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
Zhang, Lu
Second Committee Member
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
Citation
Threlfall, K. (2022). A Versatile Python Package for Simulating DNA Nanostructures with oxDNA. Computer Science and Computer Engineering Undergraduate Honors Theses Retrieved from https://scholarworks.uark.edu/csceuht/99
Included in
Computer and Systems Architecture Commons, Molecular, Cellular, and Tissue Engineering Commons, Nanoscience and Nanotechnology Commons, Numerical Analysis and Scientific Computing Commons
