[MediaMole]

The actual virus infected Windows systems used to program the industrial controllers. The virus then used those systems to put a rootkit into the actual industrial control systems, and reprogramed those systems with instructions that couldn’t be seen by the operators.

So, Stuxnet implanted programming into the actual systems that controlled the centrifuges. Apparently, the instructions caused the motors to run erratically, running over speed and slowing suddenly to cause physical damage.

Some of the equipment could very well have suffered permanent physical damage.

[gandalftb]

The centrifuges don't have a braking system and cannot slow suddenly, power is just shut off and friction with the air slows them down. Again, sensors report every anomaly, anything out of parameter shuts the power off and the centrifuge winds down on its own.

The reason so many P-1's are off line is that Iran cannot get spare parts for the crude inverters they are using and that are getting hot and acting erratically independent of any program bug.