ABSTRACT Many currently approved gene therapies use adeno‐associated virus (AAV) to deliver DNA sequences encoding protein(s)‐of‐interest into cells. The AAV viral genome forms stable, circular DNA structures called episomes after entering the nuclei. Therapeutic proteins are then generated in vivo from transcription and translation of these episomes, and long‐term durability thus depends on episome stability. Prior modeling work has utilized differential equation‐based models to characterize AA