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Multi-dimensional computational efforts using comprehensive and skeletal kinetics have been made to investigate the cool flame region in HCCI combustion. The work was done in parallel to an experimental study that showed the impact of the negative temperature coefficient and the cool flame on the start of combustion using different fuels, which is now the focus of the simulation work. Experiments in a single cylinder CFR research engine with n-butane and a primary reference fuel with an octane number of 70 (PRF 70) were modeled. A comparison of the pressure and heat release traces of the experimental and computational results shows the difficulties in predicting the heat release in the cool flame region. The behavior of the driving radicals for two-stage ignition is studied and is compared to the behavior for a single-ignition from the literature. Model results show that PRF 70 exhibits more pronounced cool flame heat release than n-butane.