We investigate the thermopower of a metal-molecule-metal junction taking into account thermal effects on the junction. Based on analytical expressions and numerical simulations, we show that the thermoelectric potential reveals valuable information on the mechanisms controlling the electron transfer process, including coherent transmission and thermalized hopping. We also show that at high temperatures, the position of the Fermi energy relative to the molecular states can be easily deduced from the thermoelectric potential. Standard current-voltage measurements are insensitive to this information.
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