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The effects of the physical and chemical properties of biodiesel fuels on the combustion process and pollutants formation in Direct Injection (DI) engine are investigated numerically by using multi-dimensional CFD models. In the current study, methyl butanoate (MB) and n-heptane are used as the surrogates for the biodiesel fuel and the conventional diesel fuel. Detailed kinetic chemical mechanisms for MB and n-heptane are implemented to simulate the combustion process. It is shown that the differences in the chemical properties between the biodiesel fuel and the diesel fuel affect the whole combustion process more significantly than the differences in the physical properties. While the variations of both the chemical and the physical properties between the biodiesel and diesel fuel influence the soot formation at the equivalent level, the variations in the chemical properties play a crucial role in the NO emissions formation.