The thermal conductivity of carbon nanotubes with Stone-Wales (SW) defects was investigated using non-equilibrium molecular dynamics method. The defect effects were analyzed by the temperature profile and local thermal resistance of the nanotubes with one or more SW defects and further compared with perfect tubes. The influences of the defect concentration, the length, the chirality and the radius of tubes and the ambient temperature were studied. It was demonstrated that a sharp jump in the temperature profile occurred at defect position due to a higher local thermal resistance, thus dramatically reducing the thermal conductivity of the nanotube. As the number of SW defects increases, the thermal conductivity decreases. Relative to the chirality, the radius has greater effects on the thermal conductivity of tubes with SW defects. With the similar radius, the thermal conductivity of armchair nanotube is higher than that of zigzag one. The shorter nanotube is more sensitive to the defect than the longer one. Thermal conductivity of the nanotube increases with ambient temperature, reaches a peak, and then decreases with increasing temperature.

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