There's two emissions systems on these trucks. One is called the Diesel Particulate Filter (DPF) and the other is a catalytic converter. The DPF traps unburnt fuel in the form of small particles. Normally the exhaust temperatures should get hot enough to burn off anything caught in the DPF. However if it hasn't seen any hard driving or high RPMs there is the potential that it will get clogged. Basically the system checks the air pressure drop across the DPF and if that drop gets too high it goes into a mode called regeneration. What the system does is spray extra fuel into the cylinder during the exhaust stroke which will burn out the particles caught in the filter. In order for this to work you need to be driving at highway speeds (some load on the engine).
DEF is used as a catalyst to convert NOx into nitrogen, water, and CO2.
DEF is used as a catalyst to convert NOx into nitrogen, water, and CO2.