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Experimental studies of soot particles showed that the intensity ratio of amorphous and graphite layers measured by Raman spectroscopy correlates to soot oxidation reactivities, which is very important for regeneration of the diesel particulate filters and gasoline particulate filters. This physical mechanism is absent in all soot models. In the present paper, a novel two-layer soot model was proposed that considers the amorphous and graphite layers in the soot particles. The soot model considers soot inception, soot surface growth, soot oxidation by O2 and OH, and soot coagulation. It is assumed that amorphous-type soot forms from fullerene. No soot coagulation is considered in the model between the amorphous- and graphitic-types of soot. Benzene is taken as the soot precursor, which is formed from acetylene. The model was implemented into a commercial CFD software CONVERGE using user defined functions. A diesel engine case was simulated.