We use the Schrieffer-Wolff transformation (SWT) to analyze Josephson junctions between superconducting leads described by the charge-conserving BCS theory. Starting from the single-electron tunneling terms, we directly recover the conventional effective Hamiltonian, $-E_{J}cos\widehat{\phi }$, with an operator-valued phase bias $\widehat{\phi }$. The SWT approach has the advantage that it can be systematically extended to more complex scenarios. We show that if a Bogoliubov quasiparticle is present its motion couples to that of Cooper pairs, introducing correlated dynamics that reshape the energy spectrum of the junction. Furthermore, higher-order terms in the SWT naturally describe Josephson harmonics, whose amplitudes are directly related to the microscopic properties of the superconducting leads and the junction. We derive expressions that could facilitate tuning the ratio between the different harmonics in a controlled way.

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• Josephson junctions
• Superconductivity
• BCS theory
• Perturbative methods