Is there anything known about the spatial configuration of the quarks within a proton of pion? Or are they just considered to be two or three overlapping points?
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The parton distribution functions (PDFs) are momentum distributions sorted by flavor. The Fourier transforms of them give you the position distributions.
You can get similar, though sometimes less specific (i.e. no flavor information) from the form-factors or structure functions.
See also: What is an intuitive picture of the motion of nucleons? for the same kind question about the motion of the nucleons in the nucleus.
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Do you have a link to the paper about a lattice simulation of quarks within proton? I vaguely recall a figure with Y-like strings with three quarks on the ends of them. – firtree Aug 24 '14 at 16:48
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1@firtree As far as I know that is not a serious visualization, but a casual representation that is about as accurate as the typical nucleus-with-three-ellipses-around-it drawing of an atom. And while I don't follow lattice QCD, last I heard a realistic simulation of a nucleon was still a goal. PDFs, structure functions and form-factors come from data except for the heavy quark mesons whee the lattice guys can do a good job. – dmckee --- ex-moderator kitten Aug 24 '14 at 16:53
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More specifically: just a static proton, no other particles or something. It was a 3D plot of 2D spatial distibution of something, so I don't think it was a freehand draw. About middle of 2000s. – firtree Aug 24 '14 at 17:00