  With the objective to understand microscopic principles governing thermal
energy flow in nanojunctions, we study phononic heat transport through
metal-molecule-metal junctions using classical molecular dynamics (MD)
simulations. Considering a single-molecule gold-alkanedithiol-gold junction, we
first focus on aspects of method development and compare two techniques for
calculating thermal conductance: (i) The Reverse Nonequilibrium MD (RNEMD)
method, where heat is inputted and extracted at a constant rate from opposite
metals. In this case, the thermal conductance is calculated from the
nonequilibrium temperature profile that is created on the junction. (ii) The
Approach-to-Equilibrium MD (AEMD) method, with the thermal conductance of the
junction obtained from the equilibration dynamics of the metals. In both
methods, simulations of alkane chains of growing size display an approximate
length-independence of the thermal conductance, with calculated values matching
computational and experimental studies. The RNEMD and AEMD methods offer
different insights on thermal transport, and we discuss their relative benefits
and shortcomings. Assessing the potential application of molecular junctions as
thermal diodes, the alkane junctions are made spatially asymmetric by modifying
their contact regions with the bulk, either by using distinct endgroups or by
replacing one of the Au contacts by Ag. Anharmonicity is built into the system
within the molecular force-field. Using the RNEMD method, we show that, while
the temperature profile strongly varies (compared to the
gold-alkanedithiol-gold junctions) due to these structural modifications, the
thermal diode effect is inconsequential in these systems -- unless one goes to
very large thermal biases. This finding suggests that one should seek molecules
with considerable internal anharmonic effects for developing nonlinear thermal
devices.
