Gene Expression Across Growth Stages (GEAGS): Modeling Circuit Dynamics in Batch Cultures.

The dynamics of recombinant gene expression in bacterial systems are often modeled under the assumption of constant growth. However, most synthetic gene circuit assays are performed in enclosed batch cultures, where nutrient depletion and physiological transitions from exponential to stationary phase substantially influence transcription, translation, mRNA degradation, and protein dilution. This chapter introduces the Gene Expression Across Growth Phases (GEAGS) framework-a dual-scale modeling approach that couples molecular reaction networks with logistic population growth through growth-dependent rate modifier functions (RMFs). The framework enables accurate simulation of gene expression dynamics under time-varying growth rate and resource competition. We provide step-by-step methods to construct GEAGS models, starting from a minimal constitutive reporter system and extending to complex applications involving optogenetic regulation and layered feedback control. This protocol establishes a generalizable computational workflow for synthetic biologists aiming to model the effects of growth, molecular crowding, and resource limitation on gene expression dynamics in batch culture.