  We report detailed atomistic simulations combined with high-fidelity
conductance calculations to probe the structural origins of conductance
fluctuations in thermally evolving Au-benzene-1,4-dithiolate-Au junctions. We
compare the behavior of structurally ideal junctions (electrodes with flat
surfaces) to structurally realistic, experimentally representative junctions
resulting from break junction simulations. The enhanced mobility of metal atoms
in structurally realistic junctions results in significant changes to the
magnitude and origin of the conductance fluctuations. Fluctuations are larger
by a factor of 2-3 in realistic junctions compared to ideal junctions.
Moreover, in junctions with highly deformed electrodes, the conductance
fluctuations arise primarily from changes in the Au geometry, in contrast to
results for junctions with non-deformed electrodes, where the conductance
fluctuations are dominated by changes in the molecule geometry. These results
provide important guidance to experimentalists developing strategies to control
molecular conductance for device applications, and also to theoreticians
invoking simplified structural models of junctions to predict their behavior.
