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System level modeling was used to develop a suitable control strategy for Diesel Homogeneous Charge Compression Ignition (HCCI) transient operation. Intake temperature and pressure, engine speed, engine load, cylinder wall temperature, exhaust gas recirculation, etc. all significantly affect combustion phasing generating a scenario where simple ECU mapping techniques prove inadequate. Two-stage fuels such as diesel fuel pose additional challenges for accurate combustion control. Low-temperature cool-flame chemical heat release can significantly alter the thermodynamic state of the trapped gaseous mixture and hence combustion phasing. Operator and environmentally induced transients can rapidly alter combustion phasing parameters suggesting a need for model-based control. A model-based control strategy featuring the identified essential physics has been developed to control diesel HCCI combustion phasing through transient operation.