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Despite the fact that urea-based selective catalytic reduction (SCR) of NOx is a key technology for achieving on- and off-highway diesel emission standards, significant control challenges remain. Transient operation, combined with dramatic changes in catalyst dynamics over the operating range, cause highly nonlinear system behavior. Moreover, these effects depend on catalyst formulation and new catalysts continue to be developed. With many controllers, any difference in catalyst formulation, converter size, and engine emissions calibration require control system re-tuning. To minimize control development effort, this paper presents a novel “generic” controller for SCR systems. Control action is grounded in a physics-based, nonlinear, embedded model. Through the model, controller parameters are adjusted a priori for catalyst formulation and converter size. The few remaining tuning levers are quite intuitive, and require no special knowledge of controls theory.