burgeoning topic of research within the fields of conservation behavior, animal behavior, ecology and wildlife management. Accumulated data from these efforts, mostly correlative and rarely-experimental, suggest that traffic noise induces a myriad of species-specific changes to population dynamics, breeding behavior and acoustic structure of avian song. However, the degree of generalizability of these findings is confounded by the limited variety of behaviors studied within a relatively small sample of species. This original research provides experimental evidence of the effects of simulated and real traffic noise on previously …

Femtosecond Laser Patterned Templates And Imprinted Polymer Structures, Deepak Rajput

Doctoral Dissertations

Femtosecond laser machining is a direct-write lithography technique by which user-defined patterns are efficiently and rapidly generated at the surface or within the bulk of transparent materials. When femtosecond laser machining is performed with tightly focused amplified pulses in single-pulse mode, transparent substrates like fused silica can be surface patterned with high aspect ratio (>10:1) and deep (>10 μm) nanoholes. The main objective behind this dissertation is to develop single-pulse amplified femtosecond laser machining into a novel technique for the production of fused silica templates with user-defined patterns made of high aspect ratio nanoholes. The size of the …

Fluorescence Spectroscopy With Correlated Atomic Force Microscopy Of Gold Nanoparticles And Meso-Scale Ribbons, Meredith Marie Therrien

Doctoral Dissertations

Studies on the optical properties of gold nanoparticles are of great interest due to the size and shape control and easy adaptability through functionalization to most any application, everything from nanomedicine to nanosensing. Gold nanoparticle optical properties change with size, morphology, and environment. Gold nanospheres were explored to determine the effect of environmental change, from many particles in solution to a single particle immobilized and in air, on fluorescence peak position. A statistical distribution of single gold nanorod fluorescence spectra demonstrate the spectral changes associated with slight variations in size. In solution, gold nanorods self-absorb and only exhibit bulk gold …

Toward Message Passing Failure Management, Wesley B. Bland

Doctoral Dissertations

As machine sizes have increased and application runtimes have lengthened, research into fault tolerance has evolved alongside. Moving from result checking, to rollback recovery, and to algorithm based fault tolerance, the type of recovery being performed has changed, but the programming model in which it executes has remained virtually static since the publication of the original Message Passing Interface (MPI) Standard in 1992. Since that time, applications have used a message passing paradigm to communicate between processes, but they could not perform process recovery within an MPI implementation due to limitations of the MPI Standard. This dissertation describes a new …

Nature And Degree Of Aqueous Alteration Of Outer Main Belt Asteroids And Cm And Ci Carbonaceous Chondrites, Driss Takir

Doctoral Dissertations

CM (Mighei-like) and CI (Ivuna-like) carbonaceous chondrites are primitive meteorites that consist of some of the most pristine matter known in the Solar System. They are thought to be genetically related to outer Main Belt asteroids (C-, D-, G-, F-, T-, and B-types) that span the 2.5 < a < 4.0 AU region. They are also thought to be the source that might have delivered water and organics to terrestrial planets during their accretion. The goal of this dissertation is to develop reliable 3-µm [micron] spectral indicators that can place constraints on the degree and location of aqueous alteration in the outer Main Belt region, and on the nature of phyllosilicate mineralogy on the surface of these asteroids. To that end, we have undertaken combined petrologic, geochemical, and spectroscopic analyses of CM and CI chondrites and outer Main Belt asteroids. Using the SpeX spectrograph/imager at NASA Infrared Telescope Facility (IRTF), we measured near-infrared (NIR: 0.7-4.0 µm) spectra of 40 outer Main Belt asteroids that allowed the identification of four 3-µm spectral groups, each of which presumably reflects a distinct surface mineralogy. We also measured spectra of 9 CM chondrites (in addition to the CI chondrite Ivuna) in the laboratory under asteroid-like conditions. These measurements revealed three spectral groups of CM chondrites, all of which are distinct from the spectrum of Ivuna on the basis of the 3-μm band center and shape of spectra, showing that distinct parent body aqueous alteration environments experienced by different carbonaceous chondrites can be distinguished using reflectance spectroscopy. All CM and CI chondrites in the present study are found to be similar to the group of asteroids that are located in the 2.5 < a < 3.3 AU region and exhibit a sharp 3-µm feature, attributed to OH-stretching in hydrated minerals. However, no meteorite match was found for asteroids with a rounded 3-µm feature that are located farther from the Sun (3.0 < a < 4.0 AU), or for groups with distinctive spectra like 1 Ceres or 52 Europa.

Tuning Sol-Gel Phase Diagrams Of Doubly Thermosensitive Hydrophilic Diblock Copolymers In Water, Naixiong Jin

Doctoral Dissertations

This dissertation presents the synthesis of stimuli-responsive hydrophilic diblock copolymers and the study of their behavior in water under various conditions. The polymers were made by “living”/controlled radical polymerization. Chapter 1 presents a background of this dissertation. Chapters 2-4 describe a family of doubly thermosensitive diblock copolymers with a small amount of carboxylic acid groups incorporated into either one or both blocks. The lower critical solution temperature (LCST) of the weak acid-containing block increases with increasing pH due to the ionization of carboxylic acid. Chapter 5 presents the preparation of pH-sensitive diblock copolymer micelle-embedded agarose hydrogels.

Chapter 2 describes the …

Quantitative Techniques For Pet/Ct: A Clinical Assessment Of The Impact Of Psf And Tof, Joshua Donald Schaefferkoetter

Doctoral Dissertations

Tomographic reconstruction has been a challenge for many imaging applications, and it is particularly problematic for count-limited modalities such as Positron Emission Tomography (PET). Recent advances in PET, including the incorporation of time-of-flight (TOF) information and modeling the variation of the point response across the imaging field (PSF), have resulted in significant improvements in image quality. While the effects of these techniques have been characterized with simulations and mathematical modeling, there has been relatively little work investigating the potential impact of such methods in the clinical setting. The objective of this work is to quantify these techniques in the context …

Resonance Hyper-Raman Characterization Of Nonlinear Chromophores, Christopher Bennett Milojevich

Doctoral Dissertations

Hyper-Raman spectroscopy is a nonlinear optical probe which can be used to explore the multi-photon properties of molecules. Three studies are presented in this dissertation. The first study is a combined experimental investigation of the surfaceenhanced hyper-Raman scattering with a theoretical study of the electronic states of the Rhodamine 6G molecule. This study demonstrates that hyper-Raman spectroscopy can be used to probe electronic states which are one-photon inaccessible. The second study involves a comparison of experimentally measured resonance hyper-Raman spectra to first-principles calculations of the resonance hyper-Raman scattering. This study shows the utility of coupling hyper-Raman spectroscopy and hyper-Raman calculations …

Hydraulic Properties Of Variably-Saturated Porous Media Determined Using Quantitative Neutron Radiography, Misun Kang

Doctoral Dissertations

The theoretical understanding of fluids in unsaturated porous media has improved substantially over the last several decades. Water retention curves remain a central pillar in the theoretical framework for modeling of water flow in unsaturated porous media. Use of the average water retention function in models to simulate water flow in porous media can result in inaccurate predictions due to the variations in water content and matric potential with elevation within the medium. As a result, point water retention curve data are needed for testing existing numerical and analytical models and for improving our ability to predict unsaturated water flow. …

Automating Large-Scale Simulation Calibration To Real-World Sensor Data, Richard Everett Edwards

Doctoral Dissertations

Many key decisions and design policies are made using sophisticated computer simulations. However, these sophisticated computer simulations have several major problems. The two main issues are 1) gaps between the simulation model and the actual structure, and 2) limitations of the modeling engine's capabilities. This dissertation's goal is to address these simulation deficiencies by presenting a general automated process for tuning simulation inputs such that simulation output matches real world measured data. The automated process involves the following key components -- 1) Identify a model that accurately estimates the real world simulation calibration target from measured sensor data; 2) Identify …

Haldane Pseudopotentials And Landau Level Mixing In The Quantum Hall Effect, Rachel Elizabeth Wooten

Doctoral Dissertations

The discovery of the quantum Hall effect in 1980 opened to physics one of the simplest systems for studying many-body correlations. Numerical techniques and trial wavefunctions have proven useful for describing the novel collective behavior of the electrons, but have not fully explained all features of the fractional quantum Hall effect. For example, it is predicted that Landau level mixing should have a moderate effect on the system for all but the very strongest magnetic fields, but this effect has not been extensively studied. Among the tools most useful to modeling and describing the quantum Hall system is the Haldane …

Alkane Adsorption On Mgo(100): Volumetric Isotherm, Inelastic Neutron Scattering, And Computational Studies, Andrew Spencer Hicks

Doctoral Dissertations

Volumetric adsorption isotherms and computational molecular dynamics (MD) simulations were performed for nonane and decane adfilms on MgO(100) nanocubes. From the isotherms, variety of thermodynamic quantities are calculated. These values, along with visual inspection of the isotherms, indicate a layer by layer trend from 2D to 3D behavior. This is attributed to the increasing importance of vertical adsorbate-adsorbate interactions as distance from the surface increases. Additionally, a 2D phase transition is observed for the first adsorbed layer as indicated by the evolution of the widths of the isotherm first derivative peaks. These experimental results are complemented by the MD calculations, …

Quorum Sensing And Metabolism In Marine Environments, Amanda May

Doctoral Dissertations

Quorum sensing (QS) is a phenomenon that allows bacteria to communicate with each other. Small molecules known as autoinducers are synthesized and released by bacteria, and once enough members of the community are around to ensure survival, i.e. quorum, a phenotype, e.g. bioluminescence, is expressed. There are two types of QS molecules, intra- and inter-species.

S-4,5-Dihydroxy-2,3-pentanedione (DPD) is a byproduct of the activated methyl cycle which recycles methionine. This has led to the discussion as to whether DPD is a metabolic byproduct or is the interspecies signal as proposed previously. The detection and quantitation of DPD however, has not …

Three Dimensional Equation Of State For Core-Collapse Supernova Matter, Helena Sofia De Castro Felga Ramos Pais

Doctoral Dissertations

The core-collapse supernova (CCSN) phenomenon, one of the most explosive events in the Universe, presents a challenge to theoretical astrophysics. Stellar matter in supernovae, experiencing most extreme pressure and temperature, undergoes transformations that cannot be simulated in terrestrial laboratories. Construction of astrophysical models is the only way towards comprehension of CCSN. The key microscopic input into CCSN models is the Equation of State (EoS), connecting the pressure of stellar matter to the energy density and temperature, dependent upon its composition. Of the large variety of forms of CCSN matter, we focus on the transitional region between homogeneous and inhomogeneous phases. …

Synthesis And Characterization Of Stimuli Responsive Polymer Brushes, Chaitra Vasant Deodhar

Doctoral Dissertations

Polyelectrolytes (PE) are the least understood polymeric systems due to their complex behavior that arises because of the intimate connection between charge and conformation. To address this challenge, my research focuses on understanding the responsive behavior of weak polyelectrolyte brushes to different stimuli such as pH, type of ion and ionic strength. In this work, weak polyelectrolyte brushes made of poly(methacrylic acid) (PMAA) and random copolymer brushes incorporating hydroxyethyl methacrylate (HEMA) as co-monomer were studied. The polymer brushes were synthesized by both “grafting to” and “grafting from” approaches and were characterized mainly by ellipsometry and neutron reflectometry.

Several methods for …

Growth And Electric Field Control Of Phase Separated Manganites, Hangwen Guo

Doctoral Dissertations

Perovskite Manganites have received numerous attentions due to exotic behaviors such as colossal magnetoreistance (CMR) and electronic phase separation (EPS). The purpose of my research is to answer fundamental questions about the growth properties of manganites and electric field control of the EPS properties.

Experimental study was conducted on controlling the growth mode of La_0.7Sr_0.3MnO₃[Lanthanum Strontium Manganese Oxide] thin films using pulsed laser deposition. Different thin film morphology, crystallinity and stoichiometry have been observed depending on growth parameters. To understand the microscopic origin, the thermodynamic processes were theoretically analyzed and a growth diagram was …

Analysis Of Ecological Change In Marine Ecosystems Via Novel Imaging And Spectroscopic Techniques On Microalgae Cells, Morgan Breonne Mcconico-Lewis

Doctoral Dissertations

With the increase in anthropogenic pollutants such as: atmospheric CO₂ [carbon dioxide], fossil fuel combustion and fertilizer run off, the fate of the environment is of great importance. Through industrialization, the greenhouse gas, CO₂, is a major contributor to global warming; while nitrogen based fertilizer, causes the production of toxins due to harmful algal blooms. Both chemical impacts dissolve into marine ecosystems effecting the chemical composition of organisms such as microalgae. Microalgae remediate these changes by sequestering carbon and nitrogen; thus there is a need to understand how these impacts affect the ecosystem by detecting the change …

Martian Dune Fields: Aeolian Activity, Morphology, Sediment Pathways, And Provenance, Matthew Chojnacki

Doctoral Dissertations

Wind has likely been the dominant geologic agent for most of Mars’ history. The wide-spread nature of sand dunes there shows that near-surface winds have commonly interacted with plentiful mobile sediments. Early studies of these dunes suggested minimal activity, dominantly unidirectional simple dune morphologies, and little variations in basaltic sand compositions. This dissertation examines martian sand dunes and aeolian systems, in terms of their activity, morphologies, thermophysical properties, sand compositions, geologic contexts, and source-lithologies using new higher-resolution orbital data. Although previous evidence for contemporary dune activity has been limited, results presented in Chapter II show substantial activity in Endeavour Crater, …

Quantitative Integration Of Multiple Near-Surface Geophysical Techniques For Improved Subsurface Imaging And Reducing Uncertainty In Discrete Anomaly Detection, Megan Estelle Carr

Doctoral Dissertations

Currently there is no systematic quantitative methodology in place for the integration of two or more coincident data sets collected using near-surface geophysical techniques. As the need for this type of methodology increases—particularly in the fields of archaeological prospecting, UXO detection, landmine detection, environmental site characterization/remediation monitoring, and forensics—a detailed and refined approach is necessary. The objective of this dissertation is to investigate quantitative techniques for integrating multi-tool near-surface geophysical data to improve subsurface imaging and reduce uncertainty in discrete anomaly detection. This objective is fulfilled by: (1) correlating multi-tool geophysical data with existing well-characterized “targets”; (2) developing methods for …

Modeling The Genetic Consequences Of Mutualism On Communities, Carrie E. Eaton

Doctoral Dissertations

Three models of coevolutionary dynamics between mutualistically interacting species are developed. The first is a three loci, haploid model describing a general plant-pollinator system, such as Greya moth and its host plant. In this case, the system will always collapse to a single plant type and pollinator type. In a community with an mutant plant type, it is possible for a host-switch to occur, governed by the initial relative abundance plant type and the pollinator choosiness. In addition, genetic diversity can be maintained if the pollinator has no differential host preference, only adaptation to a host. Next, this model is …

Big Homotopy Theory, Keith Gordon Penrod

Doctoral Dissertations

Cannon and Conner developed the theory of "big fundamental groups." This is meant to expand on the notion of fundamental group and is a powerful tool that can be used for distinguishing spaces that are not distinguishable using the fundamental group. Turner proved several classical results, such as covering theory and Seifert-VanKampen for big fundamental groups. The purpose of this paper is to expand on the the theory, to refine the definitions, and to give more examples. Also, in this paper, we define big higher homotopy groups analogous to the way classical higher homotopy groups are defined.

Multiplicative Sets Of Atoms, Ashley Nicole Rand

Doctoral Dissertations

It is possible for an element to have both an atom factorization and a factorization that will always contain a reducible element. This leads us to consider the multiplicatively closed set generated by the atoms and units of an integral domain. We start by showing that for a nice subset S of the atoms of R, there exists an integral domain containing R with set of atoms S. A multiplicatively closed set is saturated if the factors of each element in the set are also elements in the set. Considering polynomial and power series subrings, we find necessary and sufficient …

Multiscale Modeling Of Enzyme-Catalyzed Methanol Production By Particulate Methane Monooxygenase, Katherine K. Bearden

Doctoral Dissertations

In this work, the conversion of methane to methanol by the particulate Methane Monooxygenase (pMMO) enzyme is investigated using a multi-scale modeling approach. This enzyme participates in carbon cycling and aids in the removal of harmful atmospheric methane, converting it to methanol. The interaction between pMMO and a neighboring enzyme that is present in the same organism is studied, and the unknown pMMO active site is elucidated and tested for methane oxidation towards the production of methanol.

Fundamental knowledge of pMMO's mechanism is not fully understood. Understanding how this enzyme works in nature will provide information towards designing efficient synthetic …

Location Based Services In Wireless Ad Hoc Networks, Neelanjana Dutta

Doctoral Dissertations

"In this dissertation, we investigate location based services in wireless ad hoc networks from four different aspects - i) location privacy in wireless sensor networks (privacy), ii) end-to-end secure communication in randomly deployed wireless sensor networks (security), iii) quality versus latency trade-off in content retrieval under ad hoc node mobility (performance) and iv) location clustering based Sybil attack detection in vehicular ad hoc networks (trust). The first contribution of this dissertation is in addressing location privacy in wireless sensor networks. We propose a non-cooperative sensor localization algorithm showing how an external entity can stealthily invade into the location privacy of …