Every mitochondrion in the scene tracks a membrane potential ΔΨm (0–1). Random ROS/stress impulses knock it down; a constant repair current pulls it back up:
dΔΨm/dt = k_repair·(1 − ΔΨm) − impulse(p = stress_rate·dt)
PINK1/Parkin quality control: PINK1 is normally imported through the inner membrane and degraded — but only while ΔΨm stays high. When ΔΨm drops below a threshold, import stalls and PINK1 accumulates on the outer membrane instead:
dPINK1/dt = +k_acc·(threshold − ΔΨm) if ΔΨm < threshold
dPINK1/dt = −k_deg·PINK1 otherwise
Once PINK1 crosses 1.0 it phosphorylates ubiquitin and recruits Parkin with probability equal to the recruitment efficiency slider — modelling how well the E3 ligase actually gets to work. Success starts ubiquitination → autophagosome engulfment → degradation, after which a fresh mitochondrion appears (biogenesis replacing what was removed). Failure leaves the damaged organelle circulating with PINK1 capped at 1, waiting for the next recruitment roll.
Fusion rescue: at the fusion-rate probability per second, a flagged mitochondrion exchanges contents with a random healthy neighbour, averaging their ΔΨm — the real complementation effect of MFN1/2 + OPA1-mediated fusion, which can pull a damaged organelle back above threshold before it is ever cleared.
PD Mutant Toggle snaps recruitment efficiency down to ~5%, mimicking loss-of-function PINK1/PARKIN mutations found in autosomal-recessive Parkinson's disease: PINK1 keeps accumulating but Parkin is almost never recruited, so damaged, low-ΔΨm mitochondria pile up instead of being cleared — the proposed mechanism linking defective mitophagy to dopaminergic neuron loss.
This 2D view lays the population out in a flat cytoplasm disc instead of a 3D volume — the state machine and kinetics are identical to the source model, verified against it directly. Drag the view to pan, scroll/pinch to zoom.