RISC Slicer — RNA Interference Gene Silencing

This simulator renders the core catalytic step of RNA interference in 3D: siRNA-loaded RNA-Induced Silencing Complexes (RISC/AGO2) diffuse through a modeled cytoplasm, encounter freshly transcribed mRNA, and — when seed-region complementarity clears a mismatch threshold — bind, dwell, and slice the transcript into two fragments that drift apart and degrade. Because AGO2 is a catalytic slicer rather than a stoichiometric binder, each freed RISC goes on to silence further transcripts, exactly as it does inside a real cell. Sliders control siRNA dose (RISC count), competing gene transcription rate, seed-pairing mismatch tolerance, and cytoplasmic thermal motion, while live readouts track transcript count, percent knockdown, and the cleavage event rate — reproducing the birth–death balance between transcription and RNAi-driven decay that determines steady-state knockdown in real experiments.