I'm searching for a good way to animate a molecule-like structure with nice transitions between the spheres and the cylinders. So far, I'm using a skin modifier for the structure and a particle system to generate the spheres, but I'm afraid in this setup it would be hard to built in the tapering effect. I also tried to model the transition, but that resulted in a lot of z-fighting between the different links.
Here is a simplified setup to start with. On another layer, you can also find a modeled link, with the desired transition softness for reference, or to use in a different setup.