Date of Graduation


Document Type


Degree Name

Bachelor of Science


Computer Science and Computer Engineering


Patitz, Matthew

Committee Member/Reader

Zhang, Lu

Committee Member/Second Reader

Jin, Dong


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.


DNA, nanotechnology, oxDNA, simulation