The animation is built around a class called MechanicsCanvas which "knows" how to draw springs and particles (it also double-buffers the animation). A particular animation can then subclass MechanicsCanvas to get a smoothly animated schematic drawing.
The Stop/Go button creates a new thread, which runs at the lowest priority, to animate the picture.
This is the result of a simple Newtonian model of a water molecule. There are three normal modes with non-zero angular frequency which you can select by using the drop-down choice panel.