Physical Sciences and Mathematics Commons^™

Aspects Of Stochastic Geometric Mechanics In Molecular Biophysics, David Frost

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In confocal single-molecule FRET experiments, the joint distribution of FRET efficiency and donor lifetime distribution can reveal underlying molecular conformational dynamics via deviation from their theoretical Forster relationship. This shift is referred to as a dynamic shift. In this study, we investigate the influence of the free energy landscape in protein conformational dynamics on the dynamic shift by simulation of the associated continuum reaction coordinate Langevin dynamics, yielding a deeper understanding of the dynamic and structural information in the joint FRET efficiency and donor lifetime distribution. We develop novel Langevin models for the dye linker dynamics, including rotational dynamics, based …

Leveraging Artificial Intelligence For Team Cognition In Human-Ai Teams, Beau Schelble

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Advances in artificial intelligence (AI) technologies have enabled AI to be applied across a wide variety of new fields like cryptography, art, and data analysis. Several of these fields are social in nature, including decision-making and teaming, which introduces a new set of challenges for AI research. While each of these fields has its unique challenges, the area of human-AI teaming is beset with many that center around the expectations and abilities of AI teammates. One such challenge is understanding team cognition in these human-AI teams and AI teammates' ability to contribute towards, support, and encourage it. Team cognition is …

Hydrothermal Synthesis Of First-Row Transition Metal Polyanions Towards The Design Of Frustrated Magnetic Materials, Megan Smart

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Novel modern materials are constantly being discovered as humanity seeks constantly better improvement to the optics and electronics around us, from lasers used in medical therapies to the magnets and supercomputing chips in our phones. Inorganic oxides commonly draw inspiration from naturally occurring minerals to template new discoveries through substitution of similarly behaving elements with the goal of inducing certain desired properties, such as ferroelectricity or creating the elusive quantum spin liquid. While many minerals are silicates, its periodic table neighbor germanium(IV) has a rich and under-explored crystal chemistry that could contain many new structures and magnetic materials. Another common …

Zero-Knowledge Reductions And Confidential Arithmetic, Marvin Jones

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The changes in computing paradigms to shift computations to third parties have resulted in the necessity of these computations to be provable. Zero-knowledge arguments are probabilistic arguments that are used to to verify computations without secret data being leaked to the verifying party.

In this dissertation, we study zero-knowledge arguments with specific focus on reductions. Our main contributions are:

1. Provide a thorough survey in a variety of zero-knowledge techniques and protocols.
2. Prove various results of reductions that can be used to study interactive protocols in terms of subroutines. Additionally, we identify an issue in the analogous definition of zero-knowledge for …

Studies On Electrochemical Hydrogen Isotope Separation, Liyanage Mayura Sankalpa Silva

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Graphene-integrated Proton Exchange Membrane (PEM) electrochemical cells have emerged as a novel area of scientific investigation in the realm of hydrogen isotope separation. Chemical Vapor Deposited (CVD) graphene has been especially useful due to its large-scale production capability for scaling-up purposes. The research described in this dissertation explores the role that inadvertent introduction of cations, notably ammonium and copper, during the CVD graphene transfer onto PEM substrates, such as Nafion, might play in affecting hydrogen ion transport and isotope separation in PEM electrochemical cells. An extensive review of existing literature exposed a gap concerning unintentional cation introductions during graphene transfer, …

Atomistic And Mesoscale Modeling Of Microstructure Development During Solid-State Sintering, Omar Marwan Isa Hussein

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Interfaces are ubiquitous in materials systems, and they influence the processing and properties of nearly all engineering and functional materials. Examples include grain boundaries (GBs) in polycrystalline materials, free surfaces in nanoparticles, and phase boundaries in multiphase materials. Therefore, understanding and controlling interfacial processes is a key aspect of materials design and discovery efforts. Recent developments in advanced manufacturing and synthesis techniques have enabled the fabrication of materials architectures with intricate nanoscale features. Of particular interest is solid-state sintering, known for creating complex and high-precision geometries with controlled microstructures. While sintering science has been the subject of active research, very …

New Preconditioned Conjugate Gradient Methods For Some Structured Problems In Physics, Tianqi Zhang

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This dissertation concerns the development and analysis of new preconditioned conjugate gradient (PCG) algorithms for three important classes of large-scale and complex physical problems characterized by special structures. We propose several new iterative methods for solving the eigenvalue problem or energy minimization problem, which leverage the unique structures inherent in these problems while preserving the underlying physical properties. The new algorithms enable more efficient and robust large-scale modeling and simulations in many areas, including condensed matter physics, optical properties of materials, stabilities of dynamical systems arising from control problems, and many more. Some methods are expected to be applicable to …

Hpc-Enabled Fast And Configurable Dynamic Simulation, Analysis, And Learning For Complex Power System Adaptation And Control, Cong Wang

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This dissertation presents an HPC-enabled fast and configurable dynamic simulation, analysis, and learning framework for complex power system adaptation and control. Dynamic simulation for a large transmission system comprising thousands of buses and branches implies the latency of complicated numerical computations. However, faster-than-real-time execution is often required to provide timely support for power system planning and operation. The traditional approaches for speeding up the simulation demand extensive computing facilities such as CPU-based multi-core supercomputers, resulting in heavily resource-dependent solutions. In this work, by coupling the Message Passing Interface (MPI) protocol with an advanced heterogeneous programming environment, further acceleration can be …

An Investigation Of The Accretion Processes In T Tauri And Herbig Ae/Be Systems Using High Resolution Optical And Near-Infrared Spectroscopy, Joshua Kern

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Star and planet formation is intimately tied to the accretion of material from the environments in which they form. During the formation process, disks of gas and dust develop in young stellar objects through which material is facilitated to the star and forming planets. Theoretical models of these accretion processes invoke viscous spreading via hydrodynamics, as well as more complex interactions with magnetic fields be it from the stellar component or the formation environment in order to catalyze these mass flows. These accretion models predict various scenarios including magnetospheric accretion as well as supersonic accretion flows in the disk atmosphere …

Understanding The Interaction Of Environmental Contaminants With Polystyrene Nanoparticles And Dna Using Nuclear Magnetic Resonance Spectroscopy And Density Functional Theory, Saduni Arachchi

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The objective of the thesis is to study the effect of environmental pollutants on polystyrene nanoparticles and biomolecules. This is done in two different techniques, particularly NMR and density functional theory. In this thesis, we use a combination of 1H NMR, Saturation-Transfer Difference (STD) NMR and relaxation experiments to study the interactions, kinetics and dynamics of antibiotics with polystyrene nanoparticles. (PS NPs) Density functional theory (DFT) is used to study the binding of commonly used non-oxidative hair dyes to biomolecules (DNA and amino acids) and PS particles.

Damage Detection With An Integrated Smart Composite Using A Magnetostriction-Based Nondestructive Evaluation Method: Integrating Machine Learning For Prediction, Christopher Nelon

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The development of composite materials for structural components necessitates methods for evaluating and characterizing their damage states after encountering loading conditions. Laminates fabricated from carbon fiber reinforced polymers (CFRPs) are lightweight alternatives to metallic plates; thus, their usage has increased in performance industries such as aerospace and automotive. Additive manufacturing (AM) has experienced a similar growth as composite material inclusion because of its advantages over traditional manufacturing methods. Fabrication with composite laminates and additive manufacturing, specifically fused filament fabrication (fused deposition modeling), requires material to be placed layer-by-layer. If adjacent plies/layers lose adhesion during fabrication or operational usage, the strength …

Computationally-Driven Insights Into The Ligand Environments Of Materials For Catalysis And Separations, Stephen Vicchio

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Designing new catalytic and sorption materials is necessary to limit global temperature rise below 1.5 ◦C by 2050, while also meeting global energy demands. Climate change and energy production are not mutually exclusive; global population growth has direct impacts on global energy demands and climate. In both catalysis and adsorption applications, new technologies are needed to address these challenges. Catalysis can provide alternate, low-energy routes for converting low-value gases into higher-value chemical commodities, thus altering our current energy production. Likewise, new sorption materials can capture previously emitted CO₂ from decades of energy production from fossil fuels, thus helping to …

Atomistic And Mesoscale Modeling Of Microstructure Development During Solid-State Sintering, Omar Hussein

All Dissertations

Interfaces are ubiquitous in materials systems, and they influence the processing and properties of nearly all engineering and functional materials. Examples include grain boundaries (GBs) in polycrystalline materials, free surfaces in nanoparticles, and phase boundaries in multiphase materials. Therefore, understanding and controlling interfacial processes is a key aspect of materials design and discovery efforts.

Recent developments in advanced manufacturing and synthesis techniques have enabled the fabrication of materials architectures with intricate nanoscale features. Of particular interest is solid-state sintering, known for creating complex and high-precision geometries with controlled microstructures. While sintering science has been the subject of active research, very …

Controlled Manipulation And Transport By Microswimmers In Stokes Flows, Jake Buzhardt

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Remotely actuated microscale swimming robots have the potential to revolutionize many aspects of biomedicine. However, for the longterm goals of this field of research to be achievable, it is necessary to develop modelling, simulation, and control strategies which effectively and efficiently account for not only the motion of individual swimmers, but also the complex interactions of such swimmers with their environment including other nearby swimmers, boundaries, other cargo and passive particles, and the fluid medium itself. The aim of this thesis is to study these problems in simulation from the perspective of controls and dynamical systems, with a particular focus …

Nonlinear Charge And Spin Currents In Non-Centrosymmetric Electron Systems, Aniruddha Pan

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In this thesis, we discuss the existence of spin and charge currents in systems with broken spin inversion symmetry proportional to the magnitude square of the driving electric and thermal fields. This outcome is predicated on symmetry considerations in the momentum space, whereby the product between the current operator and the out-of-equilibrium distribution function has to be even.

First, we derive the second-order correction to the particle distribution function $\delta f^{(2)}$ in a semi-classical approximation, considering the local change in the equilibrium distribution function caused by external fields. Our approach departs significantly from the previous theory where $\delta f^{(2)}$ is …

High-Energy Storm Events And Their Impacts On Carbon Storage In Tidal Wetlands Of South Carolina, Gavin Gleasman

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Atmospheric carbon dioxide (CO₂) concentrations have been increasing at an accelerating rate for the past two centuries, profoundly impacting global climate change. Atmospheric CO₂ concentrations are influenced by the global carbon cycle through physical and biogeochemical pathways. Tidal wetland environments play a vital role in the global carbon cycle by offsetting atmospheric CO₂ concentrations through their natural physiochemical processes of high autotrophic productivity, allochthonous organic matter deposition, anoxic soils, and continuous accretion which promotes carbon sequestration with long-term storage at the land-ocean margin. The Intergovernmental Panel on Climate Change (IPCC) and United States Global Change Research …

The Effects Of Primary And Secondary Task Workloads On Cybersickness In Immersive Virtual Active Exploration Experiences, Rohith Venkatakrishnan

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Virtual reality (VR) technology promises to transform humanity. The technology enables users to explore and interact with computer-generated environments that can be simulated to approximate or deviate from reality. This creates an endless number of ways to propitiously apply the technology in our lives. It follows that large technological conglomerates are pushing for the widespread adoption of VR, financing the creation of the Metaverse - a hypothetical representation of the next iteration of the internet.

Even with VR technology's continuous growth, its widespread adoption remains long overdue. This can largely be attributed to an affliction called cybersickness, an analog to …

Zeros Of Modular Forms, Daozhou Zhu

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Let $E_k(z)$ be the normalized Eisenstein series of weight $k$ for the full modular group $\text{SL}(2, \mathbb{Z})$. It is conjectured that all the zeros of the weight $k+\ell$ cusp form $E_k(z)E_\ell(z)-E_{k+\ell}(z)$ in the standard fundamental domain lie on the boundary. Reitzes, Vulakh and Young \cite{Reitzes17} proved that this statement is true for sufficiently large $k$ and $\ell$. Xue and Zhu \cite{Xue} proved the cases when $\ell=4,6,8$ with $k\geq\ell$, all the zeros of $E_k(z)E_\ell(z)-E_{k+\ell}(z)$ lie on the arc $|z|=1$. For all $k\geq\ell\geq10$, we will use the same method as \cite{Reitzes17} to locate these zeros on the arc $|z|=1$, and improve the …

Expansion Of The Diazacyclobutene Motif For Antiparasitic Evaluation, Brock Alexander Miller

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Molecules containing N-heterocycles are prevalent in pharmaceutical settings. The ability to generate highly functionalized molecules containing N-heterocycles in very few synthetic operations is valuable for drug discovery. Our group has developed a two-step synthesis to access a rarely studied diazacyclobutene scaffold via a formal [2+2] cycloaddition between 4-phenyl-1,2,4-triazolinedione and electron-rich thioalkynes. Our interest in this scaffold increased exponentially from promising preliminary biological evaluations against a protozoan parasite, Trypanosoma brucei. While we were able to double the number of historical examples of this scaffold, there were significant limitations in our methodology. The most notable limitations were the lack …

Atom Economical Reactions Of Terpenoids And Post-Consumer Plastics With Sulfur, Charini Maladeniya

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The production of Ordinary Portland Cement (OPC) and its uses have a complicated environmental impact, which is influenced by infrastructure development and building operations as well as CO₂ emissions, which account for 7% of all worldwide CO₂ emissions. Due to the increasing population, production is still ongoing. The search for cement and construction materials produced with zero to low CO₂ emissions is therefore continuous. Finding recyclable, CO₂ gas-free biocomposites with high sulfur content that can rival the mechanical properties of popular building supplies like Portland cement is the primary objective of the research discussed in this …

Cosmic Diffuse Neutrino And Gamma-Ray Backgrounds In The Mev Regime, Ilukpitiye Samalka Anandagoda

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Cosmic Multi-Messenger backgrounds include relic diffuse components created in the early Universe and contributions from individual sources. In this dissertation, I present the work done in Anandagoda (2019); Anandagoda et al. (2020, 2023) where type Ia (SNe Ia) and core-collapse supernovae (CCSNe) contributions to the diffuse neutrino and gamma-ray backgrounds in the MeV regime are studied. These backgrounds are referred to as DSNB and DSGB respectively. Based on this work, the diffuse SN Ia background is ~10⁶ times lower (for electron antineutrinos) than the CCSN background making it negligible. The predicted DSNB electron antineutrino flux at earth in the …

Motion Synthesis And Control For Autonomous Agents Using Generative Models And Reinforcement Learning, Pei Xu

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Imitating and predicting human motions have wide applications in both graphics and robotics, from developing realistic models of human movement and behavior in immersive virtual worlds and games to improving autonomous navigation for service agents deployed in the real world. Traditional approaches for motion imitation and prediction typically rely on pre-defined rules to model agent behaviors or use reinforcement learning with manually designed reward functions. Despite impressive results, such approaches cannot effectively capture the diversity of motor behaviors and the decision making capabilities of human beings. Furthermore, manually designing a model or reward function to explicitly describe human motion characteristics …

Study Of Highly Charged Ion Charge Exchange With Applications To X-Ray Astrophysics, Richard Mattish

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Highly charged ions (HCIs) exist in many hot astrophysical environments where they play an important role in plasma dynamics. Charge exchange involving highly charged ions has been shown to be responsible for many observed X-ray emissions from a variety of astrophysical sources. Proper modeling of these environments requires an understanding of this process, including the electronic structure of each ion species as well as their charge exchange cross sections. This dissertation investigates charge exchange processes with highly charged ions which are present in astrophysical environments via a laboratory-based study.

The Clemson University electron beam ion trap (CUEBIT) laboratory was utilized …

A Framework For Statistical Modeling Of Wind Speed And Wind Direction, Eva Murphy

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Atmospheric near surface wind speed and wind direction play an important role in many applications, ranging from air quality modeling, building design, wind turbine placement to climate change research. It is therefore crucial to accurately estimate the joint probability distribution of wind speed and direction. This dissertation aims to provide a modeling framework for studying the variation of wind speed and wind direction. To this end, three projects are conducted to address some of the key issues for modeling wind vectors.\\

First, a conditional decomposition approach is developed to model the joint distribution of wind speed and direction. Specifically, the …

Composite And Polymer Formulation Employing Sulfur And Bio-Olefin Feedstocks, Claudia V. Lopez

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Environmental sustainability represents a challenge for society since industrial growth has a direct impact on natural resources and waste production. New technologies that effectively incorporate waste into renewable resources are critical to the development of a sustainable and circular economy. The manufacturing of structural materials like Portland cement (OPC) is responsible for >8% of the global anthropogenic emissions of carbon dioxide, with ~ 1 kg of CO₂ released to the atmosphere for every kilogram of OPC produced. For instance, the development of sustainable structural materials is a key factor to reduce the greenhouse emissions and to attenuate the climate …

Acceleration Methods For Nonlinear Solvers And Application To Fluid Flow Simulations, Duygu Vargun

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This thesis studies nonlinear iterative solvers for the simulation of Newtonian and non- Newtonian fluid models with two different approaches: Anderson acceleration (AA), an extrapolation technique that accelerates the convergence rate and improves the robustness of fixed-point iterations schemes, and continuous data assimilation (CDA) which drives the approximate solution towards coarse data measurements or observables by adding a penalty term.

We analyze the properties of nonlinear solvers to apply the AA technique. We consider the Picard iteration for the Bingham equation which models the motion of viscoplastic materials, and the classical iterated penalty Picard and Arrow-Hurwicz iterations for the incompressible …

Algebraic And Integral Closure Of A Polynomial Ring In Its Power Series Ring, Joseph Swanson

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Let R be a domain. We look at the algebraic and integral closure of a polynomial ring, R[x], in its power series ring, R[[x]]. A power series α(x) ∈ R[[x]] is said to be an algebraic power series if there exists F (x, y) ∈ R[x][y] such that F (x, α(x)) = 0, where F (x, y) ̸ = 0. If F (x, y) is monic, then α(x) is said to be an integral power series. We characterize the units of algebraic and integral power series. We show that the only algebraic power series with infinite radii of convergence are …

The Influence Of Allostery Governing The Changes In Protein Dynamics Upon Substitution, Joseph Hess

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The focus of this research is to investigate the effects of allostery on the function/activity of an enzyme, human immunodeficiency virus type 1 (HIV-1) protease, using well-defined statistical analyses of the dynamic changes of the protein and variants with unique single point substitutions ¹. The experimental data¹ evaluated here only characterized HIV-1 protease with one of its potential target substrates. Probing the dynamic interactions of the residues of an enzyme and its variants can offer insight of the developmental importance for allosteric signaling and their connection to a protein’s function. The realignment of the secondary structure elements can …

Concentration Theorems For Orthonormal Sequences In A Reproducing Kernel Hilbert Space, Travis Alvarez

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Let H be a reproducing kernel Hilbert space with reproducing kernel elements {Kx} indexed by a measure space {X,mu}. If H can be embedded in L2(X,mu), then H can be viewed as a framed Hilbert space. We study concentration of orthonormal sequences in such reproducing kernel Hilbert spaces.

Defining different versions of concentration, we find quantitative upper bounds on the number of orthonormal functions that can be classified by such concentrations. Examples are shown to prove sharpness of the bounds. In the cases that we can add "concentrated" orthonormal vectors indefinitely, the growth rate of doing so is shown.

Asymptotic Cones Of Quadratically Defined Sets And Their Applications To Qcqps, Alexander Joyce

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Quadratically constrained quadratic programs (QCQPs) are a set of optimization problems defined by a quadratic objective function and quadratic constraints. QCQPs cover a diverse set of problems, but the nonconvexity and unboundedness of quadratic constraints lead to difficulties in globally solving a QCQP. This thesis covers properties of unbounded quadratic constraints via a description of the asymptotic cone of a set defined by a single quadratic constraint. A description of the asymptotic cone is provided, including properties such as retractiveness and horizon directions.

Using the characterization of the asymptotic cone, we generalize existing results for bounded quadratically defined regions with …