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I have a question regarding how to reconcile the observation of confinement and nuclear decay (without further hadronization).

Let's assume that the nucleus is a proton emitter and nucleon 1 (N1) is the proton which is emitted in the radioactive decay. How is it possible that the red quark in N1 does not interact with the green/blue quark in N2, N3, ... ? Especially if one takes into account that the coupling constant of strong interaction is actually larger at larger distances?

I suspect it has something to do with the orders of magnitude of the relevant quantities involved (energy or resolution, e.g. nuclear: $10^{-15}$m and particle $10^{-18}$m), but I am looking for a more detailed answer.

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Confinement happens with quarks, there are no free quarks in your graph, the three colors mean that the nucleons are color neutral.

What you are talking about is the nuclear force which is a residual force from the QCD confining potential that keeps protons and neutrons neutral in color.

The residual effect of the strong force is called the nuclear force. The nuclear force acts between hadrons, known as mesons and baryons. This "residual strong force", acting indirectly, transmits gluons that form part of the virtual π and ρ mesons, which, in turn, transmit the force between nucleons that holds the nucleus (beyond protium) together.

The residual force is not confining, but generates potentials where energy levels exist. There are successful models describing the energy levels which filled up generate the periodic table of elements and the isotopes. Instabilities and decays arise because of quark decays due to weak interactions, or binding energy levels allowing fusion or fission.

There are also proton emitters due to the balance of the electromagnetic repulsive forces and the number of neutrons shielding them. These are treated again with effective potentials due to the residual strong force, and energy levels.

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