Non-equilibrium molecular dynamics (NEMD) simulations were performed on Au-SAM (self-assembly monolayer)-Au junctions to study the thermal energy transport across the junctions. Thermal conductance of the Au-SAM interfaces was calculated. Temperature effects, simulated external pressure effects, SAM molecule coverage effects and Au-SAM bond strength effects on the interfacial thermal conductance were studied. It was found that the interfacial thermal conductance increased with temperature increase at temperatures lower than 250 K but it did not have large changes at temperatures from 250 to 400 K. Such a trend was found to be similar to experimental observations on similar junctions. The simulated external pressure did not affect the interfacial thermal conductance. SAM molecule coverage and Au-SAM bond strength were found to significantly affect on the thermal conductance. The vibration densities of state (VDOS) were calculated to explore the mechanism of thermal energy transport. interfacial thermal resistance was found mainly due to the limited population of low-frequency vibration modes of the SAM molecule. Ballistic energy transport inside the SAM molecules was confirmed, and the anharmonicity played an important role in energy transport across the junctions. A heat pulse was imposed on the junction substrate, and heat dissipation inside the junction was studied. Analysis of the junction response to the heat pulse showed that the Au-SAM interfacial thermal resistance was much larger than the Au substrate and SAM resistances separately. This work showed that both the Au substrate and SAM molecules transported thermal energy efficiently, and it was the Au-SAM interfaces that dominated the thermal energy transport across the Au-SAM-Au junctions. (C) 2009 Elsevier Ltd. All rights reserved.