Antibiotic Penetration Through a Bacterial Biofilm

Bacteria inside a biofilm are not genetically different from their free-swimming cousins, yet a dose that reliably kills a planktonic culture can leave a biofilm's core completely untouched. This simulator renders that mechanism directly: antibiotic molecules diffuse in from the biofilm's outer surface while being neutralised by the extracellular matrix — degraded by matrix-bound enzymes and non-specifically absorbed by polysaccharides and extracellular DNA — producing a steady-state concentration profile C(x) = C₀·exp(−x/λ) with penetration length λ = √(D/k). Thousands of bacterial instances are colored live from that field against their own MIC threshold, so you can watch a lethal surface dose fail to reach a fully susceptible population buried only a few penetration-lengths deep, and see how diffusivity, degradation rate, dose and biofilm thickness each reshape the kill front.