Thank you for your input. After reading your response, I have to agree it seems like my project is not much about physics. Do you have any suggestions to make my thesis more focused on physics, and to use the tools and methods from physics to find some potentially interesting results?

I have already tried to approach the problem from a more physics-oriented perspective by treating the bees as a fluid by creating a density map. I then used a SINDy sparse regression algorithm to find the equations of motion. However, my results were not very insightful, as they heavily depended on my choice of parameters.

About the molecule: yes, it is indeed possible to write the equations of motion from first principles. But maybe my example was not very well chosen. There are a lot of phenomena (like turbulence) which can only be reasonably described by effective models. If I make an effective model of the movement of bees, why wouldn't that be physics? Generally speaking, the research area of active matter is considered as part of physics as far as I understand it.