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Measurements And Modeling Of Phonon-Mediated Quasiparticle Poisoning In Superconducting Qubit Arrays, Eric Yelton

Dissertations - ALL

The realization of a quantum computer that can correct for random errors on its constituent quantum bits, or qubits, is one of the primary goals in the quantum information science community. One of the leading protocols to correct these errors on a quantum processor relies on nearest-neighbor coupling of an array of physical qubits that act collectively as a single logical qubit. Superconducting circuits are a leading implementation of a physical qubit and have been used in some of the first demonstrations of this error correction scheme. A key assumption of this protocol is that errors on the physical qubits …

Frustration And Functionality : Geometry And Topology In Mechanical Metamaterials, Sourav Roy

Dissertations - ALL

This dissertation is concerned with a study of the effect of geometry in complex few body mechanical systems. The problems that we set out to solve lie on the interface of soft condensed matter physics, geometry and topology. In the first problem, I developed an effective elasticity theory of thin mechanical metamaterial sheets. This work explored the elastic response of thin metamaterial sheets draped on a uniformly and weakly curved substrate. The model spells out an elegant screening law that shows that a metamaterial alleviates elastic stresses by actuating the soft modes accessible to it. In the second problem, we …

Deformations Of Thin Membranes In Incompatible Geometries And Interactions In Mechanical Hysteron Systems, Zachariah Schrecengost

Dissertations - ALL

Soft reconfigurable systems exhibit behaviors which are highly dependent on their geometries. Thin membranes can deform in a myriad of ways as they navigate geometries different from their own in an energy efficient manner. Behaviors in mechanical hysteron systems are influenced by the geometry of the interactions and global driving. This dissertation focuses on two different types of systems which are governed in part by their geometries: thin membranes in geometrically incompatible configurations and interacting mechanical hysterons. A thin membrane forced into a conflicting geometry with an incompatible metric will deform in highly non-trivial ways. These deformations are an attempt …

Multi-Modal Mri For The Pre-Clinical Evaluation Of Hiv-Linked Changes In The Central Nervous System, Gabriel Gauthier

Theses & Dissertations

Though the inception of anti-retroviral therapy (ART) has fundamentally changed the life expectancy of human immunodeficiency virus (HIV) patients, accessibility and outcomes vary enormously along demographic lines. Even for people living with HIV (PLWH) with perfect access and adherence to anti-retroviral drugs (ARVs), modern treatment plans are fundamentally unable to secure complete viral remission for patients. The cause of this perpetual infection is the persistence of viral reservoirs in the central nervous system (CNS), hidden beyond the reach of modern ARVs, leaving patients to deal with lifelong medication side-effects and risks of developing HIV-associated neurodegenerative disorders (HAND). Despite improving outcomes …

Intrinsic And Extrinsic Drivers Of Bioaerosol Decay: Investigating Pathogen Stability Of Bacteriophage Ms2, Sin Nombre Virus, And Sars-Cov-2 In Simulated Environments, Elizabeth A. Klug

Theses & Dissertations

The threat posed by a virus as a bioaerosol depends largely on its stability under various environmental conditions (relative humidity (RH), sunlight, ozone, etc.). This stability is typically studied through aerosol decay—how the virus' viability changes over time when exposed environmental conditions. The Goldberg rotating drum, a widely used tool for studying bioaerosols, has been the basis of such research (Goldberg et al., 1958). However, it has significant limitations, including an inability to measure initial pathogen infectivity loss and the use of small sample volumes. Additionally, it does not answer the question of what intrinsic factors (lipids, proteins, nucleic acids) …

Creasing In Thick Hemispherical Shells As A Model For Foveal Formation, Indigo Skye Peppard

Undergraduate Honors Theses

This research experimentally investigates creasing behavior on the inner surface of hemispherical shells with the ultimate goal of modelling the formation of the foveal pit, a sharp surface deformation present in the retina of the eye of many animals. Creasing is a phenomenon observed in hyperelastic materials and is characterized by sharply localized surface deformations that appear at ~35% compressive strain. The foveal pits of anoles (small iguanian lizards) are funnel-shaped and resemble creases when cut along the central axis. Furthermore, during foveal pit formation the anole eye contracts around 35% along this same axis. Given these similarities we believe …

Direct Computations Of Spatially Resolved Viscoelastic Moduli Of Biomolecular Condensates, Liwen Gu

McKelvey School of Engineering Graduate Student Theses & Dissertations

Biomolecular condensates are viscoelastic materials formed by liquid-liquid phase separations (LLPS) of biopolymers. In this study, we develop a modified graph Laplacian-based collective model to characterize viscoelastic heterogeneity within condensates based on results of lattice-based Metropolis Monte Carlo (MMC) simulations. By integrating random graph models and simulations of A1-LCD, a type of intrinsically disordered protein, we examine how network topology influences storage modulus, loss modulus, crossover frequency, and relaxation time spectra. Our results reveal a strong correlation between topological features and mechanical response, with the condensate interior exhibiting higher stiffness and faster relaxation than the interface. The relaxation spectra provide …

Simplicity From Complexity: Sensing High-Dimensional Fluctuations Via Regulatory Network, Optimality In Allocating Cellular Resources, And Recovering Functional Groups Via Data-Driven Methods, Fang Yu

Arts & Sciences Graduate Student Theses and Dissertations

Biological systems must navigate dynamic and complex environments while operating under constraints such as limited molecular resources, biochemical noise, and structural trade-offs. This dissertation investigates three distinct cases in which biological systems allocate resources and process information efficiently, revealing emergent simplicity from underlying complexity. The first study develops a generalized end-product inhibition model with cross-talk and an excess of regulators, providing a proof-of-principle that simple biochemical circuits could, in principle, dynamically adjust their responsiveness to high-dimensional environmental variation. This result highlights how such circuits may allow adaptive filtering of both dominant and subdominant fluctuation modes. The second study, conducted in …

Topological And Optical Properties Of Two-Dimensional Materials, Haonan Wang

Arts & Sciences Graduate Student Theses and Dissertations

Recent advances in condensed matter physics have revealed a wide range of novel quantum phenomena in two-dimensional (2D) materials. The discovery of unique topological, magnetic, and optical properties in solids has greatly expanded our understanding of quantum phases in electronic structures. As more material systems are proposed theoretically and realized experimentally, our research focuses on uncovering and explaining these phenomena through effective models and first-principles calculations. First, we explore topological mosaic patterns in moiré superlattices—structures composed of periodic, spatially distinct domains, each with different topological properties. These domains give rise to periodic edge states along domain walls. We explore the …

X-Ray Polarization Of Accreting Stellar-Mass Black Holes Through Accretion States, Nicole Rodriguez Cavero

Arts & Sciences Graduate Student Theses and Dissertations

In recent years, X-ray polarization has opened up a new window into our understanding of astrophysical sources. Among them are accreting stellar-mass black holes, which play a key role in testing the behavior of matter in extreme gravitational environments. These sources can be observed in different states of the accretion cycle, predominantly in the soft and hard states. Every state is dominated by a combination of thermal disk, coronal, or reflected emission—each type containing different information about the environment around the black hole that can be understood through polarization. Polarimeters such as the Imaging X-ray Polarimetry Explorer and XL-Calibur allow …

Computational Design Of Potent Sirna For Braf Oncogene Silencing For Enhancing Cancer Therapy, Muhammad Hermawan Widyananda, Ricadonna Raissa

Karbala International Journal of Modern Science

The discovery of oncogenic BRAF mutations has prompted the development of inhibitors, yet resistance remains widespread. A more effective strategy involves targeting BRAF mRNA with siRNA to overcome resistance to BRAF inhibitors. This study aims to design potent siRNA for BRAF oncogene silencing using a computational approach. The full coding sequence of BRAF was retrieved from the NCBI database and potential siRNAs were predicted using the Ui-Tei, Reynolds, and Amarzguioui rules. Identified siRNAs were further analyzed using various prediction systems and parameters, including their interaction with the hAgo2 protein. The results identified that seven siRNAs (siRNA 23, siRNA 24, siRNA …

Nonthermalizing Dynamics Of Interacting Rydberg Atoms, Nicolaus A. Chlanda

Physics and Astronomy Honors Papers

An isolated system of ultracold Rydberg atoms can come to equilibrium by exchanging energy through dipole-dipole interactions. In our experiment, a static electric field of a few V/cm shifts the energy levels of the atoms, so that the energy levels are nearly degenerate at zero field and fan out with increasing field to form a manifold. We excite atoms to energy levels near the center of the manifold, where the spacing is nearly harmonic. We allow them to interact for a few microseconds, by which time the population of each energy level has reached a steady state. The population is …

Experimental Evaluation Of Resource Allocation To Organelles In Eukaryotic Cells, Ronan Hanley

Senior Honors Papers / Undergraduate Theses

Among the hallmarks of the eukaryotic cell is its organization into spatially defined sub-compartments known as organelles. Organelles provide optimized environments for otherwise incompatible biochemical reactions within the cell. It has been shown that there is significant variation in the properties of organelles in a cell, and that cells have access to a limited pool of resources that they can allocate to organelles. This begs the question: by what principles do cells dictate how resources are allocated? To begin to explore this question, we look at resource allocation in S. cerevisiaefrom two perspectives. First, we use a combination of …

Characterization Of A Magnetically Contained Hot Filament Plasma Source With A Wide-Sweeping Langmuir Probe, Jonas Rowan

Doctoral Dissertations and Master's Theses

Ionospheric plasma research in the Space and Atmospheric Instrumentation Laboratory’s Space Plasma Chamber has been hindered by the lack of a suitable plasma diagnostic instrument and understanding of its hot-filament plasma source. This thesis describes efforts made to remedy both problems. A wide-range Sweeping Langmuir Probe was developed with a ±35 V sweeping range to fully analyze ion and electron saturation regions in the entire IV curve. A method was derived to estimate the chamber source’s filament temperatures. The new Langmuir probe was integrated into a refurbished automated system designed in Python to measure plasma parameters for various chamber conditions, …

Treatment Wastewater Of Oil Refinery By Fe2o3 Nps Produce By The Novel Alishewanella Jeotgali Strain Haq8., Hawraa Qays Al-Assdy, Wijdan Hussein Al-Tamimi, Asia Fadhile Almansoory

Karbala International Journal of Modern Science

Metal oxide nanoparticles like iron oxide (Fe₂O₃) exhibit strong reactivity and photolytic features in wastewater treatment and serve as an effective adsorbent for water purification due to its substantial surface area and affinity for different functionalized groups. Iron oxide nanoparticles) IONPs) are currently applied to treat oil-contaminated water. Fe₂O₃NPs were produced using an extracellular approach utilizing the Alishewanella jeotgali strain HAQ8. IONPs were characterized using UV-vis, FT-IR, XRD, AFM, SEM-EDX, and Zeta potential. λ max for the synthesized nanoparticles observed at (358) nm. The bands at 485 cm⁻¹ in the FT-IR spectrum confirmed the formation of …

First-Principles Studies Of Excited-State Properties In Large-Scale Systems, Du Li

Arts & Sciences Graduate Student Theses and Dissertations

Density Functional Theory (DFT) is widely used as a powerful tool for studying the electronic structure of materials. However, due to the local or semilocal nature of exchange-correlation functionals, such as the local density approximation and generalized gradient approximation functional, DFT often underestimates the electronic band gap. Many-body perturbation theory (MBPT) within the GW approximation provides more accurate quasiparticle energies calculation by incorporating many-electron screening effects. Additionally, solving the Bethe-Salpeter Equation (BSE) allows for a detailed analysis of excitonic effects in optical spectra. Despite their accuracy, GW-BSE calculations are computationally expensive, particularly for large-scale systems such as defects and substrate-supported …

First-Principles Studies Of Electrical Polarization Effects In Ferroelectrics, Antiferroelectrics And Defects, Louis Alaerts

Dartmouth College Ph.D Dissertations

Over the last few decades, density functional theory (DFT) has emerged as a formidable tool in the field of computational material science. Not only has it become a complementary method approach to experiments by rationalizing the many complex properties of materials but its formidable predictive power can also be used to identify the most promising candidates for specific applications. Point defects in semiconductors have become an important platform for the development of quantum networks due to their ability to act as spin-photon interfaces. Spectral diffusion, the broadening of the optical emission line, can significantly impact the performance of these defect-based …

The Distribution Of Ultrahigh-Energy Cosmic Rays Along The Supergalactic Plane Measured At The Pierre Auger Observatory, A. Abdul Halim, P. Abreu, M. Aglietta, I. Allekotte, K. Almeida Cheminant, A. Almela, B. Fick, K. Nguyen, D. Nitz, A. Puyleart, Et. Al

Michigan Tech Publications

Ultrahigh-energy cosmic rays are known to be mainly of extragalactic origin, and their propagation is limited by energy losses, so their arrival directions are expected to correlate with the large-scale structure of the local Universe. In this work, we investigate the possible presence of intermediate-scale excesses in the flux of the most energetic cosmic rays from the direction of the supergalactic plane region using events with energies above 20 EeV recorded with the surface detector array of the Pierre Auger Observatory up to 2022 December 31, with a total exposure of 135,000 km2 sr yr. The strongest indication for an …

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

Publications and Research

It is experimentally established that there is no ground triplet state of the natural He 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 …

Unpaired Virtual Histological Staining Of Tissue From Autofluorescence Using Regularized Cycle-Consistent Adversarial Networks, Zhesi Wen

Theses and Dissertations

We present a regularized CycleGAN with a Dense Residual U-Net to virtually stain autofluorescence images of tissue into H&E-like images. Our method outperforms standard architectures, reduces artifacts, and achieves superior FID scores, enabling efficient, label-free, and accurate digital pathology for unpaired datasets using multi-channel fluorescence inputs.

Entanglement-Enhanced Metrology With Superconducting Circuits, Xingrui Song

Arts & Sciences Graduate Student Theses and Dissertations

Circuit quantum electrodynamics provides a unique platform for investigating fundamental physics and practical quantum applications. In this thesis, I introduce the superconducting circuit platform from a foundational perspective. Drawing inspiration from quantum electrodynamics and utilizing the analog of closed time-like curves, this work achieves quantum enhancement over classical strategies. Specifically, I investigate agnostic phase estimation protocol and the associated approaches that leverage quantum entanglement to optimally estimate an unknown rotation angle without requiring prior knowledge of the rotation axis. This work not only demonstrates a proof of concept for a type of entanglement-assisted metrology but also highlights intriguing quantum effects. …

Extended Tev Halos May Commonly Exist Around Middle-Aged Pulsars, A. Albert, R. Alfaro, C. Alvarez, J. C. Arteaga-Velázquez, D. Avila Rojas, H. A. Ayala Solares, R. Babu, E. Belmont-Moreno, A. Bernal, K. S. Caballero-Mora, T. Capistrán, A. Carramiñana, S. Casanova, U. Cotti, J. Cotzomi, S. Coutiño De León, E. De La Fuente, C. De León, D. Depaoli, P. Desiati, N. Di Lalla, R. Diaz Hernandez, B. L. Dingus, M. A. Duvernois, J. C. Diaz-Velez, K. Engel, C. Espinoza, K. L. Fan, K. Fang, N. Fraija, J. A. Garcia-Gonzalez, F. Garfias, H. Goksu, M. M. Gonzalez, J. A. Goodman, S. Groetsch, J. P. Harding, S. Hernandez-Cadena, I. Herzog, D. Huang, F. Hueyotl-Zahuantitla, A. Iriarte, S. Kaufmann, D. Kieda, J. Lee, H. Leon Vargas, J. T. Linnemann, A. L. Longinotti, G. Luis-Raya, K. Malone, O. Martinez, J. Martines-Castro, J. A. Matthews, P. Miranda-Romagnoli, J. A. Morales-Soto, E. Moreno, M. Mostafa, L. Nellen, M. U. Nisa, N. Omodei, Y. Perez Araujo, E. G. Perez-Perez, C. D. Rho, D. Rosa-Gonzalez, E. Ruiz-Velasco, H. Salazar, D. Salazar-Gallegos, A. Sandoval, M. Schneider, J. Serna-Franco, Y. Son, R. W. Springer, O. Tibolla, K. Tollefson, I. Torres, R. Tores-Escobedo, R. Turner, F. Urena-Mena, E. Varela, L. Villasenor, Xiaojie Wang, E. Wilcox, H. Wu, H. Zhou

Physics Faculty Research & Creative Works

Extended gamma-ray emission around isolated pulsars at TeV energies, also known as TeV halos, have been found around a handful of middle-aged pulsars. The halos are significantly more extended than their pulsar wind nebulae but much smaller than the particle diffusion length in the interstellar medium. The origin of TeV halos is unknown. Interpretations invoke either local effects related to the environment of a pulsar or generic particle transport behaviors. The latter scenario predicts that TeV halos would be a universal phenomenon for all pulsars. We searched for extended gamma-ray emission around 36 isolated middle-aged pulsars identified by radio and …

Intercellular Stress Generation During 1d Collective Migration Of Cancer Cells, Logan Waddle

Physics Undergraduate Honors Theses

Physical forces drive many cellular processes such as migration and proliferation. A metastatic tumor will have invasive strands/chains that extend from the main tumor. These chains of cells collectively migrate away from the main tumor to establish new colonies elsewhere in the body. However, how physical forces drive this collective invasion and the required energy for this process is not well understood. Invasion of a metastatic tumor to surrounding tissues leads to a majority of cancer-associated death and is often a collective effort among cells, it is therefore important to fully understand the process behind collective cancer invasion.

The goal …

Tunable Optical Beam Focusing Using Static Water Droplets On An Electrospun Polymer Fiber, Marco Laurence M. Budlayan, Dina C. Palangyos, Jonathan N. Patricio, Susan D. Arco, Raphael A. Guerrero

Physics Faculty Publications

This work explores the use of static water microdroplets on a microfiber to vary the width of an optical beam. Varying the water droplet volume changes the beam width without replacing any optical components. A surface derived from glass deposited with polyvinyl chloride (PVC) microfibers via electrospinning was used to sustain the droplet shape on the surface. Scanning electron microscopy revealed the presence of randomly intertwined microfibers with diameters of less than 3 µm which afforded the surface a hydrophobic property. A decrease in the optical transmittance of the films and an increase in the water contact angle were also …

The Mechanics Of Angular Momentum Generation In Discus Throwing, Andreas Maheras

Track and Field Faculty Publications

Angular momentum development in the back of the ring, during the first double and first single support, is of paramount importance in discus throwing because this is where almost all the angular momentum the thrower can generate will be generated. From a purely mechanical point of view, to achieve that, the thrower should keep her arms spread apart, and also actively throw both the right leg and the left arm and shoulders CCW. Those actions will collectively contribute in slowing down the lower body, as the thrower actively chooses to pass as much angular momentum to the upper body at …

Abel Inversion Comparison Of Geant4 Simulation And Ozone Production Using Cavity Ringdown Spectroscopy In Nitrogen/Oxygen Mixtures In The Presence Of Alpha Radiation, Sidney John Gautrau

Dissertations

The effects of radioactive materials on atmospheric gases have been a topic of interest for years. Radioactive materials ionize the surrounding air, and subsequent reactions lead to molecules such as ozone and nitrogen oxides. The presence of these species above background levels can be used as a marker for radioactive materials which has desirable defense applications like remote detection of radioactive materials. The molecules created in the presence of radioactive materials have been quantified in literature using G-values, which is the number of molecules of a product produced per 100 eV of deposited energy. In this work, Cavity Ringdown Spectroscopy …

The Search For Slow Particles And Magnetic Monopoles With Nova, John Clark

Poster Presentations

Singular magnetic poles, north or south, have been theorized to exist for hundreds of years. In the modern day, the elusive singular magnetic pole still remains undiscovered. The appearance of this particle would help confirm many Grand Unified Theories, GUTs, and revolutionize our understanding of some of the fundamental forces of the universe. Fermilab's NOvA collaboration is working on ways to screen and detect magnetic monopoles and other slow-moving particles coming from outer space alongside their main mission to study neutrinos. The aim of this work is to determine and improve the Far Detector’s efficiency at identifying slow moving particles. …

Low-Field Magnetoresistance In Nanocomposites Of La₀.₇Sr₀.₃Mno₃ And Metal Oxides, Nicholas K. Thiel-Hudson

University Scholar Projects

Pure La_0.7Sr_0.3MnO₃ (LSMO) exhibits colossal magnetoresistance (CMR) with large applied magnetic field over a narrow temperature range (intrinsic behavior), limiting its application to narrow temperature ranges. In contrast, the extrinsic CMR effect originates from inhomogeneities at larger length scales, such as grain boundaries and phase separation, where the structural features act as tunneling barriers, leading to a low-field magnetoresistance (LFMR) response, thereby expanding the application of LSMO into the low-field regime over a broader temperature range. In this work, the magnetotransport behavior of pure LSMO thin film is compared to the composite layered heterostructures of …

Bismuth-207 For Purity Monitoring System For Lartpc: Dune And Proto-Dune, Rohit Raut

2025 Spring Honors Capstone Projects - Archive

The Deep Underground Neutrino Experiment (DUNE), the U.S. flagship neutrino experiment, relies on high purity liquid argon (LAr) for optimal detector performance. Ensuring and monitoring LAr purity is crucial, as electronegative impurities can degrade signal quality in detectors. As part of Proto-DUNE, a prototype detector at CERN for DUNE, this study explores the use of Bismuth-207 (Bi-207) as a novel tool for real-time LAr purity monitoring and calibration. Bi-207 emits monochromatic internal conversion electrons, allowing precise impurity assessment without interfering with standard detector operations. By simulating the behavior of radioactive Bi-207 and analyzing data from the Proto-DUNE Vertical Drift detector, …

Thin-Film Optical Filters For Selective Transmission And Black-Body Reflection In Pyroelectric Energy Systems., Cedric Cruz Silva

Electronic Theses and Dissertations

Essential to pyroelectric energy systems is the ability for a pyroelectric material to achieve high temperatures rapidly. In pursuit of augmenting this process, several thin-film optical filters were designed for transmitting laser excitation in the near-infrared region, while simultaneously reflecting black-body radiation for pyroelectric materials. Designs include a classical Fabry-Perot structure with gold and tantalum pentoxide, an induced transmittance filter with silica, hafnia, and gold, and an indium-tin-oxide filter with silica, alumina, and ITO. Performance varies depending on the design. The Fabry-Perot filter experimentally showed a maximum transmittance of 42% at 1.04 μm and an infrared reflectance of 98%. The …