A probing method based on bioluminescence was developed and applied for studies of mass transfer, kinetics and feed optimization. We present here two applications that require modelling of the process for purposes of model discrimination and parameter estimation. Oxygen diffusivity in the cell-layer of a hollow-fiber reactor is estimated matching the luminescence measurements along such a reactor with the heterogeneous model of a plug-flow reactor. The transfer mechanism of substrates from the liquid phase to the cell in a chemostat is determined by following luminescence oscillations forced by periodic pumping of the substrate. The mechanism is elucidated fot the disparity between the period of the oscillations and the reactor residence time. Mass transfer coefficients are determined for the observed amplitude.