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The structural properties of InN/GaN heterostructure nanowires (NWs) were studied using transmission electron microscope techniques to determine strain behavior. A great quantity of the misfit strain between InN and GaN was relaxed through the introduction of misfit dislocations along the interface. Geometric phase analysis revealed a strain-concentration phenomenon in the strain map of the out-of-plane components and a gradual lattice recovery in that of the in-plane components over the InN/GaN interface. Interface structures that were modulated at the atomic-scale were observed in several InN/GaN heterostructure NWs. Complex strain distributions were identified in both InN and GaN.