As known, the proton is from two up and a single down quark, while the neutron is from a single up and two down quarks. The down quark is a little bit more massive and the up, and so the neutron is also a little bit more massive as the proton. It was my naive layman's hypothese.
But the masses of the quarks (4 and 8 MeV) take only a tiny part in the whole mass of the baryons ($\approx 1\textrm{ GeV}$). Their masses are coming mainly from the gluon field around them.
And, considering the relative recent charming result of the calculation of the protons and neutrons from the principles, I think maybe this question could have a more detailed answer.
I think the mass difference is coming from the difference of the gluon field, is it okay? What is that difference?
Extension: comment says, that calculation couldn't yet differentiate between protons and neutrons. I hope, maybe the last 8 years made possible this improvement.
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