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If atoms are made up mostly of "empty space," what is in that empty space? Specifically, is there air in the empty space of an atom?
The space inside the atom is just that, empty space, i.e. vacuum. Air molecules are also made up of atoms with a central core of nucleons and electrons spinning around them. They too have empty space between their nucleons and electrons. One can picture them to be like the solar system with the sun at the center and the planets revolving around it, with just empty space (vacuum) between the sun and the planets.
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