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 dspace@kzoo.edu to request access to this material.
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Item A Spectrum Analysis of Hepatitis B Virus Strain and Drug Bound State Variances(2023-11-01) Major, Samantha; Wilson, DavidThe purpose of this research was to perform an icosahedral point array spectrum analysis on the two strains and five CPAM drug bound states of the hepatitis B virus (HBV) capsids to determine possible key structural points of the viral capsid. This project serves to further the research towards the prevention and disruption of HBV infection. This research has been done using ViperDB coordinates of each structure, VMD to visualize differences between structures and unique features of the HBV capsids, Matlab to analyze point array data for each structure and determine the fitness of each point array, and analysis using code created by Gabe Orosan-Weine (K’23) to determine the closest amino acids to each point in each point array. This data was all analyzed for each structure and compared to determine differences that may be caused by each drug and similarities that may indicate necessary features of the viral capsid. These methods produced data that suggests that point arrays 3, 4, 6, 20, 52, 53, and 54 have a high fitness for most, if not all, structures studied, meaning that the points in these arrays likely fall near key structural features of the capsid. It also showed that certain amino acids are repeatedly close to said points, implicating a probable importance to chain and capsid stability. These results provide potential targets for engineered mutations, structural changes, or other changes to the viral capsid that can disrupt or prevent viral infection of HBV.Item Elucidating the Correlation Between Pre-Ictal EEG Spikes and Calcium Dynamics in the Pedunculopontine Nucleus (PPN) Through Fiber Photometry in SCN1A Mutant Mice Subjected to Hyperthermia-Induced Seizures(2024-03-01) Akhavan Tafti, Shahriar; Erdi, Peter; Mattis, JoannaThis study investigates the involvement of the pedunculopontine nucleus (PPN) in seizure pathways using a combination of GCaMP7s Viral Injections, alongside 2-photon calcium imaging and EEG recordings, within SCN1A+/- mice models. Seizures were induced through both hyperthermia and Kainic Acid injection to simulate clinical scenarios closely associated with epilepsy, particularly Dravet Syndrome. The results demonstrated a significant correlation between calcium activity within neuronal populations and EEG-detected pre-ictal spikes, suggesting a critical role for the PPN in the initiation and propagation of seizure activity. This correlation was evident across different seizure induction methods, indicating a robust association. This study provides compelling evidence that the PPN is intricately involved in seizure mechanisms, marking it as a potential target for future therapeutic interventions aimed at modulating epileptic activity. The integration of advanced imaging techniques presents a novel approach to understanding the complex neural networks underlying epilepsy, offering new insights into potential pathways for therapeutic development.Item Locating and Predicting Ligand-Binding Epitope Regions on the Enterovirus Genus with Icosahedral Point Array Asymmetric Units(2024-06-01) Blanzy, Preston T.; Wilson, DavidVirus capsids are comprised of many copies of one or several different types of capsid protein subunits. Its function is to protect the viral genetic material located within, as well as provide aid to host cell attachment. Typically, virus capsid structure can be separated by having helical or icosahedral symmetry. Icosahedral capsids describe roughly 50% of virus families, their structure is described by 20 equilateral triangular faces, 30 edges, and 12 vertices. Viruses that pertain to this form of symmetry can be classified via Triangulation Number; a method that focuses on the arrangement of protein subunits that form the capsid. T-Number Classification leads to the use of point arrays, which provide specific geometric constraints on a viruses capsid and genetic material. This modified fitting method uses gauge points to determine the overall radial scaling, which are located on the symmetrical axes of asymmetric units. This method indicates geometric locations where viruses can be modified with care, and locations where modifications are relatively easy to perform. Antivirals and vaccines can use the information given through these point arrays to find target sites to inhibit viruses from infecting the host and fully maturing. By using the best fitting point arrays for native virus capsids, radially increasing the scaling of these PAs was hypothesized to be able to describe ligand-binding epitope regions on the capsid. Native capsids for the enterovirus genus were analyzed, then compared to their virus with its receptor bound complexed to it. The algorithms used for this method were able to locate these regions on pre-complexed viruses, verifying that point arrays are a valuable method for future research in this field.Item Engineering a Custom Car Hauler : The Benefits of Computer-Assisted Design and Finite Element Analysis(2023-09-01) Beurkens, Jonah; Beurkens, Caden; Askew, Thomas R., 1955-The design and manufacture of robust and reliable vehicles is a challenge that requires an interdisciplinary approach including mechanical analysis, materials science, and advanced simulation tools. In this research, I delineate the process of engineering the truck bed and ramps for a custom ramp truck built on a 1998 Ford E-350 Cab and Chassis. I consider a combination of mechanical and economic factors such as cost, weight, yield strength, and loading conditions to determine the most effective materials to use. Then, I employ industry-standard Computer Assisted Design (CAD) and Finite Element Analysis (FEA) software to model the proposed vehicle components and simulate their behavior under desired load conditions. Through an iterative calculation- and simulation-based process, I develop an economical, safe, and reliable design that is ready for manufacture. Insights gained from this process highlight the importance of a multifaceted approach to vehicle engineering, as well as illustrate the pivotal role of advanced simulation tools in improving and validating potential designs.Item Charge Order in the Blume-Capel Model on a Triangular Lattice(Kalamazoo, Mich. : Kalamazoo College., 2024-03-01) Nelson, Matthew; Scalettar, Richard; Tobochnik, Jan, 1953-To better understand the onset of charge ordering in high-temperature superconductors, we perform Monte Carlo simulations using the Blume-Capel model on a 2D triangular lattice. By working in the canonical and grand canonical ensemble, we identify transitions in both charge and spin ordering on the lattice. To aid in this process we introduce several new measurements focused on identifying loops of spin or charge. We also make modifications to the Binder cumulant to make it applicable to the model.