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Biodiesel fuel can be produced from a wide range of source materials that affect the properties of the fuel. The diesel engine has become a highly tuned power source that is sensitive to these properties. The objectives of this research were to measure and predict the key properties of biodiesel produced from a broad range of source materials to be used as inputs for combustion modeling; and second to compare the results of the model with and without the biodiesel fuel definition. Substantial differences in viscosity, surface tension, density and thermal conductivity were obtained relative to reference diesel fuels and among the different source materials. The combustion model revealed differences in the temperature and emissions of biodiesel when compared to reference diesel fuel.