A system for reducing environmentally harmful emissions from an internal combustion engine. The system may incorporate an exhaust after-treatment device. The exhaust after-treatment device may use selective catalytic reduction to remove certain emissions from the exhaust of the engine. Urea solution may be inserted into the exhaust emissions, which is decomposed to ammonia to become a reduction agent for reduction of NOx in the emissions. The engine may be managed by a controller and the exhaust after-treatment device may be managed by another controller. These controllers may be cascaded, or be managed by a third controller that provides hierarchical or coordinated control of engine performance and emissions reduction. The engine and the exhaust after-treatment device may be modeled to aid in designing and building a system for coordinated control of an actual engine and a selective catalytic reduction after-treatment device. The controllers may be predictive model controllers.