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Combustion and pollutant formation in a DI-Diesel engine are numerically investigated using the Eulerian Particle Flamelet Model (EPFM). A baseline case for part load operating conditions is considered as well as an EGR variation. The surrogate fuel consisting of n-decane (70% liquid volume fraction) and α-methylnaphthalene (30% liquid volume fraction) is used in the simulation. Results are compared to experimental data that has been obtained using real diesel fuel. The effect of multiple flamelets on the simulation of the auto-ignition process and the pollutant formation is discussed and a converging behavior of the model with respect to the number of flamelets is found. The effect of homogenization of the three-dimensional mixture field is investigated and it has been included in the formulation of the scalar dissipation rate.