Although there's no reason that I couldn't make Universe Sandbox work smoothly at a super small scale (it kind-of already does).
The major issue is that gravity isn't the force that works at these very small scales and that could make it complicated to make realistic and/or representative.
It is fun to zoom in on something the size of a nuclei and then zoom out further than the size of the visible Universe.
There's a new movie coming out that visualizes molecules:
Molecules to the Maxhttp://www.molecularium.com/nowplaying.html(there are two movie clips at the bottom left)
New Scientist Clip About the Movie