In this study we present a detailed, mechanism-based mathematical framework of Drosophila
circadian rhythms. This framework
facilitates a more systematic approach to understanding circadian rhythms using a comprehensive representation of the network
underlying this phenomenon. The possible mechanisms underlying the cytoplasmic interval timer created by PERIODTIMELESS association are investigated, suggesting a novel positive feedback regulatory structure. Incorporation of this additional feedback into a full circadian model produced results that are consistent with previous experimental observations of wild-type protein profiles and numerous mutant phenotypes.