1. A method comprising: operating a system including an internal combustion engine and an air handling system, the air handling system including an exhaust system and an intake system, the intake system structured to provide charge air to the internal combustion engine; determining a first set of parameters based on a set of operational states of the system including a charge flow; computing a second set of parameters based on a linear time varying model of the system as a function of the first set of parameters; computing one or more control commands based upon a minimization or maximization of a cost function over a prediction horizon, and the second set of parameters; and controlling one or more operations of the air handling system based at least in part upon the one or more control commands; wherein the acts of determining the first and second set of parameters and computing the one or more control commands are repeated over a plurality of time periods over which the first set of parameters and the second set of parameters are time variant.