In this paper, equilibrium molecular dynamics simulations were performed on Au-SAM (self-assembly monolayer)-Au junctions. The SAM consisted of alkanedithiol molecules. The out-of-plane (-direction) thermal conductance and in-plane (- and -direction) thermal conductivities were calculated. The simulation finite size effect, gold substrate thickness effect, temperature effect, normal pressure effect, molecule chain length effect, and molecule coverage effect on thermal conductivity/conductance were studied. Vibration power spectra of gold atoms in the substrate and sulfur atoms in the SAM were calculated, and vibration coupling of these two parts was analyzed. The calculated thermal conductance values of Au-SAM-Au junctions are in the range of experimental data on metal-nonmetal junctions. The temperature dependence of thermal conductance has a similar trend to experimental observations. It is concluded that the Au-SAM interface resistance dominates thermal energy transport across the junction, while the substrate is the dominant media in which in-plane thermal energy transport happens.
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