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,...
Motivated by the Navier-Stokes equations, which are a set of unsolved equations related to fluid motion in R^3, we explored the incompressibility condition and the Neumann boundary problem. After exploring, we noticed that using iterated Riesz transforms of the boundary data could be used to get information about the velocity...
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...
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...
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...
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...
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...
Currently multi-canonical, and grand canonical Monte Carlo simulations exist, but do not always give all of the necessary information of the system. When using a 1-D (only changing in one variable) broad histogram Monte Carlo method a user would need to run a range of simulations in order to get...
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...
Multivariable functions permeate physics, mathematics, and other sciences. Understanding how quantities in multivariable relationships change together – or co-vary – is important for studying physical systems. In this project, we asked junior-level physics majors to describe the covariation of quantities in a multivariable context given a 2D graph. We identified...
The ability to focus light through strongly scattering materials is opening up exciting new avenues in many fields, such as optics, computer vision, biology, and medicine, which utilize light delivery and imaging techniques. Efficient, high resolution wavefront shaping and optimization methods are crucial to enabling this new capability.
In this...
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...
Plasmon induced transparency (PIT) describes a spectral response of coupled plasmonic resonators in that coupling between bright and dark modes leads to a destructive interference resulting in a narrow transparency window. This process has many applications in material characterization and advanced optical devices such as slow light devices or ultrafast...
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...
Past studies have shown that students struggle with main concepts of potential energy, such as reading graphs, understanding that potential energy can be negative, and, most pertinent to this research project, connecting potential energy to force. I designed an activity to help introductory physics students address these struggles. The activity...
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...
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...
The thermal cross sections and resonance integrals for neutron capture by ⁷⁴,⁷⁸,⁸⁰,⁸²Se were measured using the same procedure and equipment for all of the isotopes. Uncertainty and absence of accurate previous values for several isotopes introduces a need of measuring these parameters using similar techniques. This was done using OSU’s...
Organic photovoltaics are being explored as the next generation material for semiconducting and optoelectronic devices but are limited by their stability and efficiency. One new candidate is crystallized Anthradithiophene (ADT), which is a promising photo-voltaic material due to its high quantum yield and adjustable side groups. The side derivatives TES-F,...
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 optical transition in high-fraction polymorphs of titania (TiO2) were investigated to determine the band gap behavior of the most common polymorphs—brookite, rutile, and anatase—the values of which are varied in the literature. The direct optical band gaps of brookite, rutile, and anatase, were determined to be 3.37(7)eV, 3.41(11)eV and...
The response of cells to periodic driving is important for many biological processes, particularly blood flow and heart functioning. Our research analyzes the collective shear stress response of fibroblast cells due to a periodic driving frequency. When cells experience shear stress, they release calcium into the cytosol. To quantify the...
Semiconducting materials are of immense importance due to their presence in almost all modern devices. It is possible that the surface physics of semiconductors could be used to control the nanoscale topography and properties of these materials, ultimately creating new options for device fabrication. This could result in profound implications...
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...
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 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...
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...
We computationally modeled protostellar star-disk systems with star to disk mass ratio of 10. Our computational models looked at the development of density perturbations in these systems for different geometries of the system. The ratio of the star’s height and radius (rₚ/rₑ) is varied between 0.1746 and 0.88095. We modeled...
Understanding charge transfer in organic semiconductors is important for developing devices like organic light emitting diodes and flexible electronics. Optical tweezers have been used in many disciplines for trapping, manipulating, and analyzing microscopic objects such as microspheres, micro-organisms, and other colloidal particles. Using optical tweezers, studies have measured the average...
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...
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...
Chain rules are critical to the process of solving many thermodynamics-related partial derivatives. This study evaluates the solution method and error evolution of students’ responses to a pair of chain rule problems in an upper-level undergraduate thermodynamics course. Students’ responses were categorized by solution method. Students’ solution methods included implicit...
Organic aggregates and transparent amorphous metals are transforming opto-electronic devices such as highly efficiency solar cells and flexible displays. We present a fundamental optical study of how local morphology critically impacts the device performance of both stacked, conjugated organics and In-Ga-Zn-O (IGZO) transparent metallic materials. Derivatives of anthradithiophene (ADT): ADTTES-F,...
In recent decades, the cell phone has provided a convenient form of long-distance communi-cation to the general public. Despite the technological improvements since, cell phones and their smartphone successors have suffered from a lack of clarity over a typical voice call, a result of their limited bandwidth. New phone services,...
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...
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...
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...
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...
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...
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...
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...
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....
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...
High field time-domain terahertz spectroscopy (TDS) is used to determine the time dependent transmission and the time-delay and optical-power dependent conductivity of a wafer of gallium arsenide (GaAs). Gallium arsenide is a direct band-gap semiconductor and has potential as a computer processor component. Analysis of the transmission of terahertz (THz)...
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 Laser Gravitational Wave Observatory, or LIGO, is built to observe gravitational waves as they propagate through space. Advanced LIGO is extremely sensitive
to movements of the test mass as small as 10⁻²¹ m/√Hz , which allows many signals other
than gravitational waves to be detected by the system. Pressure...
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...
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...
When a star dies in a supernova, its constituent particles are torn apart and a gaseous cloud of atoms remains. These atoms may eventually condense again into large bodies such as planets and stars. There are three main theories as to how this happens: classical, kinetic, and non-local thermodynamic equilibrium...
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...
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...
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...
An experimental apparatus is modified to allow measurements of the Seebeck coefficient and resistivity to be taken simultaneously. This apparatus is designed for bulk and thin film samples between temperatures of 10 K and 300 K. The apparatus is constructed such that these simultaneous measurements do not interfere with each...
The current model for gamma ray bursts (GRBs) assumes that internal shocks are responsible for the emission of gamma-rays. Internal shocks occur when the fast expanding shell collides with the slowly expanding shells. The light curve of a GRB depends on the initial state and the expanding speed of the...
The scattering of optical rays by small spherical particles bears a strong resemblance to the
diffusion of fission neutrons in solid materials. This work explores the feasibility of
exploiting similarities between these two systems for the purposes of reactor component analysis, education, and outreach. After a brief overview of reactor-environment...
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...
We construct the contact value approximation (CVA) for the pair distribution function,
g(²)(r₁, r₂), for an inhomogeneous hard sphere fluid. The CVA is an average of two radial
distribution functions, which each take as input the distance between the particles, |r₂ −r₁|,
and the average value of the radial distribution...
Zinc sulfide thin films on silicon wafers were analyzed for layer thickness, refractive index, and absorption using reflection spectroscopy (RS), spectroscopic ellipsometry (SE), and modeling programs. RS and refractive index values from literature were used to model film thickness based on reflection and the SCOUT modeling program was used to...
The Min protein system in Escherichia coli helps the cell division process by identifying the center of the cell [1, 7]. This system has been modeled succesfully computationally under standard conditions. There has been recent experimental interest in the cell division process for significantly perturbed cell shapes. We take the...
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...
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...
High resolution images of a dim companion in a binary star system can be obtained using a Digital Micromirror Array (DMA) as an optical mask. Imaging can be problematic because the intense light from the main star can saturate the detector and leave the companion unnoticed. Placement of the DMA...
This thesis presents a measurement of the resonance integral and thermal cross section – which together represent the total neutron absorption cross section – of the naturally occurring isotopes of platinum that emit gamma radiation upon neutron absorption. The measurements were made via neutron activation analysis. Platinum samples were bombarded...
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...
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...