1. A system for controlling a variable geometry turbine and an EGR valve during engine operation, the system comprising: an internal combustion engine; and a controller configured to: develop a non-linear model using engine operating parameters; develop a linear quadratic model predictive controller, based on the non-linear model, for each engine operating zone; and generate a rate based contractive predictive model based on the linear quadratic model, and use the rate based contractive predictive model responsive to engine intake manifold pressure and EGR valve flow rate to generate requested engine turbine lift and requested EGR flow rate.