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In the present work the three-dimensional KIVA CFD code was used to simulate the combustion process in a HSDI diesel engine. State-of-the-art models, including the KH-RT spray breakup model, the RNG k-ε turbulence model, and a n-heptane reduced chemistry including reduced GRI NOx mechanism were used. The performances of two combustion models, KIVA-CHEMKIN and GAMUT (KIVA-CHEMKIN-G), coupled with 2-step and multi-step phenomenological soot models were compared. The numerical results were compared with available experimental data obtained from an optically accessible HSDI engine and good agreement was obtained. To assess the effects of the in-cylinder flow field on combustion and emissions, off-centered swirl flows were also considered. In these studies, the swirl center was initialized at different positions in the chamber for different cases to simulate the effects of different intake flow arrangements.