system
Given the following post, respond as if you're commenting on Reddit:
human
If atoms are 99.9999% empty space....

How far is each atom in relation to the other?  Are the nuclei closer together?  Do electron paths cross over into the adjacent atoms' space? Am I asking completely the wrong questions? 

I find this fact extremely mind boggling, yet very interesting!
gpt
The space in the atom is fully occupied by electron(s). It is not empty in any reasonable sense. When an electron is in a bound state in an atom, it is not just that we don't know exactly where it is, it is that it literally does not have a specific position. It is like a standing wave, where the ripples are mostly concentrated in a rough sphere with a radius on the order of half a nanometer or so.

It is only when you fire something like a high energy x-ray at the atom that the scattering between the x-ray and the electron takes place in a smaller and more well defined region of space in the atom. But once you resolve the position of the electron in this manner, and say 'it is right over here', it is no longer bound to the atom, it is being shot right out of the system with incredible momentum.

When people say that the electron behaves like a point particle, they are referring to a hypothesized internal structure. If you shoot very energetic x-rays or gamma rays at an electron, no matter where you resolve the position to be, the electron seems to be a singular object.

The proton is different as it has internal parts. The position of the proton can be smeared out all over space like an electron, but no matter where it is its parts are very close together (mostly within 10^-15 meters) of each other. You can tell that it has parts because if you hit it with a high energy particle, it behaves like a bag of stuff, not like a singular particle.

If the electron has parts, then they must be confined to a region within about 10^-18 m or so. So if you fire a super high energy gamma ray at an atom and hit the electron, you will change its state to occupy a very precise volume, but you will find that all of its pieces are mostly in that volume. Right now, there is no indication that an electron has any such internal structure, so people think of it as a point particle when it is hit by super high energy particles.