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.The initial goal of this project was to develop a physics-based approach to controlling engines with a cam-less or fully flexible valvetrain system. The model and control strategies that were developed can be applied to many internal combustion engine applications. The HCCI application in particular benefits the most from this technology because of the improved control of cylinder air mass and mixture composition. The real time one-dimensional flow model and the individual cylinder model developed during this project are explained. A single cylinder spark ignition research engine with cam-phasing and interchangeable camshafts was used for evaluating model parameter estimation and engine control performance. Test data is shown comparing estimated and measured pressures in the intake manifold and cylinder. The applicability of this control strategy to HCCI is discussed.