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The methyl ester of soybean oil, known as biodiesel, is receiving increasing attention as an alternative fuel for diesel engines. Biodiesel is a nontoxic, biodegradable, and renewable fuel with the potential to reduce engine exhaust emissions. However, previous results have shown that biodiesel-fueled engines produce a higher fraction of soluble organic material (SOF) in their exhaust particulate matter than when petroleum-based diesel fuel is used even when the total particulate emissions are lowered. Most researchers have also observed that unburned hydrocarbon (HC) emissions decrease with biodiesel. In this project, the formation of SOF in exhaust particulates under different measurement conditions and the possibility of deposition of HC vapor in the sampling lines of the HFID detector were studied experimentally and theoretically when the diesel engine was fueled with biodiesel.