That atoms are tiny universes with little planets orbiting them with microscopic beings

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Actually, when you get to relativity, you’ll find out that
matter and energy are indistinguishable on a nuclear
scale. An atomic nucleus is closer to a little ball of fire
than solid particles.
Infinite reduction doesn’t work in quantum mechanics.
On the other hand, that puts us near the absolute
minimum in the scale of the universe.
Go figure.

The only problem with that is that atoms bond strongly with other atoms. If whatever their macro representation is in our universe had a bond with another one, the result would be pretty catastrophic. 

— that and atoms don’t behave exactly with the laws of physics, which is why we have quantum physics. 

If something lives on those little things, they definitely don’t live in the same way we do. Additionally, they would need something that would help them conduct electricity in their brains. That creates a different level of complications for something sub-atomic.

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