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
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
