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The objective of the present research was to analyze the effects of using oxygenated fuels (FAMEs or biodiesel fuels) on injected fuel spray and soot formation. A 3-D numerical study which using the KIVA-3V code with modified chemical and physical models was conducted. The large-eddy simulation (LES) model and KH-RT model were used to simulate fuel spray characteristics. To predict soot formation processes, a model for predicting gas-phase polycyclic aromatic hydrocarbons (PAHs) precursor formation was coupled with a detailed phenomenological particle formation model that included soot nucleation from the precursors, surface growth/oxidation and particle coagulation. The calculated liquid spray penetration results for all fuels agreed well with the measured data. The spray measurements were conducted using a constant volume chamber (CVC), which can simulate the ambient temperature and density under real engine conditions.