Two-polaron energy diffusion in a 1D lattice of hydrogen bonded peptide units

A generalized Pauli master equation is established for describing the vibrational energy flow in a 1D lattice of hydrogen bounded peptide units. A Lang–Firsov transformation is applied so that the relevant excitations are small polarons corresponding to vibrational excitons dressed by virtual phonons. A special attention is thus paid to characterize the energy transfer mediated by two polarons. At biological temperature, it is shown that the polaron–phonon coupling is sufficiently strong to prevent any coherent motion. The polaron–polaron interaction occurring in such a nonlinear lattice does not affect the long time behavior of the energy flow which results from the diffusion of two independent polarons. This diffusive motion originates from the competition between two contributions related to phonon mediated transitions (incoherent contribution) and to dephasing limited coherent motion (coherent contribution).