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This paper presents a computational study of the effects of fuel and thermal stratifications on homogenous charge compression ignition (HCCI) combustion process in a personal car sized internal combustion engine. Stratified HCCI conditions are generated using a negative valve overlap (NVO) technique. The aims of this study are to improve the understanding of the flow dynamics, the heat and mass transfer process and the onset of auto-ignition in stratified charges under different internal EGR rate and NVO conditions. The fuel is ethanol supplied through port-fuel injection; the fuel/air mixture is assumed to be homogenous before discharging to the cylinder. Large eddy simulation (LES) is used to resolve in detailed level the flow structures, and the mixing and heat transfer between the residual gas and fresh fuel/air mixtures in the intake and compression strokes.