Channelrhodopsin Photocycle: State-Flow & Phase Portrait

This is the 2D mean-field counterpart to the stochastic channelrhodopsin-2 photocycle simulator. Instead of rendering 400 individual channel molecules hopping between states, it integrates the exact four-state kinetic model (dark-closed C1, open O1, desensitized-open O2, closed-desensitized C2) as a continuous system of population-fraction ODEs, driven by the same controllable blue-light pulse. The left panel draws the kinetic scheme as a live reaction-network diagram, with token flow along each arrow scaled to its instantaneous rate; the right panel plots the system's trajectory through (pO1, pO2) phase space, the canonical way dynamicists visualize a multi-state kinetic system's behaviour independent of any spatial layout. A live photocurrent readout uses the identical Ohmic current law as the single-channel model, including its sign flip as membrane voltage crosses the reversal potential.