About 5 years ago I read a story about scientists discovering that atoms are tiny universes/solar systems. Then at some point the scientists develope a microscope that can see the planets and their inhabitants. Later on the scientists realize that the atom people already have technology far beyond ours (because they can travel from atom to atom and colonize the planets)
I know it isn't, but it sure sounds very similar to "The Micronauts" a late 70's early 80's Marvel comic book. Good story, and J.J. Abrams was going to make what probably would have been a terrible movie adaptation of it, but he got busy with star wars and dropped it (thank god) The comic has been remade several times, usually nowhere near as good as the first run was. Good luck.