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An approach to accurately capture overall behavior in a system level model of DI Diesel HCCI engine operation is presented. The modeling methodology is an improvement over the previous effort [36], where a multi-zone model with detailed chemical kinetics was coupled with an engine cycle simulation code. This multi-zone technique was found to be inadequate in capturing the fuel spray dynamics and its impact on mixing. An improved methodology is presented in this paper that can be used to model fully and partially premixed charge compression ignition engines. A Computational Fluid Dynamics (CFD) driven model is used where the effects of fuel injection, spray evolution, evaporation, and turbulent mixing are considered. The modeling approach is based on the premise that once the initial spray dynamics are correctly captured, the overall engine predictions during the combustion process can be captured with good accuracy.