  Conventional models of Josephson junction dynamics rely on the absence of low
energy quasiparticle states due to a large superconducting gap. With this
assumption the quasiparticle degrees of freedom become "frozen out" and the
phase difference becomes the only free variable, acting as a fictitious
particle in a local in time Josephson potential related to the adiabatic and
non-dissipative supercurrent across the junction. In this article we develop a
general framework to incorporate the effects of low energy quasiparticles
interacting non-adiabatically with the phase degree of freedom. Such
quasiparticle states exist generically in constriction type junctions with high
transparency channels or resonant states, as well as in junctions of
unconventional superconductors. Furthermore, recent experiments have revealed
the existence of spurious low energy in-gap states in tunnel junctions of
conventional superconductors - a system for which the adiabatic assumption
typically is assumed to hold. We show that the resonant interaction with such
low energy states rather than the Josephson potential defines nonlinear
Josephson dynamics at small amplitudes.
