Although biodiesel has begun to penetrate the fuel market, its effect on injection processes, combustion and emission formation under diesel engine conditions remains somewhat unclear. Typical exhaust measurements from engines running biodiesel indicate that particulate matter, carbon monoxide and unburnt hydrocarbons are decreased, whereas nitrogen oxide emissions tend to be increased. However, these observations are the result of complex interactions between physical and chemical processes occurring in the combustion chamber, for which understanding is still needed. To characterize and decouple the physical and chemical influences of biodiesel on spray mixing, ignition, combustion and soot formation, a soy methyl-ester (SME) biodiesel...