This is pretty difficult to talk about with any real accuracy, because existence at these scales is so counter-intuitive. You have to throw away a lot of the ways you commonly think about things to comprehend what’s actually going on.
First of all, the “marbles with sticks” constructions that you see in chemistry class aren’t atoms. Those are *molecules*. One marble represents a single atom, and the sticks represent the ways those atoms are bonded to one another.
Atoms are, at their most basic level, comprised of two things: electrons, and quarks. Quarks come in two flavors that we care about, named “up” and “down” (because scientists are very clever…). These quarks bundle up into sets of three, which will either be a proton or neutron depending on which kind of quarks are in the triplet. 2 up + 1 down = proton, 2 down + 1 up = neutron. 3 quarks of all the same type are, uh, not allowed. Protons and neutrons clump together into a dense little nugget that we call a “nucleus”, and the electrons are… “whizzing around close by”, let’s say. The specific details are *extremely* complicated.
Electrons and quarks tend to be shown in textbooks as little spheres, implying they’re solid objects with volume. But that’s not really the case. Both of them are actually point-like. They have no volume at all. Nothing. So even if you *could* shrink down like Ant Man to try and look at them (and we pretended that light at that size worked the same way it does at regular human size) there would be nothing to see. They would literally be invisible points in space that can move around and just happen to act like tiny magnets and have gravity. Kind of boring, isn’t it?
Entire atoms, though, *do* have volume. They have a size we can measure. And so do protons and neutrons, for that matter. So atoms have volume, but are made entirely of things that *don’t* have volume, how does that work?
Y’know how when you push the north poles of two bar magnets together, you can feel them repel one another? And the closer you bring them together, the more strongly they repel? That’s what quarks and electrons do to one another. Try to push them extremely close together, and they’ll resist your push. The closer you get, the harder the push. Since they have no size, there’s no limit to how close you can get them to one another. But that also means there’s no limit to how hard they can push back.
Realistically, there is a limit to the amount of force you could ever apply to press two particles together. Therefore, they will always be separated by some nonzero amount of distance. We can use this “keep-away” distance between them as the next best thing for “volume”. The space between the particles is completely empty, but since you can’t force them together any closer, then for all serves and purposes they’re *basically* “touching”, right?
The size of a proton and neutron is defined by the “keep-away” distance that the quarks maintain with one another. The size of the nucleus is defined by the “keep-away” distance that the protons and neutrons maintain with one another. And the entire atom’s size is the “keep-away” distance that the electrons of the atom maintain with their nucleus the electrons of other atoms.
All of these “keep-away” distances around these particles and groups of these particles are either perfectly spherical, or very close to spherical most of the time. That’s why textbooks (and your marble-and-stick kits) usually show them as solid spheres, even though they actually aren’t. They “keep-away” distances make them *behave* like spheres in many ways, yes. But they aren’t solid, they are in fact 100% empty. Comprised entirely of invisible points that have no volume, but can still affect one another.
At this point you are probably wondering how are we able to actually *see* anything, since I’ve been describing everything as completely invisible. *Invisible* might not be the correct word, really. The way you classically think about light is that it heads toward and object like, say, a mirror, and it “bounces off” of that object, like a ricocheting projectile. At the human scale that is accurate enough. But at the atomic scale, that’s not really how it works. Or, maybe it is, depending on how you look at it. But that’s getting into the whole “is light a particle or a wave” thing, which is… uh… complicated!
In addition to all of the topics I completely dodged or brushed away with “it’s complicated”, there’s also a lot of questions that have probably cropped up that I have to leave to keep this answer from becoming even more of a thesis than it already is. Like, “What makes the protons stick together even though they repel each other?”, or “How do neutrons stick to anything if they’re neutral?”, or “Why do quarks like to get together in sets of three?” I’ve already glossed over entire classes worth of physics in this answer, and to answer these questions adequately would need more.
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