Physical Sciences and Mathematics Commons^™

Molecular Mechanisms Of Amyloid-Like Fibril Formation, Sharareh Jalali

Dissertations

Proteins play a critical role in living systems by performing most of the functions inside cells. The latter is determined by the protein's three-dimensional structure when it is folded in its native state. However, under pathological conditions, proteins can misfold and aggregate, accounting for the formation of highly ordered insoluble assemblies known as amyloid fibrils. These assemblies are associated with diseases like Parkinson's and Alzheimer's. Strong evidence suggests that three mechanisms are critical for forming amyloid fibrils. These mechanisms are the nucleation of amyloid fibrils in solution (primary nucleation) as well as on the surface of existing fibrils (secondary nucleation) …

Exploring Topological Phonons In Different Length Scales: Microtubules And Acoustic Metamaterials, Ssu-Ying Chen

Dissertations

The topological concepts of electronic states have been extended to phononic systems, leading to the prediction of topological phonons in a variety of materials. These phonons play a crucial role in determining material properties such as thermal conductivity, thermoelectricity, superconductivity, and specific heat. The objective of this dissertation is to investigate the role of topological phonons at different length scales.

Firstly, the acoustic resonator properties of tubulin proteins, which form microtubules, will be explored The microtubule has been proposed as an analog of a topological phononic insulator due to its unique properties. One key characteristic of topological materials is the …

Bacterial Motion And Spread In Porous Environments, Yasser Almoteri

Dissertations

Micro-swimmers are ubiquitous in nature from soil and water to mammalian bodies and even many technological processes. Common known examples are microbes such as bacteria, micro-algae and micro-plankton, cells such as spermatozoa and organisms such as nematodes. These swimmers live and have evolved in multiplex environments and complex flows in the presence of other swimmers and types, inert particles and fibers, interfaces and non-trivial confinements and more. Understanding the locomotion and interactions of these individual micro-swimmers in such impure viscous fluids is crucial to understanding the emergent dynamics of such complex systems, and to further enabling us to control and …

Fluid Dynamics Of Interacting Particles: Bouncing Droplets And Colloid-Polymer Mixtures, Lauren Barnes

Dissertations

Interacting particles are a common theme across various physical systems, particularly on the atomic and sub-atomic scales. While these particles cannot be seen with the human eye, insight into such systems can be gained by observing macroscopic systems whose physical behavior is similar. This dissertation consists of three different chapters, each presenting a different problem related to interacting particles, as follows:

Chapter 1 explores chaotic trajectories of a droplet bouncing on the surface of a vertically vibrating fluid bath, with a simple harmonic force acting on the droplet. The bouncing droplet system has attracted recent interest because it exhibits behaviors …

Boundary Integral Equation Methods For Superhydrophobic Flow And Integrated Photonics, Kosuke Sugita

Dissertations

This dissertation presents fast integral equation methods (FIEMs) for solving two important problems encountered in practical engineering applications.

The first problem involves the mixed boundary value problem in two-dimensional Stokes flow, which appears commonly in computational fluid mechanics. This problem is particularly relevant to the design of microfluidic devices, especially those involving superhydrophobic (SH) flows over surfaces made of composite solid materials with alternating solid portions, grooves, or air pockets, leading to enhanced slip.

The second problem addresses waveguide devices in two dimensions, governed by the Helmholtz equation with Dirichlet conditions imposed on the boundary. This problem serves as a …

Variable Resolution Smoothed Particle Hydrodynamics Schemes For 2-D And 3-D Viscous Flows, Francesco Ricci

Dissertations

Smoothed Particle Hydrodynamics (SPH) is a Lagrangian particle-based method for the numerical solution of the partial differential equations that govern the motion of fluids. The main aim of this thesis work is to better enable the applicability of SPH to problems involving multi-scale fluid dynamics. In the first part of the thesis, the capability of the SPH method to simulate three-dimensional isotropic turbulence is investigated with a detailed comparison of Lagrangian and Eulerian SPH formulations. The main reason for this first investigation is to provide an assessment of the error introduced by the particle disorder on the SPH discrete operators …

Importance Of Vegetation In Tsunami Mitigation: Evidence From Large Eddy Simulations With Fluid-Structure Interactions, Abhishek Mukherjee

Dissertations

Communities worldwide are increasingly interested in nature-based solutions like coastal forests for the mitigation of coastal risks. Still, it remains unclear how much protective benefit vegetation provides, particularly in the limit of highly energetic flows after tsunami impact. The present thesis, using a three-dimensional incompressible computational fluid dynamics model with a fluid-structure interaction approach, aims to quantify how energy reflection and dissipation vary with different degrees of rigidity and vegetation density of a coastal forest.

In this study, tree trunks are represented as cylinders, and the elastic modulus of hardwood trees such as pine or oak is used to characterize …

Carrier Transport Engineering In Wide Bandgap Semiconductors For Photonic And Memory Device Applications, Ravi Teja Velpula

Dissertations

Wide bandgap (WBG) semiconductors play a crucial role in the current solid-state lighting technology. The AlGaN compound semiconductor is widely used for ultraviolet (UV) light-emitting diodes (LEDs), however, the efficiency of these LEDs is largely in a single-digit percentage range due to several factors. Until recently, AlInN alloy has been relatively unexplored, though it holds potential for light-emitters operating in the visible and UV regions. In this dissertation, the first axial AlInN core-shell nanowire UV LEDs operating in the UV-A and UV-B regions with an internal quantum efficiency (IQE) of 52% are demonstrated. Moreover, the light extraction efficiency of this …

Photonic Monitoring Of Atmospheric Fauna, Adrien P. Genoud

Dissertations

Insects play a quintessential role in the Earth’s ecosystems and their recent decline in abundance and diversity is alarming. Monitoring their population is paramount to understand the causes of their decline, as well as to guide and evaluate the efficiency of conservation policies. Monitoring populations of flying insects is generally done using physical traps, but this method requires long and expensive laboratory analysis where each insect must be identified by qualified personnel. Lack of reliable data on insect populations is now considered a significant issue in the field of entomology, often referred to as a “data crisis” in the field. …

Helioseismic Diagnostics Of Active Regions And Their Magnetic Fields, John T. Stefan

Dissertations

While two and a half decades of nearly constant observation by the Solar and Heliospheric Observatory (SOHO) and the Solar Dynamics Observatory (SDO) spacecraft have yielded key insights into the structure and dynamics of active regions, it is still unclear if active regions can be identified before emerging on the solar surface and, once emerged, whether the subsurface structure of an active region’s magnetic field can be measured. Regarding the dynamical processes associated with active regions, the height and mechanism of sunquake excitation remains poorly understood. To answer these questions, a comprehensive survey of active region magnetic fields and their …

Hydrodynamic Investigation Of The Discharge Of Complex Fluids From Dispensing Bottles Using Experimental And Computational Approaches, Baran Teoman

Dissertations

The discharge of non-Newtonian, complex fluids through orifices of industrial tanks, pipes, dispensers, or packaging containers is a ubiquitous but often problematic process because of the complex rheology of such fluids and the geometry of the containers. This, in turn, reduces the discharge rate and results in residual fluid left in the container, often referred to as heel. Heel formation is undesired in general, since it causes loss of valuable material, container fouling, and cross-contamination between batches. Heel may be of significant concern not only in industrial vessels but also in consumer packaging. Despite its relevance, the research in this …

Interactions Of Amyloid Peptides With Lipid Membranes, Yanxing Yang

Dissertations

The aggregation of amyloid proteins into fibrils is a hallmark of several diseases including Alzheimer’s (AD), Parkinson’s, and Type II diabetes. This aggregation process involves the formation of small size oligomers preceding the formation of insoluble fibrils. Recent studies have shown that these oligomers are more likely to be responsible for cell toxicity than fibrils. A possible mechanism of toxicity involves the interaction of oligomers with the cell membrane compromising its integrity. In particular, oligomers may form pore-like structures in the cell membrane affecting its permeability or they may induce lipid loss via a detergent-like effect. This dissertation aims to …

Stochastic Modeling Of Flows In Membrane Pore Networks, Binan Gu

Dissertations

Membrane filters provide immediate solutions to many urgent problems such as water purification, and effective remedies to pressing environmental concerns such as waste and air treatment. The ubiquity of applications gives rise to a significant amount of research in membrane material selection and structural design to optimize filter efficiency. As physical experiments tend to be costly, numerical simulation and analysis of fluid flow, foulant transport and geometric evolution due to foulant deposition in complex geometries become particularly relevant. In this dissertation, several mathematical modeling and analytical aspects of the industrial membrane filtration process are investigated. A first-principles mathematical model for …

Performance Analysis Of The Dominant Mode Rejection Beamformer, Enlong Hu

Dissertations

In array signal processing over challenging environments, due to the non-stationarity nature of data, it is difficult to obtain enough number of data snapshots to construct an adaptive beamformer (ABF) for detecting weak signal embedded in strong interferences. One type of adaptive method targeting for such applications is the dominant mode rejection (DMR) method, which uses a reshaped eigen-decomposition of sample covariance matrix (SCM) to define a subspace containing the dominant interferers to be rejected, thereby allowing it to detect weak signal in the presence of strong interferences. The DMR weight vector takes a form similar to the adaptive minimum …

Diagnostics Of Energy Release In Solar Flares With Radio Dynamic Imaging Spectroscopy, Yingjie Luo

Dissertations

Studies of the magnetic energy release and conversion process lie at the core of solar flare physics. Radio observations serve as a unique diagnostic method. In this dissertation, taking advantage of broadband radio dynamic imaging spectroscopy observations made by the Karl G. Jansky Very Large Array (VLA), studies are carried out on the flare energy release processes using different types of radio emissions.

The VLA is a general-purpose radio observatory located in New Mexico, which provides high-quality radio dynamic imaging spectroscopic observations with an ultra-fast time cadence. In the first study, stochastic decimetric radio spike bursts are observed by the …

Coupled Oscillators: Protein And Acoustics, Angelique N. Mcfarlane

Theses

This work encompassed three different vibrational energy transfer studies of coupled resonators (metal, topological, and microtubule comparison) inspired by the lattices of microtubules from regular and cancerous cells. COMSOL Multiphysics 5.4 was utilized to design the experiment. The simulation starts with an acoustic pressure study to examine the vibrational modes present in coupled cylinders, representing α-, β-tubulin heterodimers. The Metal Study consisted of 3 models (monomer, dimer, and trimer) to choose the correct height (40 mm) and mode (Mode 1) for study. The Topological Study was run to predict and understand how the lattice structure changes over a parametric sweep …

Waves And Oscillations In A Sunspot: Observations And Modeling Of Noaa Ar 12470, Yi Chai

Dissertations

Waves and oscillations are important solar phenomena not only because they can propagate and dissipate energy in the chromosphere, but also because they carry information about the structure of the atmosphere in which they propagate. Among these phenomena, the one of the most interesting ones occurs in the sunspot umbra. In this area, continuously propagating magnetohydrodynamic (MHD) waves generated from below the photosphere create the famous 3-minute sunspot umbral oscillations that affect the line profile of spectral lines due to temperature, density, and velocity changes of the plasma in the region. In the past decades, numerous observations and models have …

Nondestructive Evaluation Of 3d Printed, Extruded, And Natural Polymer Structures Using Terahertz Spectroscopy And Imaging, Alexander T. Clark

Dissertations

Terahertz (THz) spectroscopy and imaging are considered for the nondestructive evaluation (NDE) of various three-dimensional (3D) printed, extruded, and natural polymer structures. THz radiation is the prime candidate for many NDE challenges due to the added benefits of safety, increased contrast and depth resolution, and optical characteristic visualization when compared to other techniques. THz imaging, using a wide bandwidth pulse-based system, can evaluate the external and internal structure of most nonconductive and nonpolar materials without any permanent effects. NDE images can be created based on THz pulse attributes or a material’s spectroscopic characteristics such as refractive index, attenuation coefficient, or …

Investigation Of Topological Phonons In Acoustic Metamaterials, Wenting Cheng

Dissertations

Topological acoustics is a recent and intense area of research. It merges the knowledge of mathematical topology, condensed matter physics, and acoustics. At the same time, it has been pointed out that quasiperiodicity can greatly enhance the periodic table of topological systems. Because quasiperiodic patterns have an intrinsic global degree of freedom, which exists in the topological space called the hull of a pattern, where the shape traced in this topological space is called the phason. The hull augments the physical space, which opens a door to the physics of the integer quantum Hall effect (IQHE) in arbitrary dimensions. In …

Numerical Methods For Optimal Transport And Optimal Information Transport On The Sphere, Axel G. R. Turnquist

Dissertations

The primary contribution of this dissertation is in developing and analyzing efficient, provably convergent numerical schemes for solving fully nonlinear elliptic partial differential equation arising from Optimal Transport on the sphere, and then applying and adapting the methods to two specific engineering applications: the reflector antenna problem and the moving mesh methods problem. For these types of nonlinear partial differential equations, many numerical studies have been done in recent years, the vast majority in subsets of Euclidean space. In this dissertation, the first major goal is to develop convergent schemes for the sphere. However, another goal of this dissertation is …

Periodic Fast Multipole Method, Ruqi Pei

Dissertations

Applications in electrostatics, magnetostatics, fluid mechanics, and elasticity often involve sources contained in a unit cell C, centered at the origin, on which periodic boundary condition are imposed. The free-space Green’s functions for many classical partial differential equations (PDE), such as the modified Helmholtz equation, are well-known. Among the existing schemes for imposing the periodicity, three common approaches are: direct discretization of the governing PDE including boundary conditions to yield a large sparse linear system of equations, spectral methods which solve the governing PDE using Fourier analysis, and the method of images based on tiling the plane with copies of …

Type I Error Rate Controlling Procedures For Multiple Hypotheses Testing, Beibei Li

Dissertations

This dissertation addresses several different but related topics arising in the field of multiple testing, including weighted procedures and graphical approaches for controlling the familywise error rate (FWER), and stepwise procedures with control of the false discovery rate (FDR) for discrete data. It consists of three major parts.

The first part investigates weighted procedures for controlling the FWER. In many statistical applications, hypotheses may be differentially weighted according to their different importance. Many weighted multiple testing procedures (wMTPs) have been developed for controlling the FWER. Among these procedures, two weighted Holm procedures are commonly used in practice: one is based …

Model Checks For Two-Sample Location-Scale, Atefeh Javidialsaadi

Dissertations

Two-sample location-scale refers to a model that permits a pair of standardized random variables to have a common distribution. This means that if X₁ and X₂ are two random variables with means µ₁ and µ₂ and standard deviations ?₁ and ?₂, then (X₁ - µ₁)/?₁ and (X₂ - µ₂)/?₂ have some common unspecified standard or base distribution F₀. Function-based hypothesis testing for these models refers to formal tests that would help determine whether or not two samples may have come from some location-scale …

Coherent Control Of Dispersive Waves, Jimmie Adriazola

Dissertations

This dissertation addresses some of the various issues which can arise when posing and solving optimization problems constrained by dispersive physics. Considered here are four technologically relevant experiments, each having their own unique challenges and physical settings including ultra-cold quantum fluids trapped by an external field, paraxial light propagation through a gradient index of refraction, light propagation in periodic photonic crystals, and surface gravity water waves over shallow and variable seabeds. In each of these settings, the physics can be modeled by dispersive wave equations, and the technological objective is to design the external trapping fields or propagation media such …

Experimental And Computational Studies Of Functionalized Carbon Nanotubes For Use In Energy Storage Devices And Membranes, Emine S. Karaman

Dissertations

Electrolytes with good interfacial stability are a crucial component of any electrochemical device. The development of novel gel polymer electrolytes (GEs) with good interface stability and better manufacturability is important for the development of the next generation electrochemical devices. Gel electrolytes are hybrid electrolyte materials, combining benefits of both liquid and solid systems. Compared with liquid and solid electrolytes, GEs open new design opportunities and do not require rigorous encapsulation methods. In this dissertation, studies on functionalized carbon nanotubes (fCNTs) and graphene oxide (GO) doped polyvinyl alcohol (PVA) based gel electrolytes (GEs) are reported. The ionic conductivity and mechanical strength …

Electric-Field-Driven Processes In Multiphase Fluid Systems, Qian Lei

Dissertations

Advantages of using electric fields in miniaturized apparatuses for a wide range of applications are revealed by numerous experimental and theoretical studies over the last several decades as it offers a simple and efficient method for manipulation of multiphase fluid systems. This approach is considered to be especially beneficial for control of boiling processes and colloidal suspensions considered in the presented work.

Boiling. Today's trends for enhancing boiling heat transfer in terrestrial and space applications focus on removal of bubbles to prevent formation of a vapor layer over the surface at a high overheat. In contrast, this dissertation presents a …

Dependent Censoring In Survival Analysis, Zhongcheng Lin

Dissertations

This dissertation mainly consists of two parts. In the first part, some properties of bivariate Archimedean Copulas formed by two time-to-event random variables are discussed under the setting of left censoring, where these two variables are subject to one left-censored independent variable respectively. Some distributional results for their joint cdf under different censoring patterns are presented. Those results are expected to be useful in both model fitting and checking procedures for Archimedean copula models with bivariate left-censored data. As an application of the theoretical results that are obtained, a moment estimator of the dependence parameter in Archimedean copula models is …

Colloidal Quantum Dot (Cqd) Based Mid-Wavelength Infrared Optoelectronics, Shihab Bin Hafiz

Dissertations

Colloidal quantum dot (CQD) photodetectors are a rapidly emerging technology with a potential to significantly impact today’s infrared sensing and imaging technologies. To date, CQD photodetector research is primarily focused on lead-chalcogenide semiconductor CQDs which have spectral response fundamentally limited by the bulk bandgap of the constituent material, confining their applications to near-infrared (NIR, 0.7-1.0 um) and short-wavelength infrared (SWIR, 1-2.5 um) spectral regions. The overall goal of this dissertation is to investigate a new generation of CQD materials and devices that advances the current CQD photodetector research toward the technologically important thermal infrared region of 3-5 ?m, known as …

Advances In Modeling Gas Adsorption In Porous Materials For The Characterization Applications, Max A. Maximov

Dissertations

The dissertation studies methods for mesoporous materials characterization using adsorption at various levels of scale and complexity. It starts with the topic introduction, necessary notations and definitions, recognized standards, and a literature review.

Synthesis of novel materials requires tailoring of the characterization methods and their thorough testing. The second chapter presents a nitrogen adsorption characterization study for silica colloidal crystals (synthetic opals). These materials have cage-like pores in the range of tens of nanometers. The adsorption model can be described within a macroscopic approach, based on the Derjaguin-Broekhoff-de Boer (DBdB) theory of capillary condensation. A kernel of theoretical isotherms is …

Solar Flares As Observed In The Low Frequency Microwave Gyrosynchrotron Emission, Shaheda Begum Shaik

Dissertations

Solar flares involve the sudden catastrophic release of magnetic energy stored in the Sun’s corona. This dissertation focuses on investigating the low frequency, optically-thick gyrosynchrotron emission during solar flares for its spatial and spectral dynamics, characteristics, and role in the flare process.

The first part of this dissertation first addresses the spectral dynamics and characteristics of the source morphology. The high-resolution spectra of a set of microwave bursts observed by the Expanded Owens Valley Solar Array (EOVSA) during its commissioning phase in the 2.5-18 GHz frequency range with 1-s time resolution are presented here. Out of the 12 events analyzed …