Atoms aren't really mostly empty space. Although they say the nucleus has a tiny cross-section compared to the electron shell, the space inside the electron shell is filled with electrons moving in all directions at nearly the speed of light. The electron itself is not small, it is large and fuzzy. Why fuzzy? It is fuzzy because its location cannot be known at any instant, it might not even be particle-like when attached to an atom.
What do you think of the recent stories of the 5th dimension that may be measured in the lab within 3 years? 95% of the mass of the universe is said to be dark matter and dark energy, and resides in this 5th dimension. This 5th dimension is not thought to be almost immeasurably small like the rest of the superstring dimensions, but of the order of millimeters in size. Bigger than neuronal complexes in the brain. Bigger than the amount clipped off the nail with nail clippers. Heard of that? There have been a couple 5th dimension threads on FR recently.
If the nucleus of an atom were the size of this O, the electron that orbits it, would be about a quarter of a mile away.
I think that's a considerable amount of space