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One of the factors preventing widespread use of Homogeneous Charge Compression Ignition or HCCI is the challenge of controlling the process under transient conditions. Current engine control technology does not have the ability to accurately control the individual cylinder states needed for consistent HCCI combustion. The material presented here is a new approach to engine control using a physics-based individual cylinder real time model to calculate the engine states and then controlling the engine with this state information. The model parameters and engine state information calculated within the engine controller can be used to calculate the required actuator positions so that the desired mass of air, fuel, and residual exhaust gas are achieved for each cylinder event. This approach offers a solution to the transient control problem that works with existing sensors and actuators.