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In this study, the operation of npn-type GaN-based heterojunction bipolar transistors with different net acceptor concentrations in p-base regions was simulated. It was confirmed that there is a critical net acceptor concentration (NA-ND) depending on the thickness of the base region and that if the NA-ND is lower than the critical value, the collector current may anomalously increase, regardless of base current injection. This phenomenon is caused by the punch-through process via the depletion layer extending from the collector–base junction. The effect of the valence band energy offset at the emitter-base heterojunction (ΔEV) on the current gain (β) was also investigated, and the results showed that β peaks when ΔEV is 0.22–0.30 eV. This is determined by the balance between the hot-electron injection and thermal diffusion processes in the electron transport from the emitter to the base. [ABSTRACT FROM AUTHOR]