Believe it or not, acoustics. I'm sure you've heard that there's no sound in space, but that's because the universe is so rarefied. That didn't used to be the case; sound waves were the main energy transport in the early universe. The result is that you get a characteristic spectrum of density fluctuations. You can see in the following plot just how well the observed fluctuations match the theoretical acoustic spectrum:
and what accounts for the fact that the universe is mostly empty?
Gravitational collapse. The denser areas collapsed into stars, galaxies (and even larger structures), which sucked the matter out of the less dense areas.
I've run a few simulations of such cosmological structure formation using the National Scalable Cluster Project supercomputers here at Penn, using parallel code written by Prof. Paul Bode.
- This animated .gif shows the mass density of a simulated portion of the universe 100 light-years across. Black is lowest density, followed by blue, green yellow, red, and finally white as highest density. Later images show later times, when more structure forms due to gravitational attraction. As the movie plays, the universe ages from 50 million to 12.5 billion years. During this time, our simulation volume actually expands by a factor of 40, but this expansion isn't shown.
- Here is another such universe, showing more resolution (WARNING: 7 MB).
- Here is the first frame of that universe, and here is the last frame.
It's an interesting research topic.