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An integrated system based modeling approach has been developed to understand early Direct Injection (DI) Diesel Homogeneous Charge Compression Ignition (HCCI) process. GT-Power, a commercial one-dimensional (1-D) engine cycle code has been coupled with an external cylinder model which incorporates sub-models for fuel injection, vaporization, detailed chemistry calculations (Chemkin), heat transfer, energy conservation and species conservation. In order to improve the modeling accuracy, a multi-zone model has been implemented to account for temperature and fuel stratifications in the cylinder charge. The predictions from the coupled simulation have been compared with experimental data from a single cylinder Caterpillar truck engine modified for Diesel HCCI operation. A parametric study is conducted to examine the effect of combustion timing on four major control parameters. Overall the results show good agreement of the trends between the experiments and model predictions.