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Electro-pneumatic valve actuators are used to eliminate the cam shaft of a traditional internal combustion engine. They are used to control the opening timing, duration, and lift of both intake and exhaust valves. A physics based nonlinear mathematical model called the level one model was built using Newton's law, mass conservation and thermodynamic principles. A control oriented model, the level two model, was created by partially linearizing the level one model for model reference parameter identification. This model reduces computational throughput and enables real-time implementation. A model reference adaptive control system was used to identify the nonlinear parameters that were needed for generating a feedforward control signal. The closed-loop valve lift tracking, valve opening and closing timing control strategies were proposed.