Luciferase Flash Kinetics: Single-Molecule Photon Counting

Firefly bioluminescence looks like a smooth rise-and-decay flash when you average over trillions of molecules, but at the level of a single luciferin molecule it is a sequence of discrete, random catalytic events. This simulator runs a genuine Gillespie stochastic simulation algorithm: each of a fixed pool of substrate molecules waits an exponentially-distributed random time — set by the same Michaelis-Menten-with-product-inhibition propensity used in the companion 3D model — before an active luciferase site converts it to oxyluciferin and, with probability equal to the reaction's quantum yield, emits a detected photon. Watch individual molecules flip from substrate to product on the cuvette, and watch the binned photon-count histogram below build up the familiar flash shape one discrete click at a time, complete with the shot noise that real low-light photon counting shows and a smooth mean-field curve never can.