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We investigate the size effects on the structures and thermal conductivity of silicon nanoclusters (SiNCs) using molecular dynamics simulations. We demonstrate that as the diameter of the SiNCs increases from 1.80 nm to 3.46 nm, the cluster structure changes from an amorphous state to a crystalline state at 300 K, which is in good agreement with the experimental findings. Our calculated thermal conductivity of the SiNCs shows a size-dependent effect due to the remarkable phonon-boundary scattering and can be about three orders of magnitude lower than that of bulk Si.