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Detailed diesel particulates morphology, nanostructures, fractal geometry, and nitrogen oxides (NOx) emissions were analyzed for five different test fuels in a 1.7-L, common-rail direct-injection diesel engine. The accurately formulated fuels permit the effects of sulfur, paraffins, aromatics, and naphthene concentrations to be determined. A novel thermophoretic sampling technique was used to collect particulates immediately after the exhaust valves. The morphology and nanostructures of particulate samples were examined, imaged with a high-resolution transmission electron microscope (HRTEM), and quantitatively analyzed with customized digital image processing/data acquisition systems. The results show that the particle sizes and the total mass of particulate matter (PM) emissions correlate most strongly with the fuels' aromatics and sulfur content.