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Structural Optimization And Stability Enhancement Of Uba(2) And Ntl9 Using The Computational Tool: Emcast, Bahar Ghazi Esfahani

Graduate Student Theses, Dissertations, & Professional Papers

This study enhances protein stability prediction by refining EmCAST (Empirical C-Alpha Stability Tool), a computational tool used to identify stabilizing mutations in protein domains. We applied EmCAST to two model proteins: the α-helical ubiquitin-associated domain 2 (UBA(2)) and the α/β N-terminal domain of ribosomal protein L9 (NTL9). Protein stability is critical for proper function, and mutations can lead to misfolding and disease. To validate EmCAST’s predictions, guanidine hydrochloride-induced denaturation was monitored using circular dichroism (CD) spectroscopy for both wild-type and mutant variants. Results guided refinements to EmCAST’s algorithm, incorporating new experimental datasets to improve accuracy. Additionally, we examined the assumption …

Bounded Compactness From G(E)Up, Jonas Mureika, Roberto Casadio, Ilim Irfan Çimdiker, Octavian Micu

Physics Faculty Works

We analyse how different Generalised Uncertainty Principles could place bounds on the compactness of self-gravitating systems. By considering existing experimental bounds on the relevant parameters, we conclude that the compactness of large astrophysical objects is bounded above by the inverse of the GUP parameter, which would naturally be of order one. Conversely, the existence of black holes imposes stronger bounds on those parameters.

Personalized Physics Learning Through Ai: Insights From Problem Generation, Chatbot Dialogues, And Intelligent Tutoring Systems, Atharva Dange

Physics Dissertations - Archive

Artificial intelligence (AI) is poised to transform science education, yet questions remain on how best to integrate these technologies into teaching and learning. This dissertation investigates the use of AI-driven tools in university physics courses through three complementary studies. In the first study, a generative language model (ChatGPT) was used to create novel physics homework problems aligned with course objectives. Analysis showed that, after expert vetting, AI-generated questions can foster higher-order problem-solving and reduce student reliance on solution memorization, though careful instructor oversight is required to ensure accuracy. The second study embedded an AI chatbot as a learning aid in …

Development And Application Of Gpu Based Monte Carlo Simulation Techniques In Radiation Medicine, Satzhan Sitmukhambetov

Physics Dissertations - Archive

Cancer remains a significant public health challenge, with treatments like radiation therapy forming a cornerstone of modern care. To address this challenge, advanced computer simulations can improve radiotherapy in two primary ways. From one hand, mechanistic simulations help elucidate the fundamental radiobiological working principles, which could contribute to the clinical advancements from a bottom-up framework. On the other hand, modality simulations could help design better clinical systems with better detection and therapeutic capabilities. This research enhances these critical simulation tools by introducing two significant developments.

First, this work introduces a metaphase DNA model into a microscopic Monte Carlo simulation framework …

Uncertainty In Solar Wind Propagation: An Analysis Of L1 To Earth Variability And The Implications For Geospace Modeling In Space Weather Operations, Espen T. Fredrick

Physics Dissertations - Archive

As humanity's technological dependence grows, so does its vulnerability to space weather. Space weather describes solar-driven phenomena in the near-Earth space environment and their terrestrial effects. Many of these effects occur due to the interaction of the solar wind and Earth's magnetosphere. The solar wind originates at the solar corona and carries solar plasma and magnetic field outward through the solar system. This magnetic field, known as the interplanetary magnetic field (IMF) during transit, can undergo magnetic reconnection with Earth's geomagnetic field when oppositely aligned field lines converge. This process transfers energy into Earth's magnetosphere, driving space weather phenomena.

Space …

Characterizing The Earth's Magnetosheath With In Situ Measurements, Hector A. Salinas

Physics Dissertations - Archive

Earth’s magnetosheath is a region of shocked plasma that mediates energy and momentum transfer from the solar wind to the magnetosphere. The dynamics and thus the plasma structures of this region are highly dependent on upstream solar wind conditions. As such, the region is often characterized as a turbulent environment, with the most intense periods of turbulence occurring often under quasi-parallel bow shock conditions. This magnetosheath turbulence displays as variable and large-scale fluctuations with in-situ measurements. Given that turbulence is a characteristic feature of the magnetosheath, this dissertation asks two questions: (1) How are plasma structures inside the sheath affected …

Study Of Structural Changes In Bone From Osteogenesis Imperfecta Using Positron Annihilation Lifetime Spectroscopy, Pablo Kohlmann Garcia, Richard Vallery

Student Summer Scholars Manuscripts

Osteogenesis Imperfecta (OI), commonly referred to as Brittle Bone Disease, is a genetic disorder that results in increased bone fragility. There are many known variations, with four of them being the most common and each with a different level of severity. However, the exact causes of OI and their molecular and structural effects on bones are largely unknown. To investigate the relationship between nanoscale bone structure and disease severity, this research investigates OI by using positron annihilation lifetime spectroscopy (PALS) to understand whether normal bone structure differs from OI-infected bones. Using this method, positrons are directed towards mice’s bones, forming …

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 …

Quantifying The Performance Of The Sparta Toolkit For Use In Planetary Regolith Characterization Missions, Abigail S. Glover

Honors Undergraduate Theses

This research investigates the use of the Soil Properties Assessment, Resistance, and Thermal Analysis (SPARTA) Cone Penetration Tester (CPT) to quantify bulk density in lunar regolith simulant LHS-1E. Twenty-five penetration tests were conducted across five density profiles to derive slope parameters (G), which represent the rate of increase in resistance with depth. Results showed a consistent, nonlinear relationship between G and bulk density, validating the use of G slope as a diagnostic parameter and supporting the primary hypothesis that SPARTA CPT measurements vary meaningfully with density. Compared to prior work by Lucas et al. (2024), G values from SPARTA were …

Entangled Photoelectron Attosecond Spectroscopy, Jonathan Sar-Shalom

Honors Undergraduate Theses

In this thesis we propose an interferometric scheme to retrieve the dynamics of an electron wave packet emitted from two distinct residual photo-ion channels in the ionization of an atom by an ultra-short UV pulse. EPAS (Entangled-Photoelectron Attosecond Spectroscopy) works by having a non-overlapping UV and few-cycle IR pulse, where the IR is tuned near the transition frequency between two electronic bound states of the photo-ion. Using a time-dependent simulation based on a two-channel atomic model, supported by a perturbative approach, we were able to compute the resulting interference in the angular distribution of the photoelectron and retrieve the energy-dependent …

Cfd Analysis Of Hydrodynamic Cavitation Through An Orifice: Influence Of Different Inlet Pressures And Number Of Orifice Holes, Lemthong Chanphavong, Vongsavanh Chanthaboune, Keophousone Phonhalath

ASEAN Journal on Science and Technology for Development

Hydrodynamic cavitation (HC) is considered an energy-efficient process with high potential for utilization in many chemical processes. This study presents a computational fluid dynamics (CFD) analysis of cavitating flow through an orifice with a constant flow area. The Reynolds-Averaged Navier-Stokes (RANS) equations, coupled with turbulence and cavitation models, are employed to capture the complex flow behaviors. The effects of inlet pressures and number of orifice-holes on cavitation behavior are investigated. Result of the numerical simulation is validated with the existing experimental data from the literature. The CFD study revealed that cavitation initiates just behind the inlet edge of the orifice …

Gasb Nanowires Grown On A Si Substrate And Nanolaminatate Tio2/Ag/Tio2 Structure, Malina Milanova, Petko Vitanov, Nikolay Petkov, Kiril Kirilov, Hristosko Dikov, Pavlina Ralova

Physical Sciences Publications

This paper presents a comparative study of GaSb nanowire (NWs) growth on a Si substrate using Ag nanoparticles as catalyst and on a Si substrate coated with a transparent conductive TiO2/Ag/TiO2 laminate structure. Silver nanoparticles with different sizes between 30 and 70 nm were formed directly on Si surface or embedded between two TiO2 layers by RF magnetron sputtering. A thermal evaporation method was used to grow GaSb NWs via vapor–liquid-solid (VLS) mechanism. Scanning electron microscopy (SEM) and atomic force microscopy (AFM) were used to study the surface morphology of the grown structures. Two kinds of nanostructures were observed on …

High-Fidelity Tin Processing Modes For Multigate Ge-Based Quantum Devices, Sinan Bugu, Sheshank Biradar, Alan Blake, Cheewee Liu, Maksym Myronov, Ray Duffy, Giorgos Fagas, Nikolay Petkov

Physical Sciences Publications

Charge or spin-qubits can be realized by using gate-defined quantum dots (QDs) in semiconductors in a similar fashion to the processes used in CMOS for conventional field-effect transistors or more recent fin FET technology. However, to realize a larger number of gate-defined qubits, multiples of gates with ultimately high resolution and fidelity are required. Electron beam lithography (EBL) offers flexible and tunable patterning of gate-defined spin-qubit devices for studying important quantum phenomena. While such devices are commonly realized by a positive resist process using metal lift-off, there are several clear limitations related to the resolution and the fidelity of patterning. …

Theoretical Proof Of And Proposed Experimental Search For The Ground Triplet State Of A Wigner-Regime Two-Electron ‘Artificial Atom’ In A Magnetic Field, Marlina Slamet, Viraht Sahni

Physics Faculty Publications

It is experimentally established that there is no ground triplet state of the natural 𝐻𝑒He atom. There is also no exact analytical solution to the Schrödinger equation corresponding to this state. For a two-dimensional two-electron ‘artificial atom’ or a semiconductor quantum dot in a magnetic field, as described by the Schrödinger–Pauli equation, we provide theoretical proof of the existence of a ground triplet state by deriving an exact analytical correlated wave function solution to the equation. The state exists in the Wigner high-electron-correlation regime. We further explain that the solution satisfies all requisite symmetry and electron coalescence constraints of a …

Explorations Of Dna-Single-Walled Carbon Nanotube Interactions To Develop Multiplexed Molecularly Specific Biosensors For Inflammation, Amelia K. Ryan

Dissertations and Theses

Inflammatory cytokines such as interleukin-6 (IL-6) and interleukin-12 (IL-12) are central regulators of immune signaling and key biomarkers of disease, yet existing assays for their detection remain slow, invasive, and lack multiplexing ability. This dissertation advances the development of single-walled carbon nanotube (SWCNT) optical nanosensors capable of real-time, multiplexed, and molecularly specific cytokine detection through innovative use of single-stranded DNA (ssDNA) interfaces.

First, an IL-6-specific DNA aptamer was employed as both a dispersing agent and recognition probe for SWCNT fluorescence sensing. Sequence modifications, including anchor domains, truncations, and thermally induced refolding, were systematically tested to optimize sensitivity and selectivity. The …

Metasurfaces And Their Applications In Photonic Devices, Shuwei Guo

Dissertations and Theses

Metasurfaces are flat artificial optical elements composed of dielectric and/or metallic nanostructures. They can manipulate light in unprecedented ways by altering amplitude, phase, and polarization at subwavelength scales. The ability of these two-dimensional elements to perform multiple optical functions within compact optical systems—while offering high functionality, small form factors, and easy integration into optoelectronic devices—has sparked significant interest across various fields and industries. These applications span imaging, sensing, nonlinear and quantum optics, optical computing, automotive technology, augmented and virtual reality, and more.

In this dissertation, we explore and design new multifunctional metasurfaces with a focus on manipulating spectral responses. First, …

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 …

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 …

Size Dependent Thermodynamic Properties Of Dppc, Zhenghao Pan

Graduate Research Theses & Dissertations

This study explores the viability of measuring the melting transition behavior in a simple unilamellar vesicle (LUV/SUV) liposome (DPPC surfactant) system using size data from Dy- namic Light Scattering (DLS). The melting transition of phospholipid membranes has been a focal point of studies in biological systems. Conventionally, the transition temperature of a membrane system is measured using either spectroscopy or Differential Scanning Calorimetry (DSC). By assuming that the bilayer volume is conserved, it is shown that DLS provides a transition signal comparable to that of DSC and aligns with known data. The data are fit- ted using Van’t Hoff’s equation. …

Characterization Of A Large-Scale Electrohydrodynamic Vortex Confinement Flow For Particle Agglomeration, Sanjay Dangi

Graduate Research Theses & Dissertations

With industrialization and the increasing use of microplastics and nanoparticle-based products, the concentration of fine particulate matter (PM2.5) in the biosphere has increased due to the disposal of manufacturing waste and expired parts. If inhaled, PM2.5 can have detrimental health effects, as these particles can travel deep into the lungs and even penetrate blood vessels. Conventional fabric filters used for indoor air quality control have drawbacks, including the need for periodic filter replacement and a high-pressure drop across the filter over time, which leads to increased power consumption. In power plants, electrostatic precipitators (ESPs) are primarily used to collect fly …

Experimental Demonstration Of A Metallic Sub-Terahertz Structure For High-Gradient, High-Efficiency Acceleration, Brendan Leung

Graduate Research Theses & Dissertations

Future accelerator facilities are increasingly constrained by the cost and footprint of conventional radiofrequency technology. Advancing both accelerating gradient and beam-to-wake energy transfer efficiency in the sub-terahertz (sub-THz) regime offers a credible path toward compact machines. Short wavelengths strengthen beam–structure coupling and enable small-aperture, high-impedance geometries; paired with tailored drive-beam current profiles, they can simultaneously raise gradient and transformer ratio.

This dissertation reports the design, fabrication, and beam testing of a sub-THz structure-wakefield accelerating (SWFA) device evaluated at the Argonne Wakefield Accelerator (AWA). The emittance-exchange (EEX) beamline was used to generate prescribed longitudinal current profiles in two modes: (i) a …

Sensitivity Studies Of Vector-Like Quark (Vlq) Pair Production In The Full-Hadronic Channel At The High-Luminosity Large Hadron Collider (Hl-Lhc) And A 10 Tev Muon Collider, Olabisi Olayinka

Graduate Research Theses & Dissertations

Vector-like quarks (VLQs) appear in various extensions of the Standard Model that consider a new strongly interacting sector to resolve the fine-tuning problem. These new particles can provide radiative corrections to the Higgs mass while also having electroweak-singlet masses. This latter property would allow them to escape existing constraints from Higgs boson measurements and electroweak precision data, which disfavor the existence of a fourth generation of quarks.

VLQ can be produced at colliders, with a variety of production modes and decay mechanisms open for study. In this work, we investigate the pair production of VLQ Tops (T), which are assumed …

Effects Of A-Site Cation Structure And B-Site Metal On Optical And Electronic Properties Of 2d Ruddlesden-Popper Phase Tin-Based Hybrid Perovskites, Henry Pruett

Theses and Dissertations--Chemistry

Organic metal halide perovskites (HPs) are attractive materials for a variety of electronic applications due to their low cost, tunable band gaps, excellent charge transport properties, and high photoluminescence efficiency. As such, HPs are being investigated for use in solar cells, photodetectors, X-ray detectors, light emitting diodes, field effect transistors, lasers, resistive random-access memory, etc. Currently the most popular metal used in HPs is lead, but the use of lead comes with the potential for heavy metal exposure. Tin-based perovskites offer a less hazardous alternative, but their optoelectronic properties lag behind those of lead and less work has been done …

X-Ray Standing-Wave Fluorescence Study Of The Interaction Of An Anti-Microbial Peptide With A Supported Phospholipid Bilayer, Gobind Basnet

Graduate Research Theses & Dissertations

To understand the mechanism by which anti-microbial peptide penetrates biological membranes,the study uses artificial supported lipid bilayers (SLBs) deposited on solid substrates. These bilayers were prepared from a lipid mixture of 1,2-dimyristoyl-sn-glycero-3- phosphocholine (DMPC)and 1,2-dimyristoyl-sn-glycero-3-phospho-(1’-rac-glycerol (DMPG) in a 10:1 molar ratio and were incubated both with and without indolicidin. Additionally, bilayers were studied after incubation with a labeled form of indolicidin, which involved attaching a 1.8 nm diameter gold nanoparticle to the peptide’s terminal arginine group.

X-ray reflectivity (XRR) was employed to identify structural differences between SLBsincubated with indolicidin and those without it. The introduction of gold labeling facilitated the …

Optimization Of Derivation Jobs And Modernization Of I/O Integration Tests For The Atlas Epxeriment, Arthur Charles Kraus

Graduate Research Theses & Dissertations

The High-Luminosity LHC (HL-LHC) is a phase of the LHC that is expected to start toward the end of the decade. With this comes an increase in data taken per year that current software and computing infrastructure, including I/O, is being prepared to handle. The ATLAS experiment's Software Performance Optimization Team has areas in development to improve the Athena software framework that is scalable in performance and ready for wide-spread HL-LHC era data taking. One area of interest is optimization of derivation production jobs by improving derived object data stored to disk by about 4-5% by eliminating the upper-limit on …

Monte Carlo Modeling Of Spin Polarized Photoemission From Gaas At Low Temperatures And Positive Electron Affinity Surfaces, John Rison Callahan

Graduate Research Theses & Dissertations

Research and development of new photocathode materials are essential to the continuing success and productivity of accelerator technology. High-quality photocathodes characterized by high quantum efficiencies, long lifetimes, low mean transverse energies, and robustness to vacuum environments and operation loads are becoming increasingly essential to the successful operation of the next generation of high brightness accelerator applications. For nuclear and high-energy physics experiments and other applications that rely on spin-polarized electron beams, photocathodes must also demonstrate high electron spin polarizations. The development of state of-the-art spin-polarized photocathodes will require both development of methods to improve the quality of already existing cathode …

Linking Empirical Data And Numerical Simulation To Characterize Dynamic Fire Behavior Associated With Interacting Firelines, Marta Sergeevna Jerebets

Graduate Student Theses, Dissertations, & Professional Papers

Understanding fuel pattern-fire process relationships is key for predicting fire behavior and effects with follow-on benefits to proactive fire management and model validation. To characterize dynamic fire behavior, this thesis leverages empirical data and numerical simulation through two complementary studies.

In the first study, longwave thermal sensors aboard unmanned aerial systems (UAS) were used to capture fine-scale fire behavior in two experimental grass burns. A novel paired design was used to quantify the effects of fuel arrangement on fire behavior with 3.66 m diameter treatments cut to a height of 0.15 m. The treatments ephemerally reduced fire rate of spread …

Doping Hybrid Photopolymerisable Glass With Bodipy Photosensitiser: An Efficient Approach To Improve Uv-Resistance, Luca Sorridente, Tatsiana Mikulchyk, Metodej Dvoracek, Mikhail A. Filatov, Izabela Naydenova, Kevin P. Murphy

Conference Papers

The development of photosensitive materials with improved performance and extended functionality is crucial for advancing holographic technologies. This study presents the modification and characterization of a recently reported photopolymerisable glass composition, focusing on achieving an optimal balance between maximizing photosensitivity of the material during recording and minimizing the impact of UV light on the performance of the recorded holographic structure. Building on these findings, the ultimate goal is to develop UV-resistant holographic optical elements for wavefront sensing in space applications. The research approach is based on introducing a photosensitiser with weaker UV absorption than the typically used in this material …

Investigation Of A Busemann Intake At Negative Angle Of Attack, Mark E. Noftz, Andrew N. Bustard, Nicholas J. Bisek, Thomas J. Juliano, Joseph S. Jewell

Publications

A high-speed, shape-transitioned, inward-turning intake was tested in Purdue’s Boeing/AFOSR Mach 6 Quiet Tunnel. The inlet model, called the Indiana Inlet (INlet), had a total contraction ratio of 4.68:1 and a design point of Mach 6 at 0° angle of attack. The model was outfitted with a suite of high-frequency pressure transducers, and the external flowfield was imaged with high-speed schlieren photography. The INlet was tested under low freestream disturbance levels for a variety of freestream unit Reynolds numbers and at-4° angle of attack. An unsteady shockwave near the leading edge of the inlet forebody, indicative of boundary layer separation, …