Petroleum-based fuels are used in IC engines for power generation. Global demand for petroleum-based fuels has been increasing in the past decade. Meanwhile, the increase in supply is growing at a slower rate, resulting in a sharp rise in energy cost. On the other hand, diesel engine is known to have better thermal efficiency than spark-ignition engine due to higher compression ratio. Three-dimensional multi-physics simulations were conducted to characterize biodiesel combustion in compression ignition engines, using various dual injection scheme. Simulations were conducted to test various injection schemes, fuel compositions and their effects on the engine out emissions with the main focus on simultaneous reductions in NOx and soot. A robust multi-component evaporation model for droplets is developed. The model allows accurate description of the evaporation process of fuel droplets while maintaining the computational efficiency. The analysis in this should benefit any researchers developing next generation, clean combustion technologies.