A computational method to analyze the exciton energy transfer and trapping mechanisms in mixed J-aggregates featuring a donor-acceptor system is provided. For a given geometrical configuration, the intermolecular interactions are calculated using the extended dipole method. Numerical diagonalization of the aggregate Hamiltonian is performed taking into account the static disorder. The density of states, the absorption lineshapes and the relative number of coherently coupled molecules within the donor and acceptor bands are obtained. The excitation energy transfer processes among the excited states of the donor-acceptor system (intraband and interband scatterings) are described through an exciton-phonon coupling model. The scattering rates are calculated and used in a Master Equation to obtain the time evolution of the exciton populations after initial excitation. Our simulation method is used to analyze the excitation energy transfer between two kinds of closely spaced linear parallel chains featuring the so-called blue (donor) and red (acceptor) structures of pseudoisocyanine molecules (PIC). It is also applied to describe the energy transfer in the mixed J-aggregate of oxacyanine (donor) and thiacyanine (acceptor) molecules.
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