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Fluorine ions can be effectively incorporated into AlGaN/GaN high electron mobility transistor (HEMT) structures, enabling the modulation of local potential and carrier density. The physical mechanism of fluorine incorporation in AlGaN/GaN heterojunctions is of fundamental importance to the stability of fluorine ions in AlGaN/GaN HEMTs. In this work, the molecular dynamic (MD) simulation method is used to calculate the potential energies of interstitial and substitutional fluorine atoms in AlGaN/GaN material system. Ziegler-Biersack-Littmark (ZBL), Lindhard-Sorensen (L-S) and Coulomb potential functions are applied in the MD simulation. The geometric lattice structures, spontaneous and piezoelectric polarizations, and temperature dependence are also included in the simulation. The activation energies associated with interstitial-substitutional and interstitial-interstitial diffusions are obtained. It is revealed that the fluorine ions are most likely located at the substitutional group-III cation sites S(III) and the diffusion of fluorine ions should be dominated by S(III)-interstitial process which exhibits an activation energy of 1.1 eV in Al(0.25)Ga(0.75)N and 1.4 eV in GaN in the presence of group-III vacancies. It is expected that the removal of group-III vacancies can significantly suppress the fluorine diffusion, which in turn, leads to excellent fluorine stability in III-nitride materials. (C) 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim