A novel framework for intelligent design of engine systems is introduced. Existing models of engine components and processes are integrated into a multi-purpose, flexible configuration framework. Fundamental thermodynamic elements, including zero-dimensional control volumes, one-dimensional pulsating fluid lines, and continuous flow machines are identified as the constituting components of engine systems. Models of the behavior of these elements, with various degrees of thermodynamic resolution, have been implemented into the framework. The task of the engine designer is, thus, reduced into selecting appropriate thermodynamic elements to model his engine system based on his design objectives. The applicability of the present framework to a wide range of simulation problems is demonstrated. Test problems include a study of wave dynamics in three communicating, constant volume plenums; combustion in a constant volume reactor; a tuning study for the induction system of a single cylinder engine; and, finally, a simulation of a multi-cylinder, piston-compounded diesel engine concept.