Physics Commons^™

Computational Insights Into Nucleosome Dynamics In Epigenetics Using Molecular Dynamics Simulations, Rutika Patel

Dissertations, Theses, and Capstone Projects

Nucleosome core particles (NCP) are the building blocks that form a highly organized and compact chromatin structure. Nucleosomes package DNA in the nucleus of eukaryotic cells. The NCP consists of about 147 base pairs of DNA wrapped around the histone octamer, with 1.65 superhelical turns in a left-handed manner. The histone octamer is composed of two copies of H3, H4, H2A, and H2B. Together with histone H1 and linker DNA, they further assemble into a higher-order chromatin structure. The nucleosome complex is stabilized by electrostatic interactions between positively charged histone residues and the negatively charged DNA backbone. To effectively access …

1d Crust-Magnetosphere Coupling Model For Magnetars, Kennedy M. Jeter

Dissertations, Theses, and Capstone Projects

Magnetars are the most extremely magnetized objects in the universe. Their strong magnetic fields generate high-energy magnetic flares with instantaneous luminosity that can outshine their host galaxy. Previous works have explored how Hall drift in the crust affects the dynamics of magnetic field lines in the magnetosphere. This work investigates how a change in the magnetosphere, such as a flare or an outburst, can excite Hall evolution in the crust. We investigate how the twisting and untwisting of magnetic field lines in a magnetar’s magnetosphere launches Hall waves through its crust using a one-dimensional numerical model. We use the Dedalus …

Non-Perturbative Aspects Of Gauge Theories Through A Complex Parametrization, Antonina Maj

Dissertations, Theses, and Capstone Projects

This dissertation explores a complex matrix parametrization of four-dimensional non-Abelian gauge theories as a means of gaining analytical insights into (3+1)-dimensional QCD. The low-energy scale of non-Abelian gauge theories remains an elusive area of research even after decades of work. A key challenge lies in identifying physical, gauge-invariant degrees of freedom that are relevant to non-perturbative phenomena. In this dissertation we develop a complex parametrization of gauge fields on which gauge transformations act homogeneously, thereby enabling a manifestly gauge-invariant analytical formulation of the theory.

Chapter one constructs the complex gauge-invariant parametrization for gauge theories living on both complex projective space …

Nonlinear Diffusion, Hydrodynamic Cascades And Jamming In Kinetically Constrained Systems: Insights From Lattice Gas Models, Abhishek Raj

Dissertations, Theses, and Capstone Projects

This dissertation investigates non-linear diffusion processes and emergent dynamical phenomena in kinetically constrained lattice gases. Two central models are considered: a one-dimensional lattice gas exhibiting a diffusion cascade triggered by hydrodynamic nonlinearities and a triangular ladder exclusion model that undergoes a jamming transition. The former demonstrates stretched exponential decay consistent with non-perturbative long-time tails, while the latter illustrates how classical-quantum mappings yield insight into glassy dynamics and mobility constraints. Through a combination of numerical simulations, analytical perturbation theory, and mean-field approximations, the work uncovers mechanisms underlying anomalous transport, jamming transitions, and the breakdown of perturbative hydrodynamics.

Multi-Nuclear Magnetic Resonance (Nmr) Characterization Of Novel Materials, Tawhid Pranto

Dissertations, Theses, and Capstone Projects

The increasing reliance on batteries in commercial products, coupled with the environmental challenges posed by climate change and the limitations of fossil fuel consumption, has created strong financial and environmental incentives to explore innovative energy storage solutions. Renewable energy sources are being actively developed, but their intermittent nature necessitates efficient storage technologies, driving significant research into improving the performance of batteries, fuel cells, and capacitors.

This thesis focuses on the application of advanced Nuclear Magnetic Resonance (NMR) spectroscopy to study and understand novel materials for energy storage applications, with an emphasis on electrolytes for rechargeable lithium-ion batteries and all-solid-state batteries. …

Developments In The Lithographic Engineering Of Bi2sr2cacu2o8+Delta Mesa Terahertz-Emitting Devices, Sarah Elghazoly

Dissertations, Theses, and Capstone Projects

Devices microfabricated from the high-temperature superconducting cuprate Bi₂Sr₂CaCu₂O_8+𝛿 (Bi-2212) are a promising source of coherent terahertz radiation within the ’terahertz gap’ (0.3- 1.5 THz). A current-biased mesa patterned into the surface of a single crystal will produce electromagnetic radiation in the terahertz regime due to the naturally occurring Josephson junctions formed by the stacks of superconducting cuprate oxide planes in the material separated by insulating BiO and SrO barrier layers. Previous research has shown that by fabricating these mesas such that the geometry supports resonant cavity Fabry-Perot modes, the junctions within the mesa …

Quantum Entanglement Correlations In The Proton On The Light-Front, Eric Kolbusz

Dissertations, Theses, and Capstone Projects

In this work we gather results on information theory applied to proton tomography. We start by analyzing the quantum entanglement of momentum, spin-flavor, and color degrees of freedom (d.o.f.) in the leading valence-quark state of the proton on the light front using standard information theoretical tools, leveraging model wavefunctions by Brodsky and Schlumpf to obtain numerical predictions. Light-cone perturbation theory allows us to introduce the one-gluon correction in the sub-leading Fock state and study the entanglement of the gluonic d.o.f. We find weak entanglement in the spatial d.o.f. of the valence quarks, and significantly stronger entanglement in the analogous d.o.f. …

Relevant Deformations Of Brane Brick Models, Georgios P. Goulas

Dissertations, Theses, and Capstone Projects

The thesis studies relevant deformations of 2d gauge theories with $\mathcal{N}=(0,2)$ supersymmetry, realized on the worldvolume of D1-branes probing toric Calabi-Yau 4-folds. Brane brick models are the primary means for engineering such theories and streamlining their connection to geometry. In this thesis, we relevant deformations of brane brick models, focusing on a specific class of deformations in which the initial and final theories are both described by brane brick models. Relevant deformations serve as an additional, systematic way of generating these theories, as well as uncovering connections between them. Within the framework of brane engineering, these deformations acquire a geometric …

Nuclear Magnetic Resonance Characterization For The Study Of Beyond Lithium-Ion Battery Electrolytes, Allen Zheng

Dissertations, Theses, and Capstone Projects

To achieve a sustainable future, key issues in the energy and construction sectors such as the transition from fossil fuels to renewable energy sources and recycling of waste construction materials must be addressed. While fossil fuels offer a high energy density source of quick, consistent energy, renewable energy sources such as wind, solar, and hydroelectric offer intermittent energy output, requiring energy storage systems to maintain steady energy availability for consumers. Lithium-ion batteries (LIBs) are widely used in consumer electronics, electric vehicles, and grid storage due to their high energy density, low self-discharge, and rechargeability. However, they are limited by high …

Excitons And Polaritons In Two-Dimensional Materials Heterostructures - Applications As Qubits, Time Crystals, And Superfluids, Gabriel Pimenta Martins

Dissertations, Theses, and Capstone Projects

This dissertation is concerned with exploring the properties and applications of excitons and polaritons in two-dimensional (2D) materials and heterostructures. It focuses on their potential to form qubits, time crystals, and superfluids. The work is motivated by the unique electronic and optical properties of 2D materials—specifically, their ability to host strongly bound excitons and hybrid light-matter quasiparticles known as polaritons. By exploiting a combination of theoretical modeling and numerical simulations, this work examines the behavior of these quasiparticles under various physical conditions, including strain-induced pseudomagnetic fields, optical microcavities, and periodic external potentials.

The first part of this dissertation is devoted …

Nonlinear Physics Of Parity-Broken Fluids, Sudheesh Srivastava

Dissertations, Theses, and Capstone Projects

This thesis explores parity-breaking mechanisms, nonlinear wave phenomena, and localization transitions across different physical contexts. First, we examine modulation instability in parity-breaking systems, deriving modified nonlinear Schr¨odinger equations that reveal direction dependent instabilities. Next, we investigate wave turbulence, demonstrating numerically that parity-breaking dispersion significantly alters turbulent cascades and modifies their statistical properties. Lastly, we analyze localization in quasiperiodic tight- binding model based on polariton condensate lattice. Collectively, these studies illustrate the universal role of symmetries and nonlinear interactions in shaping macroscopic behaviors, facilitating interdisciplinary insights.

Novel Alchemical Methodologies For Modeling Molecular Binding, Solmaz Azimi

Dissertations, Theses, and Capstone Projects

Molecular recognition is fundamental to all biological and biochemical processes. Understanding the interactions between molecules is the foundation for drug discovery and development, for understanding biological processes, and for the design of biosensors and nanomaterials. There is tremendous interest in the development of computer models to predict molecular association equilibria. In structure-based drug discovery enterprises, predicting the strength and selectivity of a small molecule to a biological target can advance target identification, aid ligand design, and accelerate high-throughput screening of drug compounds. This work focuses on free energy models, a class of computational methodologies grounded on the fundamental physical and …

The Role Of Secondary And Tertiary Structure In The Cap-Independent Translation Of Fgf-9 And Hif-1-Alpha, Amanda Michelle Whittaker

Dissertations, Theses, and Capstone Projects

Under normoxic conditions, eukaryotes initiate translation of RNA through eIF4E recognition of the 5’ cap. However, under cellular stress, eukaryotic translation must be initiated through a 4E-independent, or “cap-independent” mechanism, involving eukaryotic initiation factor 4G (eIF4G) binding directly to the 5’ untranslated regions (5’ UTR) of the RNA. eIF4G binding then recruits the ribosome to the transcript. While this mechanism is useful for translation of apoptotic transcripts and transcripts involved in cell survival, cap-independent translation is also utilized by oncogenic RNA for tumorigenesis. Previous work by our lab and others has categorized this recruitment and initiation mechanism as either internal-ribosome-entry-site …

Underlying Mechanisms Of Quantum Emission In Hexagonal Boron Nitride, Enrique Alejandro Mejia Iv

Dissertations, Theses, and Capstone Projects

Quantum emitters in hexagonal boron nitride (hBN) have emerged as promising candidates for advancing numerous quantum technologies. Visible-spectrum quantum emitters, in particular, have gained significant attention due to their exceptional properties, including high brightness, observable spin structure, and highly tunable emission wavelengths. However, several challenges hold back the practical implementation of hBN-based quantum emitters in technological applications—namely, the unknown physical structure of the emitters, susceptibility to spectral wandering and blinking, and limited understanding of how to control their broad spectral distribution.

In this dissertation, we investigate the collective properties of highly defective hBN. To address the key challenges, we develop …

Silver-Alloyed Cigs Thin-Film Solar Cells On Flexible Stainless-Steel Substrate, Zhi Huang

Dissertations, Theses, and Capstone Projects

Our dissertation demonstrates the optimization of ACIGS (Ag-Cu-In-Ga-Se) thin-film solar cells, achieving an efficiency of 20.4% through the combined effects of silver incorporation and alkali metal post-deposition treatment (PDT). The incorporation of 2.8% Ag into the CIGS lattice enhanced crystal quality, reduced disorder, and widened the bandgap by 0.103 eV, as evidenced by a significant reduction in Urbach energy. These improvements resulted in stronger light absorption, increased carrier generation, and enhanced photovoltaic parameters, including a short-circuit current density Jsc of 35.31 mA/cm², an open-circuit voltage Voc of 0.74 V, and a fill factor (FF) of 75.8%. PDT using rubidium fluoride …

Taming Biological Complexity Through The Use Of Symmetries, Luis A. Álvarez-García

Dissertations, Theses, and Capstone Projects

The study of biological systems is, inherently, the study of very complex systems. This is essentially due to the fact that they are made up of numerous, often very complicated, interactions between an extensive number of components. Often necessitating an abundance of quantitative parameters and details for a precise description. The human brain for ex- ample, consisting of ∼ 80 billion neurons with ∼ 800 to 100 trillion connections between them, each of them depending on a large set of parameters. Even simpler examples such as bacterial organisms, such as E. coli and B. subtilis, which we focus on …

Structural, Electronic And Magnetic Properties Of Vanadium Doped Transition Metal Dichalcogenides (Tmds), Qudsia Ashraf

Dissertations, Theses, and Capstone Projects

Magnetic semiconductors are a prerequisite for spintronic devices but their ferromagnetism disappears at room-temperature hindering application in room temperature electronic devices. Enormous research has been conducted on the room-temperature ferromagnetic order in monolayer form of bulk van der Waals materials but the few layer system has not been extensively explored.

Doping is an effective approach to modulate the structural, electronic and magnetic properties of two-dimensional (2D) Transition metal dichalcogenides (TMDs) and expand their application. The effect of vanadium dopant on structural, electronic and magnetic properties of Tungsten Diselenide (WSe₂) was studied by X-ray Photoelectron Spectroscopy (XPS), Atomic Force …

Interplay Of Magnetic Impurities And Superconductivity In Topological Materials, Didier Ndengeyintwali

Dissertations, Theses, and Capstone Projects

The interplay of superconductivity and magnetism has been a long-standing topic of interest since the discovery of superconductivity. In recent years it has been shown that topological superconductivity, which has promising applications such as in topological quantum computing, could result from such interplay. Motivated by the later results I study the effect of magnetic impurities in superconducting doped topological insulators, such as Iron based topological superconductors. I show that topological character of parent materials could lead to modifications in the structure of magnetic impurity induced in-gap states. Moreover, the superconductivity induced interaction between magnetic impurities in doped topological insulator would …

Design And Characterization Of De Novo Photoactivated Charge Separating Proteins, Paul M. Molinaro

Dissertations, Theses, and Capstone Projects

Light activate charge separation can provide high energy electrons for a variety of chemical processes. Reaction center proteins serve as a scaffold for small molecules that serve as “hopping” sites for electrons. Previous reaction center designs are four helix bundles that bind at minimum two metalloporphyrin’s: a zinc porphyrin serves as a light activated electron donor, mimicking chlorophyl, and a heme molecule serving as the acceptor. The efficiency of these designs is hampered by the enhanced relaxation of the singlet excited state of zinc porphyrin molecules due to spin-orbit coupling with the paramagnetic heme acceptor. The optimal design would contain …

Shear Viscosity Of Quasi One-Dimensional Bec Tubes And Entanglement Negativity Conditions, Camilla Polvara

Dissertations, Theses, and Capstone Projects

Shear Viscosity of Quasi One-dimensional BEC Tubes

We consider layered Bose-Einstein condensates interacting via contact intra-condensate interacions and dipolar inter-condensate potentials, both of which dominate intercondensate tunneling (which we neglect for simplicity). For this system, we compute the normal modes, we study its localization properties by numerically computing the inverse participation ratio, and we compute the inter-tube shear viscosity.

Entanglement Negativity Conditions

This project explores bounds on entanglement negativity using operator inequalities, building on the results of [1]. We are looking for a way to quantify entanglement, as an alternative to calculating the full negativity, which would otherwise require the …

Modeling And Dynamics Of Capillary Bridges, Moyosore Odunsi

Dissertations, Theses, and Capstone Projects

Capillary bridges are ubiquitous in nature and have important implications in processes like inkjet printing. They are an important area of study not only because of their industrial applications but because many of the questions in capillary bridge research are applicable to other systems. For example, they exhibit pinning and unpinning patterns that are similar to those in sliding droplets. The rules underlying this pinning are essential to predicting liquid shapes and understanding how contact lines move across surfaces. Many previous studies have focused on axisymmetric capillary bridges and neglected to model the tangential forces that arise due to asymmetry. …

Aspects Of Parity Breaking In Classical And Quantum Fluids, Dylan J. Reynolds

Dissertations, Theses, and Capstone Projects

Parity-breaking is ubiquitous across many scales of physics, from the rotation of galaxies at the largest of scales, to the cyclotron orbits of electrons at the microscopic scale. In describing the collective dynamics of many particle systems, parity breaking effects typically originate from some form of chirality, such as angular momentum, at the level of the constituent particles. External forces can also induce chiral motion, with the primary examples being the Lorentz and Coriolis forces.

The effects of parity breaking are perhaps most strikingly seen in active matter, systems of complex particles that tend to convert energy into some directed …

Quantics Tensor Trains: The Study Of A Continuous Lattice Model And Beyond, Aleix Bou Comas

Dissertations, Theses, and Capstone Projects

This four-chapter dissertation studies the efficient discretization of continuous variable functions with tensor train representation. The first chapter describes all the methodology used to discretize functions and store them efficiently. In this section, the algorithm tensor renormalization group is explained for self-containment purposes. The second chapter centers around the XY model. Quantics tensor trains are used to describe the transfer matrix of the model and compute one and two-dimensional quantities. The one dimensional magnitudes are compared to analytical results with an agreement close to machine precision. As for two dimensions, the analytical results cannot be computed. However, the critical temperature …

Positron Emission Tomography In Oncology And Environmental Science, Samantha Delaney

Dissertations, Theses, and Capstone Projects

The last half century has played witness to the onset of molecular imaging for the clinical assessment of physiological targets. While several medical imaging modalities allow for the visualization of the functional and anatomical properties of humans and living systems, few offer accurate quantitation and the ability to detect biochemical processes with low-administered drug mass doses. This limits how physicians and scientists may diagnose and treat medical issues, such as cancer, disease, and foreign agents.

A promising alternative to extant invasive procedures and suboptimal imaging modalities to assess the nature of a biological environment is the use of positron emission …

Development And Application Of Magnus Expansion Based Propagators For Problems In Spectroscopy And Quantum Dynamics, Taner M. Ture

Dissertations, Theses, and Capstone Projects

Stable and accurate numerical propagators of time-evolution equations in quantum mechanics are required to capture correct dynamical behavior, especially in the long time limit. Magnus expansion (ME) provides a general way to expand the real time propagator of a time dependent Hamiltonian within the exponential such that the unitarity is satisfied at any order. Integrators are developed by truncating the ME and using explicit integration of Lagrange interpolation formulas for the time dependent Hamiltonian within each time interval. The derived approximations are studied in a numerical test and compared to other available expressions. The sixth order expression is applied to …

Unconventional Computing With Photonic Oscillator Networks, Mostafa Honari Latifpour

Dissertations, Theses, and Capstone Projects

The ever-increasing demand for data processing and the challenges in scaling traditional computing architectures are driving intensive research into alternative computing paradigms. Optical computing has garnered renewed attention since the 2010s, driven by its potential to accelerate specialized computational tasks such as combinatorial optimization and neural networks.

Coherent light sources including lasers and parametric oscillators have been around for decades and become indispensable tools in modern technology, but these photonic oscillators are also nonlinear dynamical systems that can exhibit emergent, complex phenomena, especially when coupled in arrays. These nonlinear optical systems have recently been shown to be capable of doing …

Exciton Dynamics, Interaction, And Transport In Monolayers Of Transition Metal Dichalcogenides, Saroj Chand

Dissertations, Theses, and Capstone Projects

Monolayers Transition metal dichalcogenides (TMDs) have attracted much attention in recent years due to their promising optical and electronic properties for applications in optoelectronic devices. The rich multivalley band structure and sizable spin-orbit coupling in monolayer TMDs result in several optically bright and dark excitonic states with different spin and valley configurations. In the proposed works, we have developed experimental techniques and theoretical models to study the dynamics, interactions, and transport of both dark and bright excitons.

In W-based monolayers of TMDs, the momentum dark exciton cannot typically recombine optically, but they represent the lowest excitonic state of the system …

A Causal Inference Approach For Spike Train Interactions, Zach Saccomano

Dissertations, Theses, and Capstone Projects

Since the 1960s, neuroscientists have worked on the problem of estimating synaptic properties, such as connectivity and strength, from simultaneously recorded spike trains. Recent years have seen renewed interest in the problem coinciding with rapid advances in experimental technologies, including an approximate exponential increase in the number of neurons that can be recorded in parallel and perturbation techniques such as optogenetics that can be used to calibrate and validate causal hypotheses about functional connectivity. This thesis presents a mathematical examination of synaptic inference from two perspectives: (1) using in vivo data and biophysical models, we ask in what cases the …

Thermodynamics Of Learning With Parametric Probabilistic Models, Shervin Sadat Parsi

Dissertations, Theses, and Capstone Projects

This study delves into the learning process within the Probabilistic Parametric Models (PPMs) framework from a unique thermodynamic perspective. By exploring the core concepts of thermodynamics and its innate connection with information theory, we showcase how this interdisciplinary approach can effectively contribute to the domain of machine learning. In the initial chapter, we establish the link between the learning problem in PPMs and a thermodynamic process by reframing various elements of the learning process within the context of thermodynamics. We introduce novel information-theoretic measurements that provide insights into the information learned in both the parameter space and the overall performance …

Dynamics Of Spin And Charge Of Color Centers In Diamond Under Cryogenic Conditions, Richard G. Monge

Dissertations, Theses, and Capstone Projects

Individual quantum systems in semiconductors are currently the most sought-after platform for applications in quantum science. Most notably, the nitrogen-vacancy (NV) center in diamond features a defect deep within the electronic bandgap, making it amenable for precise manipulation to help pave the way to perform fundamental quantum physics experimentation. The NV center also offers long coherence times and versatile spin-dependent fluorescent properties, making it an ideal candidate for a nanoscale magnetometer. Furthermore, multi-color excitation offers deterministic charge state manipulation. While ambient operation has been key to their appeal, bringing NVs to cryogenic conditions opens new opportunities for alternate forms of …