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Combustion simulation is an effective tool in overcoming the issues associated with gasoline HCCI engines, controlling ignition timing and extending the operating range. The research discussed in this paper commenced by optimizing the reaction mechanism from the perspective of ignition delay using the genetic algorithm (GA) method. Simulations employing the optimized reaction mechanism were then able to more accurately reproduce the ignition timing of iso-octane and primary reference fuels (PRF). Ignition times obtained from simulations showed excellent correlation with ignition times measured using these fuels in shock tube experiments, and in engines with both homogeneous and non-homogeneous fuel distributions. The use of the PRF mechanism for gasoline with an equivalent octane number enables excellent reproduction of ignition timing even when EGR is employed.