The potential energy (as far as I have studied - that is, mainly classical physics) depends on the reference level, since its absolute value cannot be calculated. It can therefore be negative as well. Recently I was taught the mass-energy equivalence in class, in context of the mass defect that arises because of the nuclear binding energy. My question is whether the rest mass energy also includes the potential energy of the particle. If it does, its value should depend on the reference level of the potential energy. Since it is given by $E=mc^2$, the rest mass should depend on the reference level. But this does not seem to make sense. And when the potential energy becomes negative, so should the rest mass. This again seems strange.
If it does not include the potential energy, then why does the nuclear potential energy show up as a mass defect? It should not, if the rest mass energy is not related to the potential energy.
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