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In this article model-based controller design techniques are investigated for the transient operation of a common-rail diesel engine in order to optimize driveability and to reduce soot emissions. The computer-aided design has benefits in reducing controller calibration time. This paper presents a nonlinear control concept for the coordinated control of the exhaust gas recirculation (EGR) valve and the variable geometry turbocharger (VGT) in a common-rail diesel engine. The overall controller structure is set up to regulate the total cylinder air-charge with a desired fresh air-charge amount by means of controlling the intake manifold pressure and estimating the fresh air-charge inducted into the cylinders. During varying engine operating conditions the two control loops are coordinated by a compensation of the EGR valve action through the VGT controller.