Combustion and emission characteristics Of compression ignition engines strongly depend upon inner-nozzle flow and spray behavior. These processes control the fuel-air mixing, which in turn is critical for the combustion process. Previous studies by us highlighted the differences in the physical and chemical properties of petrodiesel and biodiesel, which significantly altered the inner-nozzle flow and spray structure. The current study is another step in this direction to gain a fundamental understanding on the influence of fuel properties on the combustion and emission characteristics of the compression ignition engine. n-Heptane and methyl butanoate were selected as surrogates for diesel and biodiesel fuels, respectively, because the chemical: kinetic pathways were well-understood. Liquid length and flame lift-off length for diesel and biodiesel fuels were validated against data available in the literature. Liquid lengths were always higher for biodiesel because of its higher heat of vaporization, which resulted in increased interplay between spray and combustion processes under all conditions investigated. Ambient: air entrainment was also lower for biodiesel mainly because of slower atomization and breakup. The mechanism for flame stabilization is further analyzed by estimating the turbulent burning velocity for both of the fuels. This analysis revealed that neither,flame propagation nor isolated ignition kernels upstream and detached from high-temperature regions can be the mechanism for flame stabilization. Flame propagation speeds were observed to be similar for both fuels. Biodiesel predicted lower soot concentrations, which were also reflected in reduced C2H2 mole fractions. Although prompt NOx was higher for biodiesel, total NOx was lower because of reduced thermal NOx. The ignition delay and NOx emissions predicted by these simulations do. not agree with trends reported in the literature; hence, this study highlights the need for better fuel surrogates for diesel and biodiesel fuels.