Difficult part: I don't entirely understand the correspondence between eigenvalues of the matrix of a system of differential equations and the stability of the equilibrium points of the system. Granted, this was from 3-12, rather than 12-22, but for the most part, I found 12-22 to be fairly straightforward. The math seemed ugly, but since it is largely done through numerical simulation, it's fairly understandable. The only part where I would potentially balk is equations 25-29, though the only difficult part seems to be keeping track of the constants.
Reflective part: Perelson's model seems to be a good example of a model that's only as complex as it needs to be, though in this case, it needs to be fairly complicated. It would be interesting to see how the model bears out empirically and if advancements in knowledge about HIV would change any of the model's assumptions.
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