Rotaxane Molecular Shuttle Simulator

Rotaxanes are mechanically interlocked molecules — a macrocyclic ring trapped on a dumbbell axle by bulky stopper groups it can never slip past, yet free to shuttle back and forth between two binding stations. This simulator renders a live ensemble of 30 independent rotaxane shuttles, each ring executing genuine overdamped Langevin dynamics in a double-well free-energy landscape, so you can watch stochastic, thermally activated hopping build up a Boltzmann-distributed population in real time. A pH-like stimulus toggle and a continuous bias slider tilt the landscape the way protonation, redox chemistry or light switch real synthetic molecular machines, temperature sets the thermal noise driving each hop, and a barrier-height slider controls how much resistance the ring feels crossing the axle's midpoint — with live readouts of station populations, the theoretical equilibrium ratio, and the cumulative number of shuttling events observed.