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Studies on the effects of methyl soyate (biodiesel) blends with #2 diesel fuel in conjunction with various high pressure injection schemes were conducted on a single cylinder version of the Caterpillar 3400 series heavy duty diesel engine. Engine operating conditions at both high and low loads were investigated. Experiments were performed over a range of injection timings allowing particulate versus NOx trade-off curves to be generated. Phillips 66 certified #2 diesel fuel was used as the baseline; mixtures of 20% and 40% by volume of methyl soyate with the baseline fuel were used as the biodiesel blends. A blend of 20% by volume octadecene (a hydrocarbon fuel that is representative of the biodiesel hydrocarbon's composition but without the oxygen) in #2 diesel fuel was also investigated to help determine the mechanisms of emissions reduction.