This paper deals with the modeling and simulation of the thrust chamber dynamics of airbreathing pulse detonation engines (PDEs). The system under consideration includes a supersonic inlet, a rotary valve, a multi-tube combustor, and a common nozzle. The analysis treats the conservation equations of mass, momentum, energy, and species concentration in two dimensions. Chemical kinetics is modeled using a onestep global reaction scheme, which is calibrated with a detailed model for stoichiometric hydrogen/air system. The governing equations and their associated boundary conditions are numerically solved be means of a recently developed Space-Time Conservation Element/Solution Element method, which circumvents the deficiencies of existing numerical methods for treating detonation waves and shock discontinuities. The resultant computer code is further parallelized using the Message-Passing-Interface library to improve its efficiency. The combustion and gasdynamic processes in both single- and multi-tube PDEs are studied in detail. The effects of operation frequency, valve close-up time, and system geometry on the engine propulsive performance are examined. Results show that the multi-tube design substantially modifies the system dynamics and reduces the degree of the unsteadiness of the engine. It, however, only slightly improves the propulsive performance for the system considered herein.