First-principles molecular dynamics simulation based on a plane wave/pseudopotential implementation of density functional theory is adopted to investigate atomic scale energy transport for semiconductors (silicon and germanium). By imposing thermostats to keep constant temperatures of the nanoscale thin layers, the initial thermal non-equilibrium between the neighboring layers is established under the vacuum condition. Models with variable gap distances with an interval of lattice constant increment of the simulated materials are set up and statistical comparisons of temperature evolution curves are made. The equilibration time from non-equilibrium state to thermal equilibrium state of different silicon or/and germanium layers combinations are calculated. The results show significant distinctions of heat transfer under different materials and temperatures combinations. Further discussions on the equilibrium time are made to explain the simulation results. As the first work of the atomic scale energy transport spanning from heat conduction to thermal radiation, the simulation results highlight the promising application of the first-principles molecular dynamics in thermal engineering. (C) 2012 Elsevier Ltd. All rights reserved.