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This work concerns the oxidation of biodiesel surrogates in a CI engine. An experimental study has been carried out in a single-cylinder common-rail CI engine with soybean biodiesel and two biodiesel surrogates containing neat methyl decanoate and methyl decanoate/n-heptane blends. Tests have been conducted with various intake oxygen concentrations ranging from 21% to approximately 9% at intake temperatures of 25°C and 50°C. The results showed that the ignition delay and smoke emissions of neat methyl decanoate were closer to that of soybean biodiesel as compared with methyl decanoate/n-heptane blends. A reduced chemical kinetic mechanism for the oxidation of methyl decanoate has been developed and applied to model internal combustion engines. A KIVA code, coupled with the Chemkin chemistry solver, was used as the computational platforms. The effects of various intake oxygen concentrations on the in-cylinder emissions of OH and soot were discussed.