Model-based design and analysis of a reconfigurable continuous-culture bioreactor

In this paper, we present a model-based design and analysis of prototype laboratory equipment used for growing bacteria under precisely controlled conditions for systems biology experiments. Continuous-culture bioreactors grow microorganisms continuously over periods as long as several months. Depending on the particular experiment, the reconfigurable continuous-culture bioreactor we model and analyze may operate as: (a) a chemostat with constant volume, (b) a turbidostat with constant bacterial concentration as observed through turbidity (optical density), or (c) a morbidostat with constant death-rate of bacteria. Such systems have interesting safety specifications such as not overflowing beakers, maintaining bacterial concentrations within ranges, etc., that must be maintained over long experimental periods. We develop preliminary controller and plant models and analyze them through simulation in Simulink/Stateflow (SLSF), and using reachability analysis in SpaceEx by translating the SLSF models to hybrid automata. The analysis indicates that the proposed design satisfies its regulation specifications for microorganism concentration may avoid error scenarios encountered in experiments with a prior design.