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. ... [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

• Schreck, John
• Fu, Daniel
• Williams, Dewight
• Yan, Hao
• Prasad, Abhay
• Zhang, Fei
• Pradeep Narayanan, Raghu
• Reif, John

DOI

• 10.7924/r4d223179

Subject

• DNA nanotechnology

Publication Date

• November 21, 2022

ARK

• ark:/87924/r4d223179

Affiliation

• Computer Science

Publisher

• Duke Research Data Repository

Type

• Dataset

Format

• CONF
• DAT
• TOP
• PY
• JSON

Related Materials

• Fu, D. (2022). DNAxiS [source code].  https://github.com/dfu99/dnaxis.git
• Ouldridge, T. E., et al. (2011). oxDNA [source code].  https://github.com/lorenzo-rovigatti/oxDNA.git
• Fu, D., Pradeep Narayanan, R., Prasad, A., Zhang, F., Williams, D., Schreck, J. S., Hao, Y. & Reif, J. (2022). Automated design of 3D DNA origami with non-rasterized 2D curvature. Science Advances, 8(51).  https://doi.org/10.1126/sciadv.ade4455

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

License

• Creative Commons BY Attribution 4.0 International

Title

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

License

• https://creativecommons.org/licenses/by/4.0/

Repository

• Duke Research Data Repository

Thumbnail	Title	Date Uploaded		Actions
	README.txt	2022-11-22	Public	Download
	dnaxis_v1.1_archive.zip	2022-11-22	Public	Download
	iterable parameters.zip	2022-11-22	Public	Get file from Globus
	molecular dynamics inputs.zip	2022-11-22	Public	Get file from Globus
	pathway variation.zip	2022-11-22	Public	Get file from Globus
	stepwise heuristic.zip	2022-11-22	Public	Download