Abstract: A closed-loop control algorithm that reduces the increases in nitrogen oxides (NOx) commonly observed with biodiesel combustion while retaining particulate matter (PM) reductions with variable biodiesel blend fractions. One embodiment includes a control algorithm that is closed-loop with regards to combustible oxygen mass fraction (COMF) instead of exhaust gas recirculation (EGR) fraction. Yet another algorithm includes biodiesel blend estimation and “fuel-flexible” accommodation. A physics-based model has also been developed which predicts experimentally observed engine performance and emissions for biodiesel.