Well, you could construct a simple 1D thermal model (Fourier's law) and then build a simple realtionship between the heat transported, and the power applied to the TEC, and deduce the temperatures in your system.
There's nothing special about a model that can simulate cooling to -40degC.
You need to understand the equations that govern the TEC, and have a model for the way in which you eject the heat from the system (convected radiatior? Conduction to a large heatsink mass? Radiative transport? etc.)