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In this study, the effects of varying the start of injection in a Free Piston Engine (FPE) have been investigated, using the KIVA-3V CFD code. In order to simulate the FPE the code has been modified by replacing the conventional crank shaft controlled piston motion by a piston motion profile calculated using a MATLAB/SIMULINK model. In this model, the piston motion is controlled by Newton's second law and the combustion process is represented by a simplified model based on ignition delay integrals and Wiebe functions. The results were tuned using predictions from the SENKIN software which are based on the detailed chemical kinetics mechanism of a Diesel oil surrogate represented by a blend of the main aliphatic (70% n-heptane) and aromatic (30% toluene) components. In order to help analyze the emission formation resulting from the HCCI/PPCI combustion modes in the engine, a special approach based on the temperature-equivalence ratio maps has been developed.