In pure QCD in the confinement phase what happens if I add to a system of baryons, which are quarks in the condensed phase, another quark? It doesn't have any quark or antiquark to form a baryon or a meson so how does confinement work in this case?
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A quark has a color charge. This charge creates a strong attraction to another quark over a distance. The effect is similar to a string. Trying to pull two quarks apart is like stretching a string. You need to apply a force in tons to separate two quarks by a femtometer or $10^{-15}m$. So realistically your question distills to what happens if by applying enough energy we separate two quarks by a short distance? The answer is that the energy you supplied would end up creating two jets of hadrons. During this process the color string would remain between two color charged particles (not necessarily the original quarks). Once the kinetic energy is gone, the color string wins, and two color charged particles are pulled back together to either form a meson or annihilate.
Check this simple explanation of hadron jets: Higgs Boson - What are jets?
For more details: https://en.m.wikipedia.org/wiki/Jet_(particle_physics)
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