In Greg Egan's "Permutation City", an alternative set of physical rules is devised that is designed to produce a universe resembling ours, but that is computationally feasible to accurately simulate. This simulated universe is named the Autoverse.
The protagonist spends her time manipulating molecules in Autoverse simulations, trying to invent Autoverse equivalents to biochemical systems that will eventually lead to evolution.
As sci-fi "ideas" go, the Autoverse is pretty fucking awesome. Egan then takes the idea and pushes it into insanely fun territory. It's a great read (and actually I'm pretty sure I found out about it through HN).