Thanks!
The protective shield on the atoms is actually the electrons orbiting the nucleus (yes I know the Bohr model is outdated but I wasn't going to implement quantum mechanics and electron clouds!)
As for the "shield" timer, it was originally called "time", but since it depletes faster on higher levels it didn't make sense. In hindsight I probably should have called it "energy" to make it clearer that it wasn't depleting from taking damage.