Dynein is a motor protein which transports cargo along tracks inside the cell. Like related motor proteins kinesin and myosin, dynein uses cellular energy to take steps with its two foot domains. Unlike kinesin or myosin, dynein’s stepping pattern is highly varied: it can take steps between zero and 60nm...
The dynein molecule is a peculiar motor protein recognized for its unique stepping behavior. Sometimes it steps forwards. Other times it steps backwards. It has even been observed to occasionally shuffle by beginning a step with the same domain many times in row. These motions make dynein an interesting object...
A recent article by Cozzi and Kelliher [3] has demonstrated a sense of "locality" to the incompressible Euler equations which mirrors physical fluid behavior. We further develop the corresponding notion of "damping," and identify both temporal and local damping behaviors. To represent this problem, we perturb the initial condition of...
Since the advent of graphene, research on 2D materials has exploded. Countless experiments have uncovered novel properties that emerge when different layered crystals are cleaved down to only a few atomic layers in thickness. The most popular of these non-graphene 2D materials is MoS2, a semiconductor which has been of...
By alloying face centered cubic CaSe with orthorhombic SnSe, we created the heterostructural alloy
Sn1-xCaxSe. The phase separated lms created with a high deposition temperature acted as highly crys-
talline SnSe while the low deposition temperature lms acted as a mix of SnSe and CaSe. For the alloyed
lms we...
This investigation expands on earlier methods of using surface polarization reflection (SPR) to characterize the first few monolayers of a surface. Past research measured intensities of light reflecting off an SiO₂ optical flat inside a vacuum. Pressure of applied gas was changed to view a change in reflection. In an...
We examine a discrete-time quantum walk with two-step memory for a particle on a one-
dimensional infinite space. The walk is defined with a four-state memory space analogous to the
two-state coin space commonly used in discrete time quantum walks, and a method is presented
for calculating the time evolution...
Using a plastic bottle, we explore the capabilities of a reflective phase-only Spatial Light Modulator (SLM) in removing wavefront aberrations using a Zernike polynomial phase mask, with the modulators phase depth limited to 0.8π radians. Wavefront aberrations, which can be modeled with Zernike polynomials, distort image transmission through various optical...
Terahertz (THz) spectroscopy is a great tool not only to study fundamental physical processes such as many-body Coulomb interaction but also to develop ultrafast electronic devices. More specifically, intense THz fields interacting with semiconductors have exhibited strong nonlinear effect involving extreme carrier dynamics. In this experiment, intense THz radiation was...
Metal organic frameworks(MOFs) are a class of crystalline materials utilized in gas storage, chemicalsensing, and other engineering applications. Recently chemists have begun synthesizing MOFs withmoving parts in order to further these applications. A wide array of dynamic MOFs have been created andtheorized. Among them is the interlocking of a ring...
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 construct and examine the properties of Lie and Clifford algebras which are used to describe certain types of particles. These algebras are then related to the traditional theory of division algebras. Quaternions are applied to these algebras and their properties are exploited to model physical properties of particles. The...
I investigate the feasibility of a micron-sized biosensor designed to measure neural activity. The circuitry of the biosensor is composed of graphene, some photodiodes, and a light-emitting diode. Many of these biosensors would be injected into a subject’s brain, and when powered by near-infrared light, they would glow in response...
An apparatus and method for calibrating planar laser induced fluorescence using a two-dye, two-color method was developed. A laser sheet was expanded from a 473 nm laser to excite dye solutions into higher energy states then fluoresced through spontaneous emission. The two fluorescent dyes selected for research and development were...
The motor protein dynein is responsible for cellular processes such as axonal transport and cell division by delivering vital information along the microtubule track. A failed delivery can cause severe damage to the cell’s functionality and lead to neurological diseases. Despite dynein’s rich history in cellular research, the mechanism of...
The calculation of interplanetary trajectories is a numeric problem which requires a high degree
of precision for the results to be accurate. A computer program was written for this project which
uses leapfrog integration combined with Newton’s method of iterative root finding to find ideal
interplanetary trajectories. Reasonable initial conditions...
Carbon nanotubes are the subject of intense interest in virtually every field, from medicine to
nano-scale electrical components. Multi-walled nanotubes exhibit a strong nonlinear response
to high-field strength terahertz radiation. This research uses terahertz pulses with field strength
exceeding 1 MV/cm generated by means of optical rectification utilizing a lithium...
Exciton-polaritons are a form of light-matter coupling that have potential applications as photonic transistors and logic gates. In order for a photonic transistor or logic gate to be integrated with room temperature fiber-optic technology, excitons-polaritons need to be stable at room temperature and compatible with the red and near-infrared wavelengths...
A method for determining bandgap energy using diffuse reflection is presented. The method uses bifurcated fiber optic cables to measure the diffuse reflection of diffusely reflective materials. The absorption spectrum is extrapolated from the diffuse reflection spectrum and used to determine the bandgap of powdered materials. The theory of nonspecular...
A great variety of topologically protected defects exist in ordinary and exotic states of matter. Some of them are promising candidates for technological applications such as magnetic memory or quantum computers. Others possess some properties of elementary particles that could lead to potential applications in quantum fields. Nematic liquid crystals...
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...
This research investigates the electronic properties of a fungi-derived pigment, xylindein
as a novel sustainable material for organic electronics. Xylindein molecules were characterized in solution and in film. Absorption spectra and (photo)luminescence spectra were
taken at various excitation wavelengths. Xylindein’s molecular properties were computed
with the Gaussian 09 software suite....
The electrical properties of amorphous and crystalline titanium dioxide polymorphs are reported. Titanium dioxide is a widely used transparent semiconductor and it is a useful oxide model. Using variable temperature transport measurements of thin films, it was possible to establish the activation energy barrier for conduction. This was accomplished using...
Crystal morphology and dimensionality of single-crystal semiconducting materials can have dramatic effects on the optical and electrical properties. Organic photovoltaic (OPV) materials and fluorinated graphene folds are two materials that show these dependencies. Anthradithiophene (ADT), is an OPV that can be functionalized with different side groups to form different crystal...
Many biological processes are regulated by the presence and movement of cellular Ca²⁺ ions. The concentration of Ca²⁺ in a cellular environment is regulated by IP₃ sensitive channels that lie on the surface of a cell’s endoplasmic reticulum. Little is known about the macroscopic effects of intracellular Ca²⁺ activity, so...
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...
The relationship between the index of refraction and the porosity of a material is that the index decreases with respect to the porosity. This property can be used to change the index of refraction of films which allows control of the reflection of the material. This is important because being...
Current methods in traction force analysis rely on a homogeneous extra-cellular matrix and
embedded microbeads to track deformations. The efficacy of these methods decreases when the matrix is not homogeneous. In heterogeneous matrices, beads often aggregate in regions of higher matrix density and float in regions where matrix substrate is...
Quantum yield is an important, characteristic quantity to be measured for fluorescent compounds. Here, a comparative method between fluorescent compounds in solution is applied to measure unknown quantum yields. An absorption spectrometer was used to measure the absorbances of two different fluorescent quantum yield standards. The integrated fluorescence intensities were...
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...
Terahertz (THz) frequencies of the electromagnetic spectrum have been underutilized when compared to neighboring microwave and infrared frequencies, largely due to the difficulties controlling and detecting these fields. In a step toward gaining control over THz frequencies, my advisor Dr. Yun-Shik Lee’s group experimentally demonstrated optical-pulse THz-control over a plasmonic...
We developed an integration-based line detection algorithm. Existing line detection methods such as the Hough Transformation (HT) and its variants are insensitive to image noise. The reason is that HT finds lines by calculating the gradient of the image and assumes that the region where the gradient is the steepest...
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,...
Using a simple dry transfer process, I construct and characterize three nanoscale MoS2 devices using current-voltage curves, Raman spectroscopy, optical and atomic force microscopy. I compare these devices, the thinnest of which was few layer ( ≤ 10 nm) MoS₂ capable of showing photoconductance, with a current whose magnitude is...
The neutron capture cross sections of ¹⁰⁶Cd, ¹⁰⁸Cd, ¹¹⁰Cd, ¹¹²Cd, ¹¹⁴Cd and ¹¹⁶Cd
were determined in the present project. Four different OSU TRIGA reactor facilities were
used to produce redundancy in the results and to measure the thermal cross section and
resonance integral separately. When the present values were compared...
Organic semiconducting materials have emerged in the last few decades as viable alternatives to inorganics in broad applications from field effect transistors to LEDs to solar cells. Organics provide many benefits over inorganics such as flexibility, sustainability, and reduced cost. However, these materials are more susceptible to degradation in the...
Terahertz (THz) time-domain spectroscopy provides insight into electron dynamics in semiconductor heterostructures. High-field THz spectroscopy probes the excitonic nonlinear response of GaAs quantum well (QW) systems and enables the measurement of its coherent dynamics in the time-domain. Consequently, THz spectroscopy allows one to explore the fundamental properties of many-body interactions...
The equation of state for a fluid described by the Weeks-Chandler-Andersen (WCA) potential was solved to determine at what pressures and temperatures the fluid will theoretically freeze. A Monte Carlo (MC) algorithm was used to sample a system of 256 spheres for a set of thermodynamic averages to locate and...
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...
Type I collagen fibers, the connective tissue that makes up the human breast, can be easily manipulated by cells or other outside factors. In previous studies, the alignment of collagen has been associated with the beginning of metastatic cancer, possibly influencing cancerous cells to migrate from the tumor. In this...
This study used SCOUT optical modelling software to create models of the reflectance and transmittance spectra generated by mixtures of titanium dioxide (TiO2) and tin oxide (SnO2). These models enabled identification of how altering the ratio of a mixture changes the optical response. By being able to identify how altering...
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Figure 4. The imaginary part k of the index of refraction for the rutile and anatase polymorphs
Gamma ray bursts are some of the brightest events in the entire observable universe. Since the late 1960’s, thousands of gamma ray bursts have been observed and they have been researched extensively. However, there are still many mysteries which remain unsolved. One such mystery is whether or not the viewing...
Exciton polaritons are quasiparticles composed of a quantum superposition of matter and light states that arises from the coupling of a standing wave photon and an exciton. This research has two primary objectives: to design and fabricate a Fabry-Perot microcavity system in which to produce exciton polaritons; and to show...
In industry, there is considerable interest in finding sustainable, renewable materials for use in electronic devices. Pigments derived from spalting fungi are of particular interest due to their longevity in diverse environmental conditions. The focus of my project was to characterizethe properties of a novel, fungi-derived pigment, and to discover...
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...
Microelectrode array (MEA) dissolved-oxygen (DO) sensors were built and electrochemically tested in a solution of potassium ferricyanide. MEAs are becoming more popular as DO sensors because of their small size and capacity for simultaneous measurements with multiple recording sites. The ability to measure DO with multiple recording sites is useful...
We construct a Monte Carlo simulation in Python to calculate optical flashes at 5x10¹⁴ Hz peaking at 6x10³¹ erg s⁻¹Hz⁻¹St⁻¹ due to synchrotron radiation from the reverse shock of a gamma-ray burst’s jet. While analytical solutions to this problem exist, they rely on sweeping simplifications of what is necessarily a...
In this paper I present the results of Monte Carlo simulations for a soft sphere fluid with a Weeks-Chandler-Anderson (WCA) pair potential. The results are compared to Soft Fundamental Measure Theory (SFMT) results obtained by our research group. One of the research group’s goals was to show that our SFMT...
We measure the charging and discharging of two organic materials, PCBM and ADT-TES-F. These materials are studied through the noncontact method of particle trapping known as Optical Tweezers, where an IR laser is used to constrain the motion of a coated or noncoated silica sphere while its positional data is...
Impedance spectroscopy is a method of modeling materials with equivalent circuits to determine electrical properties, such as the resistivity and the dielectric constant. We explore impedance spectroscopy, both theoretically and experimentally through applying the method to samples of BaCuS1-xSexF. Grain boundary effects were dominant in the results, and although they...
This research specifically examines the collective motion of populations of MDA-MB-231 breast cancer cells under the influence of a chemo-attractant gradient. Their motion is compared to the mathematical model of a persistent random walk, measuring the persistence bias of the cells from their autocorrelation function and applying to the mean...
Spectroscopic ellipsometry (SE) is used to characterize amorphous and crystalline thin films of TiO2. Amorphous precursor films of TiO2 are deposited by radio frequency magnetron sputtering on fused silica and silicon substrates. Annealing the amorphous precursor films induces them to crystallize into either pure or mixed phases of the three...
Dynein is a motor protein which transports cargo along tracks inside the cell. Like related motor proteins kinesin and myosin, dynein uses cellular energy to take steps with its two foot domains. Unlike kinesin or myosin, dynein’s stepping pattern is highly varied: it can take steps between zero and 60nm...
Optical trapping is a tool used throughout a wide variety of disciplines rang- ing from precisely probing and manipulating sub-micron organisms in biol- ogy to analyzing fundamental charge transfer in colloidal physics. This thesis presents research involving optical tweezer force measurements of polystyrene and silica microspheres. In addition, preliminary work...
Hall measurements can be made on the unstudied alloy, Sn₁-ₓCaₓSe to determine its electrical transport properties. The Sn₁-ₓCaₓSe samples were made by laser deposition into thin films and have a variable of calcium concentration x. These samples are approximately 250 nm in thickness, were grown at 366° C and are...
The standard model (SM) of particle physics describes many of the experimentally observed subatomic particle interactions. However, there are a few discrepancies with the SM namely: matter/antimatter asymmetry and dark energy. A current extension of the SM allows for small amounts of Lorentz Violation to fix these discrepancies. Lorentz Violating...
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...
A flipped classroom provides students with course content in the form of videos, readings, and/or simulations that they complete during the time traditionally used for homework assignments while in-class time is devoted to hands-on group learning activities. Project BoxSand is gathering quantitative data on how students in a flipped classroom,...
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...
Average monthly temperatures (maximum and minimum) and precipitation patterns are expected to change as a direct consequence of anthropogenic climate change. Temperatures are expected to be warmer in the future but precise estimates vary depending on factors like number of ensembles and emission scenario. For this study, we used 100...
In 1877 John Kerr described an experiment that demonstrated a quadratic change in refractive index in a plate glass placed in a strong external electric field. This results in a nonlinear relationship between the average electric polarization within the materials and the intensity of the applied electric field. This opened...