How did physicists figure out the structure of an atom at a time when it was impossible to observe them?

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Especially, the 3 main parts of the atom – electron, proton and neutron and the fact that electron whirled around the nucleus and that the nucleus had proton and neutrons, etc.

It’s a complex structure and I am struggling to understand how they were able to hypothesize it.

In: Physics

Well I think they didn’t actually figure it out for a while (and we still haven’t completely). The standard model you’re referring to doesn’t really work like we thought it would.
The atom is a combination of probabilities not electrons whirling around a nucleus in the Way they teach you growing up.