You are changing the electronic charges on a multitude of molecules arranged at very specific locations in a very specific manner.

The problem is that the physical aspects of the computer are not what infringes the patent. They exist in the prior art. A mechanical or biological computer would infringe the same as an electrical computer because the physical aspects are irrelevant to the software. You're essentially try to claim that authors should be able to patent literary works because a pen or a printing press is a physical machine that moves all manner of ink molecules around into a particular configuration.