As I understand it, an atom is made up of a nucleus of neutrons and protons, with a load of electrons orbiting it.
Well this understanding is what, maybe more than a hundred years out of date?
As others have said, quantum mechanics changed our view of what a particle is, although the big problem is that there is no agreement within this discipline as to how to explain the results of quantum experiments.
There are still paradoxes within QM to be resolved, but what I still see in much writing is this need to believe in particles, however small or fundamental. We need to think in terms of whole systems, and maybe we also need to let go of our need for thinking of time and space as fundamental aspects of reality too.
All IMHO of course 😀
It’s a great question, but then so many aspects of our cosmos are still a mystery to us, it’s great to explore these things huh?