Another theory is that during deep sleep cells go into more of a maintenance mode, with slightly increased mitosis rates, waste removal and decreased central (nervous-system control) acting slightly more like single-celled organisms.<p>This state change seems to be partially thermally regulated but also via chemical and neuron mechanisms.<p>Yawning and stretching (pandiculation) seems to be correlated with increasing alertness and temperature so maybe it helps sync your cells back to optimal central-nervous system control and suppresses the unicellular maintenance functions. For example it's disadvantageous to have a bunch of your muscle cells in the middle of mitosis if you soon need to run from a predator or hunt.