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How the proton state is found and renormalized in lattice QCD? Is there any literature shows the method step by step? What about other bound states in QCD if we somehow know their quantum numbers?

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In general, bound states in lattice QCD are found by analyzing correlation functions of operators with the appropriate quantum numbers. This works both for baryons and mesons, even for pure-glue states like glueballs. See for example these introductory lecture notes: http://arxiv.org/abs/hep-lat/9807028. Chapter 17 should answer your questions in more detail.

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