Date of Graduation
8-2023
Document Type
Thesis
Degree Name
Bachelor of Science in Computer Science
Degree Level
Undergraduate
Department
Computer Science and Computer Engineering
Advisor/Mentor
Patitz, Matthew
Committee Member/Reader
Gauch, Susan
Committee Member/Second Reader
Gauch, John
Committee Member/Third Reader
Le, Thi Hoang Ngan
Committee Member/Fourth Reader
Nakarmi, Ukash
Abstract
Though still in its infancy, the design of DNA crisscross slats presents great potential in the algorithmic self-assembly of DNA. The provision for higher levels of cooperativity allows for fewer errors through the natural proofreading of slat placement, leading to more robust assembly. Highly accurate simulations of self-assembling DNA squares have been achieved by following the kinetic Tile Assembly Model. Building on that foundation, this study seeks to calibrate the system parameters of a kinetic simulator for self-assembling DNA slats to match experimental results and to use those ranges of parameters to perform exploratory simulations of systems not yet tested in a lab setting. Novel systems include those with fewer unique slat types to analyze the trade-off between growth rate and accuracy of each assembly.
Keywords
DNA; Self-assembly; Algorithm; Slat; Kinetic; Simulation
Citation
Vaughan, L., & Fleming, H. J. (2023). Simulation and Analysis of Self-Assembling Slat-Based DNA Ribbons. Computer Science and Computer Engineering Undergraduate Honors Theses Retrieved from https://scholarworks.uark.edu/csceuht/120