Date of Graduation

5-2022

Document Type

Thesis

Degree Name

Bachelor of Science

Degree Level

Undergraduate

Department

Computer Science and Computer Engineering

Advisor/Mentor

Patitz, Matthew

Committee Member/Reader

Zhang, Lu

Committee Member/Second Reader

Jin, Dong

Abstract

The ability to synthesize custom DNA molecules has led to the feasibility of DNA nanotechnology. Synthesis is time-consuming and expensive, so simulations of proposed DNA designs are necessary. Open-source simulators, such as oxDNA, are available but often difficult to configure and interface with. Packages such as oxdna-tile-binding pro- vide an interface for oxDNA which allows for the ability to create scripts that automate the configuration process. This project works to improve the scripts in oxdna-tile-binding to improve integration with job scheduling systems commonly used in high-performance computing environments, improve ease-of-use and consistency within the scripts compos- ing oxdna-tile-binding, and move the oxdna-tile-binding source repository to GitHub for improved distribution.

Keywords

DNA, nanotechnology, oxDNA, simulation

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