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Present observation shows that elementary particles have no internal structure, and have no real size as they are described by wavefunction.

Something that therefore confuses me is that on a lot of online "size comparison" videos and animations, elementary particles are given sizes, some much larger than others. An example.

Where exactly are the sizes for these animations coming from and how are they so precise? Are they just straight made up or are they from some other source that deals with theoretical sizes? Apologies if this question seems silly, but I've been puzzled about it for some time.

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In quantum field theory, elementary particles are represented as pointlike excitations of an underlying quantum field, which means that an electron or a quark has no size. However, there is a long tradition of identifying the "size" of certain particles as the typical extent of their wave functions. (Depending on the context, this might mean the de Broglie wavelength or the Compton wavelength or something else.) So electrons are typically described as having a size of $\sim10^{-10}$ m, since that is the typical extent of their atomic wave functions. Protons or neutrons, being composites, are not point particles, but both the size of nucleons and the spread in their wave functions are set by the range of the strong interaction at $\sim10^{-15}$ m; this is therefore identified as their "size." For more massive particles, it is commonplace to use the Compton wavelength to denote their even smaller "sizes."

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