Hello,
This is not traditionnal pixel art, but an entirely working simulation of the intel 4004... in a "pixel art" circuit.
It's a part from a secondary project I'm working on. A transistor level simulator based on bitmap images.
The animation you can see here is just a small loop from a "set all registers to 0xF" simulation. The IO are set from the simulator, with an emulated ROM to feed the CPU with custom instructions.
Here the image circuit, and here at "higher resolution" for a better visibility of transistors.
Green pixels are transistors, red pixels are pull up, and blue is ground.
The circuit was drawn by hand (it took a long time). Based on official schematics. | 
No, powdertoy use a particle based representation of an electric current. This has two major disadvantages:
- it's extremelly slow
- it's absollutelly not realistic when you try to simulate real transistors
This simulator works with real hardware and is pretty fast compared to "particle based" representations, like you can see here for example: the DIE photography, and the simulated version.
Other than powdertoy you have wireworld that uses cellular automatons. But it's also pretty slow and not realistic.