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We describe a method for simulating exciton dynamics in protein-pigmentcomplexes, including effects from charge transfer as well as fluorescence. Themethod combines the hierarchical equations of motion, which are used todescribe quantum dynamics of excitons, and the Nakajima-Zwanzig quantum masterequation, which is used to describe slower charge transfer processes. We studythe charge transfer quenching in light harvesting complex II, a proteinpostulated to control non-photochemcial quenching in many plant species. Usingour hybrid approach, we find good agreement between our calculation andexperimental measurements of the excitation lifetime. Furthermore ourcalculations reveal that the exciton energy funnel plays an important role indetermining quenching efficiency, a conclusion we expect to extend to otherproteins that perform protective excitation quenching. This also highlights theneed for simulation methods that properly account for the interplay of excitondynamics and charge transfer processes.

Coupled charge and energy transfer dynamics in light harvesting complexes from a hybrid hierarchical equations of motion approach