I'm writing my master thesis on simulation of active matter. The Chapters of my thesis are currently: Introduction, Theory, Simulations, Discussion, and Conclusion.
In my simulation chapter I introduce a model and I don't think it is immediately obvious why this model is relevant. Should I explain my thinking and argue it's importance right there in the section describing the model? An alternative could be to save such arguments for the discussion chapter where I currently mainly discuss the results from the simulations.