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I was watching a video explaining virtual particle can be drawn to the positively charged necleus which explain why there is a tiny step between the higher energy level and ground state, but I'm not convinced as to why it doesn't affect all other energy levels?

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The Lamb Shift will certainly contain contributions from all energy levels in an atomic system (including the non-bound ones), but basic perturbation theory will tell you that the contribution from higher energy levels will be negligible compared to the next-highest-level contribution (which is already quite small).

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