- 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 ... [Read More]
- Total Size
- 6 files (33.1 GB)
- Data Citation
- Fu, D., Pradeep Narayanan, R., Prasad, A., Zhang, F., Williams, D., Schreck, J., Yan, H. & Reif, J. (2022). Data from: Automated design of 3D DNA origami with non-rasterized 2D curvature. Duke Research Data Repository. https://doi.org/10.7924/r4d223179
- Creator
- DOI
- 10.7924/r4d223179
- Subject
- Publication Date
- November 21, 2022
- ARK
- ark:/87924/r4d223179
- Affiliation
- Publisher
- Type
- Related Materials
- Funding Agency
- National Science Foundation
- Grant Number
- 1909848
- 2113941
- 1931487
- 2004250
- Contact
- Daniel Fu, dfu@cs.duke.edu, http://orcid.org/0000-0001-5934-7314
- Title
- Data from: Automated design of 3D DNA origami with non-rasterized 2D curvature
- Repository
Thumbnail | Title | Date Uploaded | Visibility | Actions |
---|---|---|---|---|
README.txt | 2022-11-22 | Download | ||
dnaxis_v1.1_archive.zip | 2022-11-22 | Download | ||
iterable parameters.zip | 2022-11-22 | |||
molecular dynamics inputs.zip | 2022-11-22 | |||
pathway variation.zip | 2022-11-22 | |||
stepwise heuristic.zip | 2022-11-22 | Download |