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A 0.5 liter optical HCCI engine firing a mixture of n-heptane (50%) and iso-octane (50%) with air/fuel ratio of 3 is studied using large eddy simulation (LES) and laser diagnostics. Formaldehyde and OH LIF and in-cylinder pressure were measured in the experiments to characterize the ignition process. The LES made use of a detailed chemical kinetic mechanism that consists of 233 species and 2019 reactions. The auto-ignition simulation is coupled with LES by the use of a renormalized reaction progress variable. Systematic LES study on the effect of initial temperature inhomogeneity and turbulence intensity has been carried out to delineate their effect on the ignition process. It was shown that the charge under the present experimental condition would not be ignited without initial temperature inhomogeneity. Increasing temperature inhomogeneity leads to earlier ignition whereas increasing turbulence intensity would retard the ignition.