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Southwest Research Institute, as part of the Clean Diesel IV consortium, built a multi-cylinder HCCI engine that ran in the HCCI combustion mode full-time. The engine was used to develop HCCI fuels, demonstrate the potential operating range of HCCI, and to demonstrate the feasibility of transient control of HCCI. As part of the engine design, a hardware based method of decoupling control of air and EGR was developed and patented [ 1 ]. The system utilized a positive displacement supercharger with a controlled bypass valve for air-flow control, and a high-pressure loop EGR system with variable geometry turbocharger to control the EGR rate. By utilizing the system, the required precision from the air and EGR control in the engine controller was reduced.