Space said:
If, inside of an atom is mostly space, how do we have stuff, that is made of atoms?
Your question is more nuanced than you may realize. It involves asking, "how big are fundamental particles?" And that's not an easy question to answer. When we detect a fundamental particle, we can always localize it (find it) within some small volume of space, and we can make that volume as small as we want and find the particle within it and not outside of it.
For example, a pixel on a camera sensor will detect a photon while the other pixels nearby do not. You won't have a partial detection on multiple pixels, it will always be detected by one and only one pixel. We can make our pixels as small as we like and we will still detect a photon at one and only one pixel. Now, real camera sensors have a minimum size to their pixels, but the idea applies to other detection methods as well.
So what we have is, in effect, that fundamental particles don't have a size. Or, rather, don't have a
minimum size, in the sense that we can localize them to as small a volume of space as we like. But we also know that particles interact with each other at a distance, so then we have to ask, "do they have a maximum size?"
Unfortunately this isn't any easier to answer than the first question. What do we mean by "size"? For large, macroscopic objects this is easy to answer. I take out my ruler and I measure a cube and say that it's 3x3x3 inches, to within some measurement error. But that's only because we can't see all the details down at the subatomic level with our naked eye.
How would we even measure the size something like an electron? We can't use a ruler, so we have to be more creative. Well, electrons repel each other, so one way is to shoot electrons at each other and see how they bounce off of other electrons. On our everyday scale objects either hit each, or they miss completely. There doesn't seem to be an in-between. You don't see bowling balls miss the pins by half an inch yet still somehow bounce off of them. But it's different for electrons. Since the electromagnetic force is infinite in range, there is no distance that the electrons wouldn't repel each other. Surely this can't mean that electrons have
infinite size, right?
Well, perhaps the EM force isn't the right one to look at. Surely there is some way to tell how big an electron or other fundamental particle is, right? Well, no. No matter what experiments we do, no matter which particular forces we focus on, there simply isn't a clear, unambiguous way to define or measure the size of a fundamental particle. They seem to be able to be as small as we can measure, they can interact across infinite distances, and they will do very, very strange things like tunnel through solid barriers, rotate around twice to get back to their starting orientation, and many other things that don't make any sense to us if we try to compare them to macroscopic objects.
So, how big are fundamental particles? We can't answer that at this time, and there may not even be an answer. One way to view things is to say that the particles are delocalized until they are detected. So if I put an electron in a box, I can say that the electron is somewhere in the box (assuming it hasn't quantum tunneled out), but I don't know where. It wouldn't be incorrect to say that the electron is delocalized and occupies the entire box until I do something to measure its position. The same is true for an atom. I know a hydrogen atom has a proton and an electron, but I can't say that either particle is in a certain position until I measure their positions. So both particles, and the atom itself, is delocalized.
Moving back to the original question, what is in the 'empty space' in atoms? We can't answer that except to say that the notion of 'empty' vs 'non-empty' space isn't clear-cut in this context. Personally I would say that the particles making up an atom are delocalized, meaning that they don't have a definite position. And since they don't have a definite position it would be reasonable to some to say that an atom doesn't have empty space. The space is filled with the delocalized particles that make up the atom. Or you could say it's filled with intense fields. OR you could say that the space is never empty, just filled with excited and un-excited regions of underlying fields (EM field, electron field, quark field, etc).
It's quite complicated.
