A method for controlling an internal combustion engine having a controller controlling a variable geometry turbine and an EGR valve during engine operation, the method comprising: developing a non-linear model using engine operating parameters; defining at least one engine operating zone about a center linearization point for engine speed ranges and fuel rate ranges; linearizing the non-linear model at a center linearization point within an engine operating zone; developing a second order reduced linear model based on the non-linear model; developing a linear quadratic model predictive controller for each engine operating zone, based on the non-linear model; generating a rate based predictive model as a derivative of the linear model; generating the linear model as a linear quadratic model in the form of a piecewise affine control law wherein: u k + 1 = u k + T s F i x aug + G i, if H i x aug ≤ K k, where i ∈ {1,...,n r} denotes the i th polyhedral region, ( F i x aug +G i) gives the requested control rates, u̇, u denotes the vector of outputs, d denotes the vector of disturbances, and x aug = ξ ^ k u k d ̇ k o k r k where ξ̂ k is the estimated plant model state; estimating an engine state; determining a region of the piecewise affine control law based on the estimated engine state; applying feedback gain associated with the selected region of the piecewise affine control law to determine a control rate; and integrating the control rate to determine a control value to be applied to one engine input using the rate based predictive model in the controller, responsive to engine intake manifold pressure and EGR valve flow rate, to generate requested engine turbine lift and requested EGR flow rate; and controlling by the controller a variable geometry turbine and an EGR valve during engine operation in response to the intake manifold pressure and the requested EGR valve flow rate to generate turbine lift and EGR flow rate. developing a non-linear model using engine operating parameters; defining at least one engine operating zone about a center linearization point for engine speed ranges and fuel rate ranges; linearizing the non-linear model at a center linearization point within an engine operating zone; developing a second order reduced linear model based on the non-linear model; developing a linear quadratic model predictive controller for each engine operating zone, based on the non-linear model; generating a rate based predictive model as a derivative of the linear model; generating the linear model as a linear quadratic model in the form of a piecewise affine control law wherein: u k + 1 = u k + T s F i x aug + G i, if H i x aug ≤ K k, where i ∈ {1,...,n r} denotes the i th polyhedral region, ( F i x aug +G i) gives the requested control rates, u̇, u denotes the vector of outputs, d denotes the vector of disturbances, and x aug = ξ ^ k u k d ̇ k o k r k where ξ̂ k is the estimated plant model state; estimating an engine state; determining a region of the piecewise affine control law based on the estimated engine state; applying feedback gain associated with the selected region of the piecewise affine control law to determine a control rate; and integrating the control rate to determine a control value to be applied to one engine input using the rate based predictive model in the controller, responsive to engine intake manifold pressure and EGR valve flow rate, to generate requested engine turbine lift and requested EGR flow rate; and controlling by the controller a variable geometry turbine and an EGR valve during engine operation in response to the intake manifold pressure and the requested EGR valve flow rate to generate turbine lift and EGR flow rate.