Date of Graduation

8-2023

Document Type

Thesis

Degree Name

Bachelor of Science in Computer Science

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

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