We have studied self-coordinated transportation systems using SU-8 microstructures in open microchannels and here present a stochastic model for the bacteria-driven microbarge that is designed to mimic the motion of this system with and without chemical gradients or other external stimuli and compare experimental results with the outcomes of simulations. Our ultimate goal is to use our mathematical model as a workbench to propose various closed loop control schemes applicable for the real system.