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In this paper, a model-based linear estimator and a non-linear control law for an Fe-zeolite urea-selective catalytic reduction (SCR) catalyst for heavy duty diesel engine applications is presented. The novel aspect of this work is that the relevant species, NO, NO2 and NH3 are estimated and controlled independently. The ability to target NH3 slip is important not only to minimize urea consumption, but also to reduce this unregulated emission. Being able to discriminate between NO and NO2 is important for two reasons. First, recent Fe-zeolite catalyst studies suggest that NOx reduction is highly favored by the NO 2 based reactions. Second, NO2 is more toxic than NO to both the environment and human health. The estimator and control law are based on a 4-state model of the urea-SCR plant. A linearized version of the model is used for state estimation while the full nonlinear model is used for control design.