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We investigated the structural characteristics and defect states of intrinsic GaN epi-layers in a high power device structures grown on GaN and sapphire substrates by metal–organic chemical vapor deposition (MOCVD). From X-ray diffraction, Raman spectroscopy, and photoluminescence measurements, the structural properties of the GaN epi-structures were improved clearly using GaN substrates. Through optical conductance deep level transient spectroscopy analysis, four traps were observed in all the GaN layers. The activation energies of these traps were 0.93 eV (H1), 0.61 eV (H2), 0.50 eV (H3), and 0.2 eV (H4) above the valance band edge, and their capture cross-sections were 3.41 × 10–14 cm2 (H1), 3.04 × 10–14 cm2 (H2), 1.35 × 10–12 cm2 (H3) and 2.90 × 10–16 cm2 (H4), respectively. The origins of the H4 and H1 traps may be related to gallium vacancy (VGa) and VGa-related defects, and the H2 and H3 traps were from nitrogen vacancy (VN). The total defect density of GaN epi-layers estimated using the space charge limited current method was reduced to 1.18 × 1015 cm−3 on GaN substrates from about 1.52 × 1017 cm−3 on sapphire substrates.