Physics Senior Integrated Projects

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This collection includes Senior Integrated Projects (SIPs, formerly known as Senior Individualized Projects) completed in the Physics Department. Abstracts are generally available to the public, but PDF files are available only to current Kalamazoo College students, faculty, and staff. If you are not a current K College student, faculty, or staff member, email us at to request access to this material.


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Now showing 1 - 5 of 335
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    Alternative Methods for Ultrasonic Welding of Advanced Thermoplastic Composites
    (2022-11-01) Carman, Vaughn A.; Short, Matt; Askew, Thomas R., 1955-
    The fusion bonding of advanced thermoplastic composites has a variety of applications in aerospace, automotive, medical, consumer electronics and energy markets. High-power ultrasonic welding is a state-of-the-art manufacturing process being used to join these materials. This welding process uses high frequency, moderate force, and low amplitude mechanical vibrations to generate heat. When adequate temperatures are reached at the weld interface, localized melting occurs and upon cooling, an intermolecular bond is formed between the materials. It is the viscoelastic nature of polymers that facilitates heating, enabling the bonding process. This project was done in collaboration with Agile Ultrasonics Corp, an American company based out of Hilliard, OH. Agile entered the industry in 2017, specializing in the joining and consolidation of thermoplastic materials, including carbon-fiber-reinforced polymers (specifically: PEEK - Polyether ether ketone, PAEK - Polyaryletherketone, PEKK - Polyetherketoneketone, PPS - Polyphenylene sulfide) [1]. Agile collaborates with industry-leading manufacturers of aerospace and consumer electronic components on a variety of system design projects. They have been developing a unique process that continuously joins fiber reinforced thermoplastic tape, braid, or pre-consolidated plate materials. One of the primary objectives of this project is to help refine this process and make it more robust. The majority of the content in this report focuses on investigating anvil materials with properties that can improve the quality of the scan welds being produced by Agile. More specifically, this project investigates the effect that the elastic modulus within compliant anvil materials has on the amount of heat being generated at the weld joint. The first section will focus on background information, and the following two will go into the work that was performed and the test results. Data was collected on various materials and a variety of tests were designed and performed to find an array of compliant substrates that can be used by Agile.
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    Utilizing Combined Point Array’s in Hepatitis B Virus Drug-Bound State Investigative Research
    (2022-11-01) Phillips, Mary; Wilson, David
    Viruses attach to a host cell by administering a molecular hijacking and in turn, replicating the genetic material enveloped within their capsid shells to spread viral particles. Viruses are complex in nature, coming in a multitude of different shapes and sizes. A promising feature of spherically shaped viruses like the Hepatitis B virus, is that they orient themselves to a set of distinct points called point array’s. A virus's genetic material is positioned at multiple radial levels within an icosahedral capsid. Point array’s give the geometric constraints that viruses with spherical icosahedral symmetry adhere to. By combining a virus’s network of best fitting point arrays, meaning the arrays that are the smallest distance away from capsid protrusions, we are able to compare the mechanism of the assembly and disassembly of viral capsid formations and essentially capsid stability. Within this study, a combined point array analysis was applied to the two strains of the Hepatitis B virus and five separate drugs that cause the mis-assembly and distortion of Hepatitis B virus capsids. The most significant locations on these drugs were identified in an analysis where specific amino acid sequencing at these locations were identified and compared. The results showed the most prominent locations in which HBV is dismantled and the capsid is changed after the drugs have induced mis-assembly. These locations were then compared to the ADYW strain of the HBV for similarities and differences in the virion capsid structure.
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    Engineering a Rotating Sample Cell for Ultrafast Two-Dimensional Electronic Spectroscopy
    (2021-11-01) Wade, Carter E.; Cole, Arthur; Ogilvie, Jennifer P.
    Two-dimensional electronic spectroscopy (2DES) is a collection of techniques that allow us to track energy and charge transfer by exciting pigments with lasers and tracking the frequencies emitted following a range of delay times. While working with the Ogilvie Group at the University of Michigan’s physics REU, I was tasked with developing a rotating sample cell to prevent the same area of sample from being targeted twice in a row. In this paper, I discuss the techniques and advantages of 2DES, the limitations that we still face which motivated my work, and the development of my Rotating Sample Cell.
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    Surveying Features of Spherical Viruses
    (2023-01-01) Orosan-White, Gabe; Wilson, David
    The main research goal was to investigate the relationship between gauge points and other capsid properties. Data was collected from online databases: ViperDB (VIrus Particle ExploreR database), RCSB (Research Collaboratory for Structural Bioinformatics), and SCOP (Structural Classification of Proteins). I wrote code to streamline and automate this process, analyze capsid data, and compile a database, then I made a website to visualize the results. Dr. Wilson already had a MatLab script called SC_frankencode.m (which I will refer to as GP.m) to find gauge points given a capsid’s PDB (Protein Data Bank) coordinates from ViperDB, so I wrote scripts to perform other analysis on PDB and point array files. The first thing I worked on was developing a script called to detect which amino acids were nearby (<5Å) each point in a given point array and write the results to an Excel file. I then made a shell script to loop over a folder of point arrays and later used pyinstaller to create an executable of the Python script, as well as a corresponding adapted PA-folder script. Next I created a pipeline that downloaded all of the capsid coordinate files from ViperDB and performed all the steps involved in collecting the gauge point and amino acid data. This consisted of: creating a list of all PDB IDs using the API, downloading each of their coordinate files, running to create the full capsid of the AU in the coordinate file, to get the XYZ coordinates, to load the capsid, my version of GP.m which writes the output to an Excel file (along with the points of the 5 closest Point Arrays to protrusions), and on each point array. This produced ~1,200 Excel files (available here - full_*.xlsx files contain amino acid data, others contain gauge point data). I made an iPython notebook file called xlfiles_json.ipynb to compile a database with the results, additional data from scraping SCOP, RCSB, and ViperDB, and the output of some other analysis scripts (detailed in the data section below). The last stage of my work has been focused on making a website where you can search, filter, and create visualizations for information stored in the database.
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    Synthesis & Characterization of Entropy Stabilized YBCO Superconductors
    (2023-01-01) Wennen, Elias; Need, Ryan; Raghavan, Aditya
    The nuanced causes of the ability of certain materials to obtain superconductivity, or zero resistance, are still a topic of debate. To further developments in this area of study, the synthesis and characterization of novel superconducting materials is essential. A relatively young method in materials science, entropy stabilization dopes lattice sites of a crystalline structure, which produces a large amount of electromagnetic and configurational disorder. This method has not been applied to the YBa2Cu3O7−δ (YBCO) superconductor, a well studied, high temperature, superconducting cuprate. In this paper, we present data gathered from entropy stabilized samples of YBCO using X-ray diffraction, and electrical transport. Expected results were found for Series A, whereas difficulties in finding a temperature entropy dominant Gibbs free energy for Series B led to phase impurities and insulating behaviors.
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