The engine-out emissions of the CI Core Engine model referred to in your question responds dynamically to dynamic changes in the following control inputs to the engine: fuel mass, boost pressure, intake manifold gas temperature, intake oxygen percent, and fuel pressure to the extent that those inputs affect engine dynamic engine torque. The CI Core Engine model then uses the dynamic engine torque together with engine speed to look up quasi-steady engine-out emissions from lookup tables based on warmed up conditions. Our engine-out emissions can be calibrated to take into account air system and fuel system dynamics given a fixed engine calibration in the CI Controller, but not cylinder wall warmup dynamics.
If you want to focus on transient emissions for aftertreatment control and calibration, and account for cylinder wall warmup dynamics, you can make empirical dynamic emissions models using our Mapped CI Engine block, which allows a temperature input to affect emissions as the engine system warms up. You can fill 3-D lookup tables in the Mapped CI Engine block from measured engine-out emissions data using engine speed, fuel mass/inject, and coolant temperature/cylinder wall temperature as inputs. A coolant temperature/cylinder wall temperature model can be made using our Simscape family of products. Of course this empirical approach involves laboratory access and labor to calibrate the 3D lookup tables of the emissions.