DNA Strand-Displacement Logic Gate

Toehold-mediated strand displacement is the core reaction that DNA computing runs on: a short single-stranded "toehold" lets an invader strand nucleate on a duplex and then out-compete an incumbent strand base pair by base pair, with no enzymes involved. This simulator builds a two-input AND gate from that reaction — an output strand held quenched by two protector strands, each guarding one flank via its own toehold. Add Input A and Input B (in either order) and watch each one dock at its toehold and branch-migrate the matching protector off, base pair by base pair; only once both protectors are gone does the reporter domain light up. A toehold-length slider and a concentration slider drive a real rate law, k(b) rising sigmoidally with toehold length toward the diffusion limit, with the predicted half-time read out live.