Does the two-level atom picture of a josephson junction have a theoretical foundation in BCS?
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Yes, except that the rigorous equations are nonlocal and involve the internal pair coordinates. 1974.
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Rogovin, D., & Scully, M. O.
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Rogovin, D||Scully, Marlan O
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http://dx.doi.org/10.1016/0003-4916(74)90175-4