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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.

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  • Can you explain the strength of "argue" here? Is there not a huge difference between giving a broad explanation, which might be expected on initial presentation, and a detailed exposition or "argument" which might well be reserved for later discussion? May 26 at 19:37
  • @RobbieGoodwin I think in this case an explanation might be a better description. A motivation as to why I am doing things this way and why it makes sense. Jun 2 at 13:22
  • Thanks and don't you think the initial presentation might be an appropriate place for a brief outline of why the model is relevant, and a later discussion more suitable for details? Otherwise, why are there separate presentation and discussion sections? Jun 2 at 18:34

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If it is not obvious why the model is relevant, then yes, explaining why/how it is relevant should be in your methods section (or when you introduce the model). This is because model selection is part of your methods, and what your considerations were in selecting it is an important part when replicating your results. However, you would keep the importance of your model (or more detailed explanations) for the discussion.

You have a little more freedom with the structure of theses, unlike papers, too. But even in papers which are to be as concise as possible, briefly explaining/stating why certain materials and methods are used is required. And, it is more helpful to the reader to understand why as soon as possible (i.e. when it is first introduced).

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