dnafold enables dynamic modeling of DNA origami unfolding, which is inaccessible to oxDNA in reasonable time and computing power12. dnafold is a mesoscopic model that represents DNA at a resolution of 8 nt per bead. It utilizes a switchable force field to model the properties of ssDNA and dsDNA. With this coarse-grained representation, Brownian dynamics simulations are conducted that capture the full assembly of DNA origami structures from scaffold and staple components.
References
- DeLuca, M. et al. Mechanism of DNA origami folding elucidated by mesoscopic simulations. Nat Commun 15, 3015 (2024).
- DeLuca, M. marcello-deluca/dnafold (2025).