DNA Origami Annealing — Cooperative Nucleation-and-Growth (2D)

DNA origami folds a long scaffold strand into a target shape by base-pairing it with hundreds of short "staple" strands, each of which must find its own binding site inside a narrow thermal window during a slow cooling anneal. The companion 3D simulator models each of ~330 sites as an independent coin-flip against its own melting temperature. This 2D top-down version instead models a real cooperative effect: a site's already-hybridized lattice neighbors mechanically reinforce it, so its effective binding rate rises with local neighborhood occupancy. The result is genuine nucleation-and-growth behavior — folded domains nucleate at a handful of sites and spread outward across the lattice, the same qualitative dynamics described by classical Avrami-type crystallization kinetics — rather than every site filling in independently. A toggle lets you switch off the neighbor coupling to compare directly against the independent-site baseline under an identical cooling program, and a live strip chart traces bath temperature and folding yield across the whole anneal.