Cell signaling under external stimulation is a critical mechanism that governs many biological processes such as cell proliferation, cell migration, and cell apoptosis, etc. For multicellular organisms, the ability to synchronize heterogeneous individual cellular responses through intercellular communication is crucial to maintain normal functionality. However, even though the biological pathways...
The utility of high-throughput, computational screening has become an invaluable asset to the field of materials science. In the hierarchy of computational methods, the most accurate methods are often the most computationally expensive. However, as both the efficiency and fidelity of numerical techniques advance, high-quality screening of large materials datasets...
Quantum mechanics is increasingly being taught with a spins-first approach where instructors use simple spin systems to introduce the principles of quantum mechanics rather than systems with wavefunctions. One of the defining characteristics of a spins-first approach is that systems studied have discrete bases, whereas systems with wavefunctions have continuous...
Transparent conductive oxides (TCO) are at the forefront of technology with their uses in
touch screen phones and televisions, solar cells and more. Titanium dioxide and tin dioxide are two TCOs that have been studied in depth on their own, so to further explore these TCOs, this project focuses on...
Physicists solve problems and communicate their work using many external representations, such as equations, words, diagrams, graphs, sketches, pictures, and more. To learn physics, then, students must learn to use external representations. In this dissertation, I present three manuscripts. Each manuscript discusses how upper-division Paradigms in Physics students use multiple...
Given the recent advancements in the field of pulsar timing pertaining to the detection of a stochastic gravitational wave background (GWB), it is now the perfect time to perform tests of gravity via exploration of the correlation signature between the timing data of pairs of pulsars induced by the polarization...
The North American Nanohertz Observatory for Gravitational Waves (NANOGrav) is an international collaboration that seeks to use perturbations in the time of arrivals of pulsar signals to detect gravitational waves in the nanohertz range of frequencies. The 15-year data set will be released as of June 2023. It is a...
Crystals are solid materials with periodic and symmetric molecular patterns. The structure of a crystalline solid determines its properties, making it essential to study its structures. From the principle of minimum energy, a crystal will choose a structure with the lowest free energy F = U – TS. At low...
Loop quantum gravity is a theoretical framework which aims to quantize general relativity. One of the unique aspects of this theory is that it imposes a discrete structure on space-time. One toy model of loop quantum gravity is loop quantum cosmology, which maintains the idea of a discrete spatial structure...
Brownian motion is the movement of a particle in a fluid resulting from collisions with surrounding molecules. It has modern applications in simulating fluid dynamics and the motion of proteins in biophysics. Brownian motion simulations generally evolve the initial state by applying Newton’s second law to every particle. These simulations...
Loop quantum gravity is a framework for quantizing general relativity which imposes a discrete structure on space. In exploring the structure of loop quantum gravity, researchers have investigated loop quantum cosmology, a toy model with reduced degrees of freedom while maintaining a discrete space. Polymer quantum mechanics is a framework...
Semiconductors serve an integral role in our technologies today. However, with new advancements in ultra-fast electronics, we are approaching the fundamental speed limits of traditional silicon-based semiconductors. Silicon-based semiconductors typically exhibit photocarrier dynamics in nanosecond timescales. Transition metal dichalcogenides (TMDs) are 2D materials shown to exhibit photocarrier dynamics in picosecond...
Nuclear fusion reactors comprise a significant field of study due to their potential to provide a limitless, clean, and sustainable source of energy. The inertial electrostatic confinement fusor is a type of fusion-generating device that accelerates deuterium gas to the conditions required for fusion. The goal of this research was...
Organic semiconductors are a promising alternative to the traditional inorganic semiconductors, such as silicon. Organics are solution-processable, low-cost, sustainable, and have interesting optoelectronic properties. One such property is the formation of exciton-polaritons, quantum quasi-particles formed by an electron-hole pair in the semiconductor and a photon. This process can be induced...
I examine the strong co-variability between the surface divergence and vorticity and how it varies with latitude in the Pacific Ocean using surface vector winds from reanalysis and satellite scatterometer observations. This analysis was motivated in part by a significant correlation between divergence and vorticity over the global oceans that...
I had to write again. My research lay in science, and it was a science of three parts. The first part made a careful, introductory chapter, begged for by things that were lacking. It summarizes the von Neumann measurement model, derived from the Stern-Gerlach experiment, and it explains how weak...
We present a classical density functional to model the soft, repulsive potential of a Weeks-Chandler-Andersen (WCA) fluid using Soft Fundamental Measure Theory (SFMT) with temperature-dependent parameters inspired by the Barker-Henderson method. Our functional uses soft spheres to model the soft-sphere WCA potential, and gives results that are in good agreement...
I led a collaborative project involving a search for an evidence of a gravitational wave background (GWB) with all the spatial correlations allowed by general metric theories of gravity using NANOGrav’s 12.5 year data set. The search found no substantial evidence in favor of the existence of such correlations.
The...
Freshwater flux from the Greenland Ice Sheet has the capacity to affect regional and global circulation as well as contribute to sea level rise. Outlet glaciers are an important part of this process. They provide pathways for inland glaciers and ice sheets to melt and drain into the surrounding oceans....
With the unique conceptual and mathematical backgrounds of every introductory physics student, there is no way to design a rigid curriculum that anticipates and meets every student’s needs. We can employ machine learning to explore the correlations that exist in the voluminous data from educational settings. That is, institutional, gradebook,...
Computational statistical mechanics leans heavily on the class of Markov Chain Monte Carlo Algorithms. Many such algorithms exist, and simulations can run for several weeks, making the selection of algorithms a difficult, but critical task. In this work, we introduce a benchmark system of two quadratic wells with an analytical...
In this thesis, we explore a general method for constructing path sums in a discrete spacetime using a jump amplitude matrix. This is accomplished by deriving a composition law that relates jump amplitudes to the propagator. Then properties of causal sets are used to average this relationship over sprinklings. This...
Fast neutron detection is important to the detection of illicit nuclear materials and can help prevent those materials from being used or transported without discovery. Previous research has shown that Heavy Oxide Inorganic Scintillator crystals can be used to detect fast neutrons by capitalizing on their high inelastic scattering cross...
By studying gravitational waves, we can gain new insights into the merging events between massive objects such as black holes as well as neutron stars. Moreover, studying low-frequency waves allows us to observe merging events between supermassive black holes at the centers of galaxies, which in turn allows us to...
The North American Nanohertz Observatory for Gravitational Waves (NANOGrav) times periodic signals from pulsars as a method of detecting gravitational waves. NANOGrav detects waves emitted in the nanohertz frequency range, a range lower than those previously explored by other organizations. This allows for the study of rarely observed sources such...
Microtubules (MT) are highly dynamic cylindrical-like structures within cells whose growth is controlled by motor proteins, a class of biological machines that walk along the MT while simultaneously regulating MT growth. Here we are interested in the behavior of kinesin-14 motor proteins. Although processive behavior of kinesin-14 motors has been...
Ice-penetrating radar produces detailed images of the internal ice layers in a glacier. Because the layers form from each year's snowfall, the curving of the internal layers is a record of the climate conditions that the glacier experienced as it flowed throughout the millennia. The Hiawatha Glacier lies on top...
Electron behavior in semiconductor materials critically determines electronic applications. Previous research has shown carrier temperature higher than the lattice temperature of LEDs due to energy differences in the quantum well. Study of these findings requires a novel set-up to dig out weak signal in a thermal-noise filled environment; analytical methods...
Recent observations of tidewater glaciers find that the currently accepted model for predicting ice melt vastly underestimates observed melt rates. The release of pressurized air bubbles into the ocean from pores in the ice is one process that can amplify glacier melt. To incorporate this process into models, we need...
TiO₂ typically crystallizes into three polymorphs: brookite, rutile, and anatase. The phase selection problem in TiO₂ is the lack of understanding what conditions cause amorphous TiO₂ to crystallize into one of its three polymorphs during an annealing process. It has been recently shown that phase selection in TiO₂ is highly...
This thesis conveys the key technical features and scientific applications of a particle-particle ballistic simulation tool (SpaceLab) as well as a high level overview of experiments it was designed for and executed on. SpaceLab simulates spherical particle interactions under any combination of self-gravity, sliding friction, rolling friction, Van-Der-Waals (VDW) cohesion...
Electrostatic gating of nanomaterials allows researchers to control carrier density and shape potential barriers that confine carriers. Lithographic patterning followed by metal deposition is the standard technique to define electrostatic gates; however, the methods of fabricating these devices often involve harsh processing. For example, taking a material to high temperatures...
Organic semiconductors have attracted considerable attention due to their applications in low-cost, solution-processable (opto)electronic devices. An important class of high-performance organic semiconductors is pentacene derivatives, which exhibit high charger carrier mobilities in field-effect transistors and ultrafast singlet fission in photovoltaic devices. These derivatives have served as benchmark materials for systematic...
Taking long-term electrical measurements of a large number of neurons simultaneously is required for many modern neuroscience experiments. However, such experiments are currently limited by the shortcomings of traditional neurosensing technology. For example, there is a significant mechanical mismatch between rigid silicon probes and soft biological tissues. This mismatch can...
At the intersection of basic science research and clinical relevance, cancer metastasis and cell invasion is a multifaceted problem that has been investigated for the past several decades. Importantly, cancer cell plasticity, the ability of a single cell to change its phenotype without genetic mutations in response to environmental cues,...
Gamma Ray Bursts (GRBs) are the most energetic explosions in the Universe, producing up to $\sim10^{53}$ ergs of energy in the first few seconds of their emission -- the so-called prompt phase that is dominated by high energy X-ray and $\gamma$-ray photons. The very large luminosities released in these events...
Fluorescent proteins have emerged as an essential toolset for bioimaging, creating a demand for engineering proteins with new and improved fluorescent properties. In this thesis, I explore the atomistic structure of REX-GECO1, a newly engineered protein biosensor that has unique optical properties. Since this protein has no available crystal structure,...
In this work, we systematically explore the effectiveness of optical aberration correction over a wide range of optical depths using the Segmented and Zernike Polynomial bases. We manufacture a set of 16 optical phantom samples consisting of a clear polyester resin substrate embedded with varying concentrations of aluminum oxide (Al₂O₃)...
Solutions to Einstein's equations are usually found by considering ideal, simplified models. However, if the real world always matched ideal physics models, then farmers would milk black and white spheres. To combat this, Regge calculus was developed as a numerical approximation scheme for general relativity. In Regge calculus curved manifolds...
Organic semiconductors are of interest for (opto)electronic applications due to their low cost, solution processability, and tunable properties. Natural product-derived organic pigments have attracted attention due to their extraordinary environmental stability and unexpectedly good optoelectronic performance, in spite of only partially conjugated molecular structures. Fungi-derived pigments are a naturally sourced,...
Different models show the effects of environmental decoherence on a quantum system
due to various environments of interest. One important quantity within these models is
the decoherence time, which tells us how quickly environments wash away the coherence of
local measurements. We can describe this effect as the quantum system...
The ring disclination is a topological defect that may be suitable for light polarization inside of a nematic liquid crystal. Due to its stability and chirality, the ring disclination could also allow for theoretical applications to quantum and classical field theories as a model for fundamental particles. In order to...
The purpose of this project is to verify scattering mechanisms in semiconductors by measuring transport properties and producing data that reflects existing research. The Hall effect is utilized to measure the resistivity, mobility and charge carrier concentration of the semiconductors: indium tin oxide (ITO), p-type silicon, and n-type silicon. By...
Instance segmentation, the classification and localization of objects in an image, is a problem in cellular biophysics due to the physiological relevance of cell morphology. Particularly, cancer cells migrate in tissue space by changing their body shape similarly to how humans extend their limbs to swim through water. Monitoring such...
A new class at Oregon State, PH 317: Experimental Physics, is designed to simulate a traditional laboratory research experience for undergraduate students. Several weeks of the class is devoted to Brownian motion experiments. Although this is a common topic for undergraduate lab classes, the experiment still needed some basic exploration...
The study of carrier transport in light-emitting diode (LED) has been researched extensively in the past. However, most studies were implementing voltages above the turn-on voltage of the LED. Research on LEDs well below the turn-on voltage threshold is comparatively scarce for good reasons. When the supply voltage is below...
Detecting gravitational waves is a topic at the forefront of physics. The first gravitational wave was detected by LIGO in 2015. This wave had a frequency in the 10s of Hz. This project is focused on detecting gravitational waves on the nanohertz spectrum using a pulsar timing array. This array...