We report on a series of controlled computational experiments based on nonequilibrium molecular dynamics and show that at the nanoscale, the thermal rectification is determined by the thermal boundary resistance, i.e., the thermal resistance of the interface, and cannot be explained without it. In the graphene–bilayer graphene system that we study, the sign of the thermal rectification is opposite to the value predicted from bulk-derived models, i.e., phonons preferentially flow in the opposite direction. This behavior derives from the temperature dependence of the thermal boundary resistance and from the fact that the latter, at the nanoscale, has large relative weight compared to the total thermal resistance. These results outline the importance of properly accounting for the active role of the interface.

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