||Transport and metabolism are modeled using the constraint-based method flux-balance analysis (FBA). Briefly, FBA assumes that bacteria have evolved to maximize growth, and poses transport and metabolism as the optimization of cellular building block and energy production subject to available nutrients, and allowed chemical reactions. FBA models are typically constrained by experimentally measured transport and diffusion rates. In addition to these constraints, we constrain constrain our FBA module by our model's predicted enzyme abundances, and by experimentally measured kinetic parameters. These additional constraints yield a more accurate model of transport and metabolism. Furthermore, we use our other modules to obtain a more extensive and accurate metabolic objective than used in earlier FBA models.
Computes reaction bounds based on
specific transport rate
Computes optimal reaction fluxes which maximize biomass production
Computes integer-valued production of biomass components
Updates amounts of biomass components
molecules/(gram dry biomass)/s