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Being mostly empty space, we cannot pass through walls unimpeded any more than a magnet can pass through another magnets field unimpeded- and largely for the same reasons.
I don't think they need physical boundaries as they're held "together" (despite the distances being large) by the orbit of the electrons around the nucleus.
I don't think it's contained. More like the area of the empty space is defined by the boundaries of the "orbit" of the electron.
I'm not sure if this helps you though, sorry.
originally posted by: Words
This does help quite a bit, thank you. This is what I thought. But the trouble is, if this is so, the idea in pop-culture that atoms are little spheres in which empty space is contained is a mathematical and abstract notion, with little concrete reality.