The current boom in natural gas from shale formations in the United States has reduced the price of natural gas to less than the price of petroleum fuels. Thus it is attractive to convert high horsepower diesel engines that use large quantities of fuel to dual fuel operation where a portion of the diesel fuel is replaced by natural gas. The substitution is limited by emissions of unburned natural gas and severe combustion phenomena such as auto-ignition or knock of the mixture and high rates of pressure rise during the ignition and early phase combustion of the diesel and natural gas-air mixture. In this work, the combustion process for dual fuel combustion was investigated using 3D CFD. The combustion process was modeled using detailed chemistry and a simulation domain sensitivity study was conducted to investigate the combustion to CFD geometry assumptions. A baseline model capturing the onset of knock was validated against experimental data from a heavy-duty dual-fuel engine. The model was then applied to different operating conditions exhibiting varying levels of knock strength. The modeling results were then used to monitor the low temperature combustion phenomena by evaluating the formation of formaldehyde and other combustion radicals. These reactive species reacted easily with natural gas, leading to auto-ignition. As the consumption of natural gas increased, the heat release increased and knock occurred.