We simulate each of those things from the level below. Artificial neural networks are made from toy models of the behaviours of neurons, cells have been simulated at the level of molecules[0], molecules e.g. protein folding likewise at the level of quantum mechanics.
But each level pushes the limits of what is computationally tractable even for the relatively low complexity cases, so we're not doing a full Schrödinger equation simulation of a cell, let alone a brain.
