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Coupled-resonator optical waveguides made from coupled high- Q photonic crystal nanocavities are investigated for use as cavities in mode-locked lasers. Such devices show great potential in slowing down light and can serve to reduce the cavity length of a mode-locked laser. An explicit expression for the cold-cavity transmission spectrum is derived and used to interpret numerical investigations performed to characterize the parameter regime of active mode-locked operation. It is found that the modulation frequency relative to the centerband nearest supermode (SM) frequency shift determines the quality of the emerging pulse train. A range of tuning around this frequency allows for effective mode locking. Finally, noise is added to the generalized single-cavity eigenfrequencies in order to evaluate the effects of fabrication imperfections on the cold-cavity transmission properties and consequently on the locking of SMs.