Q: If atoms are 99.99% space, what “kind” of space is it? Is it empty vacuum?
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However, electrons aren’t really particles (which is why it’s impossible to actually specify their size); they’re waves. Electrons are more like the “ringing” of the bell and less like a fly buzzing around the bell. The math that describes the “quantum wave function” of electrons in atoms and the math that describes vibrations in a bell have some things in common. In quantum physics things tend spread out between a lot of states (in this case those different states include different positions). The atom picture is from here.