Data from: Automated design of 3D DNA origami with non-rasterized 2D curvature


This data set includes molecular dynamics simulation data for DNA nanostructures discussed in the associated publication. Simulations are performed in oxDNA, a coarse-grained molecular dynamics simulator for DNA. Each simulation begins from an initial configuration of the molecular data generated by DNAxiS, which is a DNA nanostructure design software that utilizes heuristic algorithms for calculating designs for curved and enclosed DNA origami with multiple layers. Molecular dynamics simulations are performed in 3 steps to first relax energies in the initial configuration to conform to the DNA model of oxDNA, then briefly run again to reach a relaxed state similar to its expected physical conformation, then run again for much longer to sample molecular configurations of the structure in its relaxed state. Initial configurations, endpoints of each simulation step, and sample trajectories of the molecular dynamics simulation process have been provided to observe or reproduce the published data.

Data Access

Duke Authors

Cited Authors

  • Reif, J; Fu, D; Williams, D; Yan, H; Zhang, F; Prasad, A

Published Date

  • November 22, 2022

Digital Object Identifier (DOI)

  • 10.7924/r4d223179