Autophagy ("self-eating") is the cell's recycling program: a cup-shaped membrane called the phagophore grows around damaged organelles or misfolded proteins, seals into a double-membrane autophagosome, then fuses with a lysosome so acid hydrolases can break the cargo down into reusable building blocks.
Falling mTOR (mechanistic target of rapamycin) activity releases the ULK1 kinase complex, which nucleates LC3-tagged membrane patches — shown here as small glowing instanced tiles — around a cargo particle. The formation rate follows R = R₀ + k·(1 − mTOR): the lower the mTOR gauge, the faster new phagophores are nucleated. Once a cup closes around its cargo it becomes a sealed autophagosome (torus), drifts to the lysosome, fuses, and the cargo shrinks away as it is degraded.
Nutrient-state preset sets baseline mTOR; the AMPK/starvation slider further suppresses it; simulation speed scales the whole clock; auto-rotate toggles a slow orbiting camera that always keeps the cell in frame.
Yoshinori Ohsumi won the 2016 Nobel Prize in Physiology or Medicine for discovering the core autophagy genes in baker's yeast — machinery that turned out to be almost unchanged in human cells.
Autophagy is the cell's own recycling program. Watch falling mTOR activity release the ULK1 complex, which nucleates a ring of LC3-tagged membrane patches around a damaged mitochondrion; the patches close into a sealed autophagosome, drift to a lysosome, fuse, and the cargo is broken down and recycled.
The simulation models the core autophagy pathway: mTOR suppression under nutrient stress triggers phagophore nucleation (LC3 puncta), cup closure into an autophagosome, transport to a lysosome, membrane fusion, and enzymatic degradation of the engulfed cargo.
Pick a nutrient-state preset or drag the AMPK/starvation slider to push mTOR activity down and watch new autophagosomes nucleate faster; the speed slider scales the whole simulation, and auto-rotate keeps the whole cell in frame while you watch a cup close and fuse.
Yoshinori Ohsumi won the 2016 Nobel Prize in Physiology or Medicine for identifying most of the core autophagy genes using baker's yeast — machinery later found to be conserved almost unchanged in human cells.