Physics Commons^™

Evaluation Of Presage® As A 3d Dose Verification Tool In Proton Beams, Mitchell Carroll

Dissertations & Theses (Open Access)

Radiotherapy techniques have advanced and radiation dose plans have become much more complex over the last decade. This is especially true in proton therapy, which involves extremely steep dose gradients as a result of positioning the Bragg peak to cover the volumes to be treated. The Bragg peak can be shifted significantly in the patient as a result of nonuniformities in the tissue composition in its path, which can result in treatment complications. Some traditional dose verification tools used in proton beam commissioning and treatment plan verification are film, TLD, and ionization chambers. Such 0D and 2D dosimeters are incapable …

Nonlinear Sliding Mode Observer Applied To Microalgae Growth, Rebecca J. Griffith

Doctoral Dissertations and Master's Theses

Modeling biological processes, such as algae growth, is an area of ongoing research. The ability to understand the multitude of parameters that influence this system provides a platform for better understanding the dynamics of microalgae growth. Empirical modeling efforts look to understand sources of driving nutrients that influence harmful algal blooms (HABs). These harmful algal blooms are dense aggregates that have an increasingly negative impact on local economics, marine and freshwater systems, and public health. They result from a high influx of nitrogen and nutrients that drive the algae biomass to exponentially grow. This growth blocks out the sun, potentially …

Plasmonic Enhancement Of Photoluminescence And Photobrightening In Cdse Quantum Dots, David Alan French

Graduate Theses and Dissertations

Quantum dots are gaining recognition not just in the physics and chemistry community, but in the public eye as well. Quantum dot technologies are now being used in sensors, detectors, and even television displays. By exciting quantum dots with light or electricity, they can be made to emit light, and by altering the quantum dot characteristics the wavelength can be finely tuned. The light emitted can be also be made more intense by an increase in the excitation energy. The excitation light can be increased via plasmonic enhancement, leading to increased luminescence. Aside from the relatively steady-state response, quantum dots …

Innate Immunity, The Hepatic Extracellular Matrix, And Liver Injury: Mathematical Modeling Of Metastatic Potential And Tumor Development In Alcoholic Liver Disease., Shanice V. Hudson

Electronic Theses and Dissertations

The overarching goals of the current work are to fill key gaps in the current understanding of alcohol consumption and the risk of metastasis to the liver. Considering the evidence this research group has compiled confirming that the hepatic matrisome responds dynamically to injury, an altered extracellular matrix (ECM) profile appears to be a key feature of pre-fibrotic inflammatory injury in the liver. This group has demonstrated that the hepatic ECM responds dynamically to alcohol exposure, in particular, sensitizing the liver to LPS-induced inflammatory damage. Although the study of alcohol in its role as a contributing factor to oncogenesis and …

Equilibrium Partitioning Of Binary Polymer Mixtures Into Biological Nanopores, Mehmet Alphan Aksoyoglu

Doctoral Dissertations

The cell interior, enclosed by membrane barriers, is a condensed solution of inorganic ions, polymers, carbohydrates, polynucleotides, and a large number of other organic molecules. Within cells, transport of metabolites and biopolymers, such as polynucleotides and proteins, occurs partly through specific transmembrane pores (mesoscopic ion channels) spanning cellular compartments. Examples of such functions are translocation of matrix RNA molecules from cell nucleus through nuclear pore complexes, ejection of viral genome from bacterial virus capsids into host bacterial cells, and translocation of protein factors across toxin channels in biological membranes. All these processes, that occur in the cellular milieu, are mediated …

Supercharged Models Of Intrinsically Disordered Proteins And Their Utility In Sensing, Peter J. Schnatz

Dissertations, Theses, and Capstone Projects

In this thesis I show that greatly increasing the magnitude of a protein’s net charge using surface supercharging transforms that protein into a ligand-gated or counterion-gated conformational molecular switch. To demonstrate this I first modified the designed helical bundle hemoprotein H4 using simple molecular modeling, creating a highly charged protein which both unfolds reversibly at low ionic strength and undergoes the ligand-induced folding transition commonly observed in signal transduction by intrinsically disordered proteins in biology. Due to the high surface charge density, ligand binding to this protein is allosterically activated by low concentrations of divalent cations and the polyamine spermine. …

Structure And Thermodynamics Of Polyglutamine Peptides And Amyloid Fibrils Via Metadynamics And Molecular Dynamics Simulations, Riley Workman

Electronic Theses and Dissertations

Aggregation of polyglutamine (polyQ)-rich polypeptides in neurons is a marker for nine neurodegenerative diseases. The molecular process responsible for the formation of polyQ fibrils is not well understood and represents a growing area of study. To enable development of treatments that could interfere with aggregation of polyQ peptides, it is crucial to understand the molecular mechanisms by which polyQ peptides aggregate into fibrils. Many experimental techniques have been employed to probe polyQ aggregation, however, observations from these studies have not lead to a unified understanding of the properties of these systems, instead yielding competing, fragmented theories of polyQ aggregation. This …

Investigation Of Stereotactic Body Radiation Therapy Delivery Accuracy On An Elekta Linear Accelerator, Addie Barron

LSU Master's Theses

Purpose: This work investigated the delivery accuracy of high-dose lung and spine stereotactic treatments delivered with the Elekta Infinity and Versa HD platforms. The accuracy of these platforms will be used for consideration in implementing a spine stereotactic radiosurgery (SSRS) program at Mary Bird Perkins Cancer Center.

Methods: A geometric phantom was used to perform Winston-Lutz type tests that assessed the relevant degrees of freedom (gantry, collimator, and couch) of the delivery system. A lung stereotactic body radiation therapy (SBRT) and spine SRS treatment plan were generated for use in end-to-end testing. Delivery accuracy was tested using a novel diode …

The Computational Study Of Fly Swarms & Complexity, Austin Bebee

Senior Theses

A system is considered complex if it is composed of individual parts that abide by their own set of rules, while the system, as a whole, will produce non-deterministic properties. This prevents the behavior of such systems from being accurately predicted. The motivation for studying complexity spurs from the fact that it is a fundamental aspect of innumerable systems. Among complex systems, fly swarms are relatively simple, but even so they are still not well understood. In this research, several computational models were developed to assist with the understanding of fly swarms. These models were primarily analyzed by using the …

Photonic Tools For Advanced Sensing And Imaging At The Nanoscale., Jafar Hamed Ghithan

Electronic Theses and Dissertations

This dissertation reports a novel bio-sensing strategy based on single-mode, electro-active, integrated optical waveguide (SM-EA-IOW) platforms. It also reports the development of a super-resolved far-field optical imaging tool to enable optical, electronic, and spectroelectrochemical investigations at the nanoscale. SM-EA-IOW platforms with its outstanding sensitivity for spectroelectrochemical interrogation was combined with a sandwich bioassay for the development of a novel immunosensing based strategy for label-free detection of infectious pathogens. The strategy begins with the functionalization of the electroactive waveguide surface with a capturing antibody aimed at a specific target analyte. Once the target analyte is bound to the photonic interface, it …

Combining Microdialysis And Electrophysiology In Cerebral Cortex To Delineate Functional Implications Of Acetylcholine Gradients, Tazima Nur

Graduate Theses and Dissertations

The neuronal network in cerebral cortex is a dynamic system that can undergo changes in collective neural activity as the organism changes its behavior. For example, during sleep and quiet restful awake state, many neurons tend to fire together in synchrony. In contrast, during alert awake states, firing patterns of neurons tend to be more asynchronous, firing more independently. These changes in population-level synchrony are defined as changes in cortical state. Response to sensory input is state-dependent, i.e., change in cortical state can impact the sensory information processing in cortex and introduce trial-to-trial variability in response to the same repeated …

The Incorporation Of Graphene To Lithium Cobalt Oxide As A Cathode To Improve The Performance Of Lithium Ion Batteries, Kenan Wang

Graduate Theses and Dissertations

One of the objectives of this thesis work was to investigate the cathode performance of lithium cobalt oxide (LiCoO2) incorporated with graphene powder in lithium ion batteries (LIBs). Graphene powder was incorporated into cathode materials to enhance the performance of LIBs. The other objective was to impede the construction of a solid electrolyte interphase (SEI) sheet using graphene sheet coating on its cathode.

The results of this work show that adding graphene powder improved the performance of LiCoO¬2 as a cathode material. With the incorporation of different weight percentages of graphene powder, the LiBs showed distinct changes in their charging …

Sex Differences In Lower Limb Biomechanics During A Single-Leg Cut With Body Borne Load, Auralea Carylon Fain

Boise State University Theses and Dissertations

Introduction: Musculoskeletal injuries are ever-increasing in military personnel, particularly females. These musculoskeletal injuries are attributed to adaptations in lower limb biomechanics while performing routine military tasks, such as a single-leg cut, with the addition of body borne load. However, it is unknown if females and males exhibit similar lower limb biomechanics with the addition of body borne load during these tasks. This study sought to compare the lower limb biomechanical adaptations exhibited by females and males performing a single-leg cut with body borne load. Methods: Eleven females and 17 males had lower limb biomechanics quantified during a single-leg cut with …

Pregnancy Induced Alterations Of Reproductive Tract Collagen And Elastin In A Murine Model, Basant K. Dhital

Dissertations, Theses, and Capstone Projects

This thesis reports on structural and dynamical modifications of reproductive tract elastin and collagen as a function of parity. Pelvic floor dysfunction, including pelvic organ prolapse (POP) is a major concern affecting female health worldwide, leading to surgeries costing billions of dollars annually. Collagen, elastic fibers, and proteoglycans are major extracellular matrix (ECM) components found in connective tissues. Vaginal child birth, advancing age, and disruption or dysfunction of connective tissue are major risk factors of POP. In the female reproductive tract, the assembly of elastic fibers is crucial for the pelvic floor support. Any disturbance in the synthesis, assembly, and …

Achieving A Stable Magneto-Optical Trap, Chasen S. Himeda

Honors Thesis

The utilization of the Magneto-Optical Trap (MOT) as a method for cooling and confining atoms is a recent development in the field of modern optical physics. Producing an effective MOT relies on a constant magnetic field throughout the trapping region and successful laser cooling, a technique used to achieve optical molasses by slowing particles using a three-dimensional intersection of laser beams. A successful MOT occurs when the trapped atoms slow down to approximately 30 cm/s at a temperature in the microkelvin range and is observable when a small bright orb of atoms is located in the center of the chamber. …

Compact Sensing Platforms Based On Localized Surface Plasmon Resonance, Zhutian Ding

Electronic Thesis and Dissertation Repository

The development of plasmonic sensors mainly focuses on the improvement of their sensitivities that are approaching the theoretical limit. This work aims to propose, fabricate and characterize compact sensing platforms that are highly adaptable and easy to be miniaturized, without compromising their sensitivities. A plasmonic sensing system that allows the excitation of localized surface plasmon resonance (LSPR) by individual waveguide modes is presented conceptually and experimentally. Another compact sensing platform is proposed based on the ensemble hypothesis developed in this thesis.

The Association Of Size Variation In The Dental Arch To Third Molar Agenesis For A Modern Population, Devin N. Williams

USF Tampa Graduate Theses and Dissertations

The frequency with which individuals do not develop their third molars, or wisdom teeth, is increasing worldwide. This current topic of human evolution is relevant to the research of anthropologists, geneticists, dentists, and other researchers involved in the study of human dentition. Many explanations have been offered to account for the prevalence of molar agenesis including, evolutionary, environmental, and genetic theories. The purpose of this research project is to determine the frequency of third molar agenesis and investigate the relationship between third molar agenesis and maxillomandibular jaw dimensions in a sample of orthodontic patients. This research tests the hypotheses that: …

Evolving Specialization In An Agent-Based Model Without Task-Switching Costs, Shane Meyer

Dissertations

This work examines the possibility of evolving the phenotypic specialization associated with division of labor in an agent-based model without task-switching costs. The model examines two groups competing for vital resources, where members of one group are capable of sharing resources with other agents in their group. Agents attempt to collect resources which allow them to reproduce, with more resources leading to a greater number of offspring by asexual reproduction. Four variants of the model are examined, with combinations of one or two resources and the presence of a foraging risk. The presence of the foraging risk can lead to …

Nadph-Cytochrome P450 Oxidoreductase: Extraction Of The Full-Length Protein And Methyl-Trosy Nmr Of The Soluble Mutants, Sara Ali Jamal Arafeh

Master's Theses (2009 -)

NADPH-cytochrome p450 oxidoreductase (CYPOR) is a membrane-bound protein in living cells. CYPOR delivers electrons to cytochrome p450 proteins (CYPs) to catalyze metabolism of drugs and synthesis of steroids. Extraction and solubilization of CYPOR from the membrane is typically done with the TritonX-100 detergent. The amount of the solubilized protein by this detergent, however, remains relatively low to structurally analyze CYPOR with NMR spectroscopy. The goal of the first project in this thesis was to optimize the amount of the extracted CYPOR from the E. coli membrane using various detergents and additives. To this aim, non-ionic detergents with variable hydrophobicity (TritonX-100, …

Information Content, Charge Transport Properties, And Computational Capacities Of Proteins, Joseph Murphy Brisendine Jr.

Dissertations, Theses, and Capstone Projects

This thesis is the beginning of an attempt to build a coherent theory of the properties of proteins based in information theory and the duality of information theory and nonequilibrium thermodynamics. Throughout, we will adopt the viewpoint that information can act as a thermodynamic potential, which is necessary to understand how biological processes are both enabled and constrained by the laws of thermodynamics. Understanding information as a form of thermodynamic potential also clarifies the description of proteins and other biological macromolecules as “molecular machines”: meso-scale structures with emergent causal powers which perform work on their environments by irreversibly dissipating energy …

Learning From Disorder And Noise In Physical Biology, Taylor Emil Firman

Electronic Theses and Dissertations

Stochasticity, disorder, and noise play crucial roles in the functioning of many biological systems over many different length scales. On the molecular scale, most proteins are envisioned as pristinely folded structures, but intrinsically disordered proteins (IDPs) have no such folded state and still serve distinct purposes within the cell. At the scale of gene regulation, realistic in vivo conditions produce stochastic fluctuations in gene expression that can lead to advantageous bet-hedging strategies, but can be difficult to characterize using a deterministic framework. Even at the organismal scale, germband extension (GBE) in Drosophila melanogaster embryos systematically elongates the epithelial tissue using …

Evaluation And Adaptation Of Live-Cell Interferometry For Applications In Basic, Translational, And Clinical Research, Kevin A. Leslie

Theses and Dissertations

Cell mass is an important indicator of cell health and status. A diverse set of techniques have been developed to precisely measure the masses of single cells, with varying degrees of technical complexity and throughput. Here, the development of a non-invasive, label-free optical technique, termed Live-Cell Interferometry (LCI), is described. Several applications are presented, including an evaluation of LCI’s utility for assessing drug response heterogeneity in patient-derived melanoma lines and the measurement of CD3+ T cell kinetics during hematopoietic stem cell transplantation. The characterization of mast cells during degranulation, the measurement of viral reactivation kinetics in Kaposi’s Sarcoma, and drug …

Hyperthermia As A Cancer Treatment- From Theory To Practice, Graham Fullerton

CMC Senior Theses

Using iron super-paramagnetic and ferromagnetic nanoparticles composed of Fe₃O₄ molecules, scientists analyze the effectiveness and practicality of this new treatment theory, hyperthermia. The problems of magnetic particle density, isothermal barriers/cellular cooling thresholds, and nanoparticle specific targeting are addressed in this review.

Iron magnetic nanoparticles were chosen due to their relatively low biological reactivates and lack of subsequent cellular toxicity. However, there are significant heating problems associated with these magnetic nanoparticles due to their relative size and short thermal time constants or thermal half-lives. Effectively, these aforementioned issues create a phenomenon where cancerous cells, surrounded by unheated healthy …

Can A Comprehensive Transition Plan To Barefoot Running Be The Solution To The Injury Epidemic In American Endurance Runners?, Michael A. Scarlett

CMC Senior Theses

Fossils belonging to the genus Homo, dating as far back as two million years ago, exhibit uniquely efficient features suggesting that early humans had evolved to become exceptional endurance runners. Although they did not have the cushion or stability-control features provided in our modern day running shoes, our early human ancestors experienced far less of the running-related injuries we experience today. The injury rate has been estimated as high as 90% annually for Americans training for a marathon and as high as 79% annually for all American endurance runners. There is an injury epidemic in conventionally shod populations that …

Compositional And Topographical Characterization Of Carbonaceous Chondritic Meteorites Moss And Murray Using Micro-Raman Spectroscopy And Sem/Eds, Aaron Stokke

All Graduate Theses, Dissertations, and Other Capstone Projects

Carbonaceous chondritic meteorites are considered some of the most primitive surviving materials from the formation of our solar system. Thus, these objects can provide information about planet formation through their physical properties (such as structure, composition, and morphology) which can be characterized using microscopy and spectroscopy techniques. In this work, the analytical methods of Raman spectroscopy, scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDS), and optical microscopy are applied to determine the mineralogical, topographical, and elemental compositions of two carbonaceous chondritic fragments: Moss and Murray. Both samples were comprised of chondrules and matrix while Moss contained chondrule rims and Murray …

First-Principles Investigation Of The Interfacial Properties Of Boron Nitride, Kevin Waters

Dissertations, Master's Theses and Master's Reports

The interactions of nanomaterial surfaces with biological compounds, e.g. proteins, DNA, etc., unites the biological regime and nanomaterial world. Hybrid systems of boron-nitride nanotubes (BNNTs) and biological compounds are well-suited for a broad range of applications. First-principles methods are used to characterize the interface of these hybrid systems. Previous work has shown that the sensing capabilities of pristine BNNT are limited by long-ranged interactions. In this study the surfaces of pristine and functionalized BNNTs are investigated. The surfaces of the functionalized BNNTs give new properties to the tubes, which may enhance their sensing capabilities, while retaining their stability and chemical …

Ecology And Virulence Capabilities Of Vibrios Isolated From The Pristine North Inlet Estuary, Savannah Leigh Klein

Theses and Dissertations

Vibrio bacteria are Gram negative, motile organisms that occur naturally in most coastal and estuarine ecosystems. Some vibrios are important human pathogens, including Vibrio parahaemolyticus and Vibrio vulnificus. The CDC estimates that vibrios cause 80,000 cases of disease each year in the United States alone. Most cases are caused by V. parahaemolyticus, which infects humans after the consumption of contaminated raw or undercooked seafood, primarily oysters. V. parahaemolyticus causes mild gastroenteritis that is self-limiting unless the patient is immunocompromised. V. vulnificus has a much lower incidence of disease (100 cases in the USA yr-1); however, this organism causes much more …

Regulation Of Cytoplasmic Dynein By Lis1 And Adenomatous Polyposis Coli, Timothy Joshua Hines

Theses and Dissertations

Cytoplasmic dynein 1 (dynein) is a microtubule motor that plays a role in mitosis, cell migration, and minus-end directed microtubule-based transport. The lissencephaly protein, Lis1, and its binding partner, Ndel1, are critical regulators of cytoplasmic dynein (Niethammer et al., 2000). In humans, haploinsufficiency of Lis1 leads to lissencephaly, a devastating developmental neurological disorder characterized by severe brain malformation, leading to cognitive and motor defects, and progressively worsening seizures (Dobyns et al., 1993). While Lis1 is known to play a role in regulating dynein-dependent functions such as neuronal migration and mitotic spindle orientation during development, the protein is still highly expressed …