We study the heat transport due to phonons in nanomechanical structures using a phase space representation of non-equilibrium Greens functions. This representation accounts for the atomic degrees of freedom making it particularly suited for the description of small (molecular) junctions systems. We show that for the steady state limit our formalism correctly recovers the heuristic Landauer-like heat conductance for a quantum coherent molecular system coupled to thermal reservoirs. We find general expressions for the non-stationary heat current due to an external periodic drive. In both cases we discuss the quantum thermodynamic properties of the systems. We apply our formalism to the case of a diatomic molecular junction.
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