Tools for simulation of complex physical effect

Hi, we are working on a novel method to measure blood glucose non-invasively (see: diamontech.com). We are using a new kind of tunable laser (quantum-cascade-laser) to specifically heat up glucose molecules in the skin. We have a working prototype and start miniaturizing the whole system right now.

In order to expedite testing of different hypothesis we'd like to simulate our whole system with all its components (optics, electronics, thermal, mechanical, in best case even sample/skin) and I was wondering what is the best approach. Commercial simulation software like Zemax, Matlab/Simulink, Solidworks seem to focus on only one subset and it's complicated to string them together. Then there are some python-libs of different quality levels to support simulations. And I found modelica, which seems to be a good candidate, but I don't know anybody who has actually used it.

Are there any best practices? Any advice?

Thanks, Thorsten