Yes, all molecules are mostly empty space, no matter how tightly packed they look the DNA double helix has a little less empty space than most because it’s REALLY tightly packed, but it’s still mostly empty space. Huge forces like the gravity in a star can compress atoms so that they’re much closer together, but that’s usually balanced out by the heat energy the star produces. However, when a star runs out of fuel, there’s nothing balancing out the gravity, so what’s left of the star crushes in on itself so hard that all the molecules really do get squished together.
Some really big stars that run out of fuel crush themselves to tightly that the electrons orbiting the nucleus of each atom are actually squished into the nucleus!
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