Physics Commons^™

Absolute Quantification And Identification Of Rna From Rna-Lipid Nanoparticles Using High Resolution Mass Spectrometry, Jason C. Funderburk, Yasir A. Alshehry, Matthew S. Halquist Phd, Sandro R.P. Da Rocha Phd

Graduate Research Posters

Background

RNA therapeutics are a rising drug category with potential use for a range of conditions encompassing infectious diseases to therapies for cancer, diseases, and genetic disorders. RNA-lipid nanoparticles (RNA-LNPs) are the prominent delivery method for these therapeutics approved products include mRNA vaccines and polyneuropathy treatments. The emergency use authorizations and orphan drug status of current RNA-LNP drugs has allowed approval without finalization of the regulatory analytical procedures for quality monitoring. The objective of the study was to develop an LC-MS assay to simultaneously measure identity and concentration of two therapeutically relevant intact RNA constructs extracted from RNA-LNPs to enhance …

Absolute Quantification And Identification Of Rna From Rna-Lipid Nanoparticles Using High Resolution Mass Spectrometry, Jason C. Funderburk

Theses and Dissertations

RNA therapeutics are a rising drug category with potential use for a range of conditions encompassing infectious diseases to therapies for cancer, diseases, and genetic disorders. RNA-lipid nanoparticles (RNA-LNPs) are the prominent delivery method for these therapeutics approved products include mRNA vaccines and polyneuropathy treatments. The emergency use authorizations and orphan drug status of current RNA-LNP drugs has allowed approval without finalization of the regulatory analytical procedures for quality monitoring. The objective of the study was to develop an LC-MS assay to simultaneously measure identity and concentration of two therapeutically relevant intact RNA constructs extracted from RNA-LNPs to enhance quality …

Medical Linear Accelerator Water Tank Measurements Optimization For Commissioning, Tyler R. Laugh

Theses and Dissertations

Beam commissioning is a critical component of linear accelerator (LINAC) implementation, requiring accurate measurement of percent depth dose (PDD), beam profiles, and output factors across a wide range of field sizes. Conventional commissioning workflows often require multiple detectors and can be time-intensive, particularly for small-field dosimetry where measurement accuracy is highly sensitive to detector characteristics. This study evaluated the performance of a plastic scintillation detector (BP-PSD) for full water tank commissioning and its potential to improve efficiency while maintaining dosimetric accuracy.

Beam data were acquired for field sizes ranging from 1 × 1 cm² to 40 × 40 cm² using …

A Mathematical Frameworks For Singular, Nonlinear Phenomena: Applications To Nematocyst Firing And Inhomogeneous Nls With Coulomb Potential, Abdulrahman Alharbi

Theses and Dissertations

Nematocysts are specialized cellular organelles found in all cnidarians, including corals and jellyfish, as well as in some single-celled protists such as dinoflagellates. These organelles display remarkable diversity in morphology and function, playing roles in prey capture and defense. The firing of a nematocyst is one of the fastest accelerations in nature, yet the underlying physical mechanisms remain not fully understood. In this work, we address key questions: how sufficient force is generated to overcome the fluid boundary layer, whether fluid–structure interaction models can reproduce observed dynamics, and what mechanisms trigger discharge.

Our research investigates models based on osmotic pressure …

A Fault-Tolerant Exchange-Coupled Spin-Ensemble Qubit At Elevated-Temperatures, Aniruddha Chakraborty

Theses and Dissertations

This thesis introduces a novel qubit architecture: the ferromagnetic exchange-coupled spin ensemble qubit (E-qubit), designed to address the noise-induced instability. In this work, the time evolution of the ensemble’s density matrix is studied using the Liouville–von Neumann equation. To benchmark against a single-spin qubit, the gate fidelity of an E-qubit is computed in the presence of thermal noise. Coherence time is also analyzed under identical thermal condition and a linear scaling is observed with qubit size . The results show that, at 6 K , the gate fidelity error (0.7 % ) of the seven- spin ensemble is an order …

Establishing A Conventional Linac-Based Electron Flash Beam, Justin Defrancisco

Theses and Dissertations

Problems: A rediscovered radiotherapy technique, FLASH, involves increasing the dose rate to >40 Gy/s. For a given dose, FLASH is shown to decrease the normal tissue complication probability without affecting the tumor control probability. More preclinical studies are necessary to confirm and enable these desirable properties on humans. Current preclinical investigations have diverse constraints, requiring FLASH apparatuses with flexible parameters and accurate control. However, there are limited FLASH platforms available, the existing ones are costly. Our institution is not in possession of any such infrastructure. Even if available, dosimetry and beam control in FLASH are extremely lacking. There is …

Dosimetric Validation Of An Electron Monte Carlo (Emc) Algorithm For Small Cutouts And Extended Ssd’S: Assessing Emc In Small Field Dosimetry, Anil Basavaaraju

Theses and Dissertations

This thesis validates the accuracy and limitations of Electron Monte Carlo (eMC) simulations in Eclipse treatment planning systems for small-field electron dosimetry and extended source-to-surface distances (SSDs). Systematic measurements were performed using a microDiamond detector across various electron energies and field sizes. The study examines the discrepancies between measured and calculated (eMC) dose distributions, validating challenges due to lateral scatter disequilibrium and extended air gaps. Our findings provide systematic data for eMC dose calculations and demonstrate that eMC performs within clinical tolerances, with the ultimate goal of enhancing the precision and safety of radiation treatments.

Periodic Trends In The Electronic And Magnetic Structure Of Superatomic 3d Transition Metal Chalcogenide Clusters, Gabriel Bohannon

Theses and Dissertations

We have systematically investigated the electronic structure of octahedral transition metal chalcogenide clusters, TM₆S₈(CO)₆, in which the transition metal atoms are from the 3d series in order to identify if periodic properties emerge. We were motivated by the identification of closed electronic shells with electron counts of 96, 100 and 114 in similar clusters from the 4d and 5d transition metal series. Further motivation was the finding of a dual-shell closing in the Fe₆S₈(CN)₆^5- cluster. This cluster is stabilized with a large spin magnetic moment due to the …

Multiphysics Modeling Of Material Response To High-Intensity X-Ray And Laser Pulses: Heating, Ablation, And Plasma Expansion, Youssef Abouhussien

Theses and Dissertations

This dissertation presents a computational framework to investigate material response under high-intensity X-ray fluxes produced by an exo-atmospheric nuclear detonation and laser-material irradiations, with a focus on heating, ablation, and plasma expansion phenomena relevant to satellite vulnerability and high-energy-density environments. A hybrid Monte Carlo and Two-Temperature Model (MC-TTM) was developed to simulate X-ray and laser energy deposition and thermal relaxation in metals and semiconductors across a range of X-ray and laser pulse durations from femtoseconds to nanoseconds. Results demonstrate distinct thermal behavior between materials, with ablation thresholds and phase transitions captured in good agreement with experimental data.

In parallel, a …

Mathematical Model For The Role Of Multiple Pericentromeric Repeats On Heterochromatin Assembly, Puranjan Ghimire, Mo Motamedi, Richard Joh

Physics Publications

Although the length and constituting sequences for pericentromeric repeats are highly variable across eukaryotes, the presence of multiple pericentromeric repeats is one of the conserved features of the eukaryotic chromosomes. Pericentromeric heterochromatin is often misregulated in human diseases, with the expansion of pericentromeric repeats in human solid cancers. In this article, we have developed a mathematical model of the RNAi-dependent methylation of H3K9 in the pericentromeric region of fission yeast. Our model, which takes copy number as an explicit parameter, predicts that the pericentromere is silenced only if there are many copies of repeats. It becomes bistable or desilenced if …

Mathematical Analysis Of Eukaryotic Pericentromere, Puranjan Ghimire

Theses and Dissertations

The centromere is crucial for chromosomal stability and their proper segregation during cell division in eukaryotes. Surrounding the centromere are pericentromeres, made of repetitive DNA elements called pericentromeric repeats, varying from 10 in fission yeast to thousands in humans. These repeats form densely packed heterochromatin, where genes are usually silenced. The silencing mechanism across different pericentromeric repeats remains unclear.

Despite variations in sequence and length, pericentromeric repeats are conserved across eukaryotes, indicating their functional importance. This dissertation presents mathematical models to quantify gene silencing in fission yeast and humans. In fission yeast, my model predicts that silencing occurs only with …

Effect Of Annealing On Photoluminescence From Defects In Gan, Oleksandr Andrieiev

Theses and Dissertations

Annealing is a critical process in modern GaN technology, essential for achieving p-type conductivity by activating the Mg_Ga acceptor, as first demonstrated by Shuji Nakamura in the early 1990s. Despite the omnipresence of hydrogen as an impurity in GaN crystals, the precise mechanisms governing hydrogen diffusion and acceptor passivation remain only partially understood. The presented research investigates the effects of annealing-induced activation and hydrogen passivation on C and Be acceptors in GaN grown by MOCVD, HVPE, and MBE methods. We explored these effects by using several annealing techniques, gas compositions, and thermal regimes. A transient behavior between the C …

Long-Wave Modeling Of Viscous Film Dynamics Inside A Tube With Time-Dependent Radius, Robert E. Hicks

Theses and Dissertations

Lung fluid dynamics is a well studied topic and relevant in the field of research surrounding patients with Chronic Obstructive Pulmonary Disease (COPD) and cystic fibrosis. However, the literature on the mathematical description of the net pulmonary fluid transport in the case of constricting and expanding airways is scarce. In this paper we aim to address how breathing contributes to airways clearance in patients with pulmonary diseases such as COPD and CF in which cilia do not function properly. We begin with the flow of a fluid-filled tube with rigid walls of fixed radius and the effects of gravity being …

Optimizing Deep Inspiration Breath Hold Technique For Personalized Breast Cancer Radiotherapy, Srinidhi Rajagopalan

Theses and Dissertations

The purpose of this research is entrenched in advancing the practice of 3D Conformal Radiation Therapy (3D CRT) for breast cancer patients by meticulously evaluating the impact of different Deep Inspiration Breath Hold (DIBH) techniques on dosimetric parameters. This study aims to ascertain the quantitative benefits of varied breathing techniques, primarily focusing on the 'Ultimate DIBH' method's efficacy in sparing critical organs such as the heart and lungs.

The comprehensive analysis of different DIBH techniques in this research is not merely an academic exercise but is geared towards substantiating the hypothesized advantages of these techniques with empirical data. By generating …

Photoluminescence Of Beryllium-Related Defects In Gallium Nitride, Mykhailo Vorobiov, Mykhailo Vorobiov

Theses and Dissertations

This study explores the potential of beryllium (Be) as an alternative dopant to magnesium (Mg) for achieving higher hole concentrations in gallium nitride (GaN). Despite Mg prominence as an acceptor in optoelectronic and high-power devices, its deep acceptor level at 0.22 eV above the valence band limits its effectiveness. By examining Be, this research aims to pave the way to overcoming these limitations and extend the findings to aluminum nitride and aluminum gallium nitride (AlGaN) alloy. Key contributions of this work include. i)Identification of three Be-related luminescence bands in GaN through photoluminescence spectroscopy, improving the understanding needed for further material …

Using Superatomic Clusters And Charge Transfer Ligands To Control Electronic Characteristics Of Phosphorene Nanoribbons And Phosphorene Monolayer, Ryan Lambert

Theses and Dissertations

Phosphorene is a two-dimensional electron poor p-type semiconductor with high carrier mobility and great promise for applications in electronics and optoelectronics. As the main theme in this dissertation, the following work represents different investigations of various electronic properties associated with phosphorene. Most notable are the findings on charge transfer doping with metal-chalcogenide superatoms which displays novel control of the two most important properties of a semiconductor – the band gap energy and the nature of carriers. By tuning the width of the gap and p-/n-type character of conduction, we gain control over a material’s capacity to play a certain role …

Innovations In Drop Shape Analysis Using Deep Learning And Solving The Young-Laplace Equation For An Axisymmetric Pendant Drop, Andres P. Hyer

Theses and Dissertations

Axisymmetric Drop Shape Analysis (ADSA) is a technique commonly used to determine surface or interfacial tension. Applications of traditional ASDA methods to process analytical technologies are limited by computational speed and image quality. Here, we address these limitations using a novel machine learning approach to analysis. With a convolutional neural network (CNN), we were able to achieve an experimental fit precision of (+/-) 0.122 mN/m in predicting the surface tension of drop images at a rate of 1.5 ms^-1 versus 7.7 s^-1, which is more than 5,000 times faster than the traditional method. The results are validated on real images …

Mechanisms Of Emulsion Destabilization: An Investigation Of Surfactant, Stabilizer, And Detergent Based Formulations Using Diffusing Wave Spectroscopy, Jordan N. Nowaczyk

Theses and Dissertations

Conventional approaches for studying emulsions, such as microscopy and macroscopic phase tracking, present challenges when it comes to establishing detailed mechanistic descriptions of the impact of emulsifier and stabilizer additives. Additionally, while a combination of sizing methods and macroscopic phase tracking can provide insights into droplet size changes and concentration, the use of multiple measurements can be cumbersome and error-prone. It is the focus of this work, to present a new method for studying water in oil (W/O) emulsions that involves using diffusing wave spectroscopy (DWS) to examine the impact of three different surface stabilizing additives at varying concentrations. By …

Strong Homotopy Lie Algebras And Hypergraphs, Samuel J. Bevins, Marco Aldi

Undergraduate Research Posters

We study hypergraphs by attaching a nilpotent strong homotopy Lie algebra. We especially focus on hypergraph theoretic information that is encoded in the cohomology of the resulting strong homotopy Lie algebra.

Comparative Investigation Of Structure And Operating Parameters On The Performance And Reaction Dynamic Of Co Conversion On Silica Aerogel And Fumed-Silica-Supported Pd Catalysts, Rola Mohammad Al Soubaihi, Khaled M. Saoud, Joydeep Dutta

VCUarts Qatar Faculty Research

The catalyst morphology, metal-support interaction, and reaction conditions greatly influence the catalytic performance and reaction dynamics. Similarly, the dispersion of the metal within the support plays a crucial role in the thermal stability and sintering of the catalyst. Furthermore, temperature-dependent conversion hysteresis is well-known to occur during ignition and extinction of exothermic CO oxidation over supported Pd catalysts due to the variation of CO adsorption on the surface or bulk oxidation of Pd and the ability of the catalyst to regenerate the active sites. Herein, the catalytic performance and the hysteresis behavior of mesoporous silica aerogel supported Pd (Pd/a-SiO2), and …

Multi-Modality Automatic Lung Tumor Segmentation Method Using Deep Learning And Radiomics, Siqiu Wang

Theses and Dissertations

Delineation of the tumor volume is the initial and fundamental step in the radiotherapy planning process. The current clinical practice of manual delineation is time-consuming and suffers from observer variability. This work seeks to develop an effective automatic framework to produce clinically usable lung tumor segmentations. First, to facilitate the development and validation of our methodology, an expansive database of planning CTs, diagnostic PETs, and manual tumor segmentations was curated, and an image registration and preprocessing pipeline was established. Then a deep learning neural network was constructed and optimized to utilize dual-modality PET and CT images for lung tumor segmentation. …

Development Of Novel Intracavitary Intensity Modulated Brachytherapy Applicators For Optimizing The Target Coverage In Gynecologic Malignancies, Monte Carlo Simulation Dosimetry, Moeen Meftahi

Theses and Dissertations

Gynecologic brachytherapy (GYN-BT) is essential for treating cervical and endometrial cancers, the most prevalent female reproductive cancers. This technique enables high radiation doses to a target with rapid dose fall-off to protect adjacent healthy organs. This dissertation aims to address some of the limitations of intracavitary GYN-BT using an intensity modulated brachytherapy (IMBT) technique and Monte Carlo (MC) simulations.

First, a novel non-invasive shielded vaginal cylinder (VC) applicator was designed to provide optimized radiation coverage for the target volume at vaginal apex, site of most recurrences without BT, for endometrial cancer BT. Physical limitations of current applicators and their resulting …

Direction Modulated Brachytherapy For The Treatment Of Cervical Cancer, Dylan Richeson

Theses and Dissertations

Purpose: To evaluate and compare the performance of 9 experimental DMBT tandem models of varying physical dimensions in relation to 24 previously planned HDR cervical cancer treatment plans from multiple institutions that used conventional tandem and rings or ovoid applicators.

Methods and Materials: The DMBT tandem is designed to be used concurrently with IGABT and is made from an MRI-compatible tungsten-alloy rod with 6 channels grooved out of its periphery. 9 experimental DMBT tandem prototypes were provided. Each of the models was of equal lengths but varied in thickness, channel diameter size, and circle channel diameter size. Replanning …

Periodic Trends In The Infrared And Optical Absorption Spectra Of Metal Chalcogenide Clusters, Alain Ward

Theses and Dissertations

We have investigated the Optical absorption, Infrared spectra, Binding Energies, and various other cluster properties to determine the existence of periodic trend for Transition Metal Chalcogenide Clusters ligated with CO ligands. We were motivated to answer the question of whether periodic behavior can be observed in properties of octahedral metal-chalcogenide clusters. We have used the Amsterdam Density Functional code to calculate the electronic structure of Transition Metal Chalcogenide Clusters using gradient-corrected density functional theory. We determined the existence of several periodic trends in properties of octahedral Transition Metal Chalcogenide Clusters TM₆Se₈(CO)₆. To investigate these …

Nanopore Detection Of Long Time-Scale Single Metallic Cluster Conformational Changes And Surface Ligand Exchange, Bobby D. Cox

Theses and Dissertations

Single molecule nanopore spectroscopy serves as an emerging tool for studying small molecules in aqueous environments without the need for additional chemical labels. Recently it has been seeing increased use as a tool for investigating small metallic nanoparticles and clusters. These clusters consist of a handful of metallic atoms (e.g. Au18) and are regularly ‘passivated’ with organic ligands to provide functionality and protect against aggregation. There has been a widening gap in research studying the surface kinetics of these passivating ligands at the single molecule level as well as during the exchange process. In this work we investigated these surface …

Equations Of State For Warm Dense Carbon From Quantum Espresso, Derek J. Schauss

Theses and Dissertations

Warm dense plasma is the matter that exists, roughly, in the range of 10,000 to 10,000,000 Kelvin and has solid-like densities, typically between 0.1 and 10 grams per centimeter. Warm dense fluids like hydrogen, helium, and carbon are believed to make up the interiors of many planets, white dwarfs, and other stars in our universe. The existence of warm dense matter (WDM) on Earth, however, is very rare, as it can only be created with high-energy sources like a nuclear explosion. In such an event, theoretical and computational models that accurately predict the response of certain materials are thus very …

Fabrication Of Metal-Silicon Nanostructures By Reactive Laser Ablation In Liquid, Eric J. Broadhead

Theses and Dissertations

Metal-silicon nanostructures are a growing area of research due to their applications in multiple fields such as biosensing and catalysis. In addition, silicon can provide strong support effects to metal nanoparticles while being more cost effective than traditionally used supports, like titania. Traditional wet-chemical methods are capable of synthesizing metal-silicon nanostructures with a variety of composition and nanoparticle shapes, but they often require high temperatures, toxic solvents, strong reducing agents, or need capping agents added to stabilize the nanoparticles. Laser processing is an emerging technique capable of synthesizing metal-silicon composite surfaces that offers a faster, simpler, and greener synthesis route …

Nebulizer-Based Systems To Improve Pharmaceutical Aerosol Delivery To The Lungs, Benjamin M. Spence

Theses and Dissertations

Combining vibrating mesh nebulizers with additional new technologies leads to substantial improvements in pharmaceutical aerosol delivery to the lungs across therapeutic administration methods. In this dissertation, streamlined components, aerosol administration synchronization, and/or Excipient Enhanced Growth (EEG) technologies were utilized to develop and test several novel devices and aerosol delivery systems. The first focus of this work was to improve the poor delivery efficiency, e.g., 3.6% of nominal dose (Dugernier et al. 2017), of aerosolized medication administration to adult human subjects concurrent with high flow nasal cannula (HFNC) therapy, a form of continuous-flow non-invasive ventilation (NIV). The developed Low-Volume Mixer-Heater (LVMH) …

Ligand Effects On Electronic, Magnetic, And Catalytic Properties Of Clusters And Cluster Assemblies, Dinesh Bista 9288522

Theses and Dissertations

Ligands commonly protect metallic clusters against reacting with outside reactants. However, ligands can also be used to control the redox properties enabling the formation of super donors/acceptors that can donate/accept multiple electrons. This thesis focuses on how the ligands can be used to control the electronic and magnetic features of clusters and ligand stabilized cluster-based assemblies, leading to nano pn junctions with directed transport, the possibility of light-harvesting, and catalysts for cross-coupling reactions. The thesis addresses three distinct classes of clusters and their applications. The first class of cluster “metal chalcogen clusters” is the central idea of the thesis focused …

Live Cell Biomass Tracking For Basic, Translational, And Clinical Research, Graeme Murray

Theses and Dissertations

Single cell mass is tightly regulated throughout generations and the cell cycle, making it an important marker of cell health. Abnormal changes in cell size can be the first indication of dysfunction in response to environmental stimuli such as cytotoxic drugs. Described here is the further development of high-speed live cell interferometry (HSLCI) to concurrently measure the changes in single cell mass of thousands of cells over time. Critically, the high-throughput nature of HSLCI provides realistic pictures of tumor heterogeneity. This throughput enabled HSLCI to correctly predict in vivo carboplatin sensitivity of three triple negative breast cancer patient derived xenografts, …