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Although tiny, a proton takes up a finite amount of space, enough to fit three quarks, a host of virtual particles, and their associated gluons. The size of a proton's radius is determined by these particles and their interactions, and so is fundamentally tied in to theories like the Standard Model and quantum chromodynamics.

We can measure the radius because the proton's charge is spread across it, which influences the orbit of any electrons that might be circling it. Measurements with electrons produce a value that's easily in agreement with existing theories. But a few years back, researchers put a heavier version of the electron, called a muon, in orbit around a proton. This formed an exotic, heavier version of the hydrogen atom. And here, measuring the proton's radius produced an entirely different value—something that shouldn't have happened.

This “proton radius puzzle” suggests there may be something fundamentally wrong with our physics models. And the researchers who discovered it have now moved on to put a muon in orbit around deuterium, a heavier isotope of hydrogen. They confirm that the problem still exists, and there's no way of solving it with existing theories...

Researchers orbit a muon around an atom, confirm physics is broken | Ars Technica

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