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In this paper, computation fluid dynamics (CFD) simulations are employed to describe the effect of flow parameters on the formation of soot and NOx in a heavy duty engine under low load and high load. The complexity of diesel combustion, specially when soot, NOx and other emissions are of interest, requires using a detailed chemical mechanism to have a correct estimation of temperature and species distribution. In this work, Multiple Representative Interactive Flamelets (MRIF) method is employed to describe the chemical reactions, ignition, flame propagation and emissions in the engine. A phenomenological model for soot formation, including soot nucleation, coagulation and oxidation with O2 and OH is incorporated into the flamelet combustion model. Different strategies for modelling NOx are chosen to take into account the longer time scale for NOx formation. The numerical results are compared with experimental data to show the validity of the model for the cases under study.