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It has been known from multi-zone simulations that HCCI combustion can be significantly affected by temperature stratification of the in-cylinder gas. With the same combustion timing (i.e. crank angles at 50% heat release, denoted as CA50), large temperature stratification tends to prolong the combustion duration and lower down the in-cylinder pressure-rise-rate. With low pressure-rise-rate HCCI engines can be operated at high load, therefore it is of practical importance to look into more details about how temperature stratification affects the auto-ignition process. It has been realized that multi-zone simulations can not account for the effects of spatial structures of the stratified temperature field, i.e. how the size of the hot and cold spots in the temperature field could affect the auto-ignition process. This question is investigated in the present work by large eddy simulation (LES) method which is capable of resolving the in-cylinder turbulence field in space and time.