Eli5 What is the mechanism that physically puts voltages on wires in the CPU.

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I have a fairly strong understanding of how code like C is compiled into machine code and how transistors form gates which can be put together to compute lots of operations which can eventually become a computer. Say you have a machine instruction that says to add the contents of register 3 and register 5 and put the result in register 6. What is physically putting the voltages on the transistors in a way that achieves the desired result given that nothing is flipping a mechanical switch?

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Other transistors. It’s transistors all the way down. The moment power comes up from the PSU, all the transistors are initialized to their “default” state (either energized or not) simply by the path their gate electrodes have to the always-on power supply wires – through other transistors and components. From there they need some input to start changing states. That’s what the clock is for – when it got power, it automatically sent a pulse into the attached crystal and started trying to establish oscillation. When it is ready, it starts sending out the clock pulse to the rest of the circuits.

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