10.6084/m9.figshare.11805963.v1 Tural Aksel Tural Aksel Nick Fong Nick Fong Christopher Maffeo Christopher Maffeo Aleksei Aksimentiev Aleksei Aksimentiev Shawn Douglas Shawn Douglas SI2:SSE: Collaborative Research: Integrated Tools for DNA Nanostructure Design and Simulation figshare 2020 NSF-CSSI-2020-Talk DNA origami Biophysics Simulation and Modelling Nanotechnology not elsewhere classified 2020-02-05 06:09:35 Presentation https://figshare.com/articles/presentation/SI2_SSE_Collaborative_Research_Integrated_Tools_for_DNA_Nanostructure_Design_and_Simulation/11805963 While the robustness of the DNA origami method has enabled researchers to fabricate a large diversity of shapes, many design choices are made according to <i>ad hoc</i> rules and heuristics derived from limited empirical data. It would be beneficial to establish a quantitative physical basis for favoring one strand routing over another for a given shape. With these goals in mind, we have developed Cadnano Toolkit (<b>CTK</b>) and Molecular Dynamics Simulations of Self-Assembled DNA Nanostructures (<b>MrDNA</b>), a suite of programs to augment several aspects of the DNA origami design process.<br>