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Operating the HCCI engine with dual fuels with a large difference in auto-ignition characteristics (octane number) is one way to control the HCCI operation. The effect of octane number on combustion, emissions and engine performance in a 6 cylinder SCANIA truck engine, fuelled with n-heptane and isooctane, and running in HCCI mode, are investigated numerically and compared with measurements taken from Olsson et al. [SAE 2000-01-2867]. To correctly simulate the HCCI engine operation, we implement a probability density function (PDF) based stochastic reactor model (including detailed chemical kinetics and accounting for inhomogeneities in composition and temperature) coupled with GT-POWER, a 1-D fluid dynamics based engine cycle simulator. Such a coupling proves to be ideal for the understanding of the combustion phenomenon as well as the gas dynamics processes intrinsic to the engine cycle.