Heterostructure transistors based on the AlGaN/GaN material structure are popular for chemical and biological sensors because of their nontoxicity and chemical inertness in biological or corrosive environments. They also offer very high sensitivity as a result of the very large gain and transconductance. Studies over the years show much research on this technology for sensing applications including pH sensing, prostate cancer detection, and breast cancer detection. However, the designs of these devices are not optimized because of nonexistent or rudimentary modeling and simulation support. Commercial software packages adept at simulating III-V-based transistors do not have applications built-in for chemical sensing capability. Current research relies on analytical models and in-house numerical programs to do specific and limited simulations. We build upon a TCAD simulation framework (FLOODS) specifically suited for III-V device simulation that is capable of self-consistent, fully-coupled simulation of reaction-dependent physics at the electrolyte/semiconductor interface. This paper outlines the simulation methodology for a pH sensor using an open-gate AlGaN/GaN High Electron Mobility Transistor (HEMT). The interfacial reactions are coupled to traditional device simulation equations, i.e. Poisson and carrier continuity. This enables surface charging reactions to be directly coupled to the device output terminal characteristics. We also solve for electrostatic field and ion transport in the electrolyte. This work will enable optimization of specific sensor technologies or exploration of the fundamental physics behind the sensing mechanism.