An engine and one or more aftertreatment subsystems integrated into one system for optimization and control. At least one controller may be connected to the engine and the one or more aftertreatment subsystems. The controller may contain and execute a program for the optimization and control of the one system. Controller may receive information pertinent to the engine and the one or more aftertreatment subsystems for the program. The controller may prescribe setpoints and constraints for measured variables and positions of actuators according to the program to aid in effecting the optimization and control of the one system.