HFSS does not simulate electrons. It only simulates fields according to Maxwell equations with minor extension to linearized LLG for ferrites. The latter is in the form of complex anisotropy only, so technically there are no equations solved, other than Maxwell eqs. That's all. So, I guess, it should not. There is a thing called QuantumATK for atomic-scale design, but I have no Idea how it works, and is it suitable for your research.
On the other hand, HFSS perfectly simulates wave resonances in any scale, so you should try getting some basic EM wave mechanics data at least for comparative study.
>add physics here manually?
no. HFSS has hard-coded solvers. Here, you probaly should look into COMSOL direction. But I am not sure, is it suitable to the scale of antenna problem.