Bacteriophage Lysis–Lysogeny Decision Switch

When bacteriophage lambda infects an E. coli cell, it must "decide" whether to replicate immediately and kill the host (lysis) or splice its DNA into the host chromosome and go dormant (lysogeny). This simulation renders the real molecular logic behind that decision: a bistable mutual-repression circuit between the CI repressor and the Cro anti-repressor, integrated live from stochastic differential equations and rendered as a population of instanced protein molecules inside a 3D bacterial cell. Multiplicity of infection and host nutrient stress bias the coin flip the same way they do biologically, molecular noise is what actually breaks the symmetry between the two stable states, and an SOS/UV-damage trigger lets you watch an established lysogen undergo prophage induction and flip to lysis in real time.