Fitting an Arduino processor on a PC Motherboard
Arduino uses an 8 bit microcontroller , it's not a processor.
You could create a custom circuit board that you could insert into a PCI slot or PCI Express slot in order to take power from those slots, but communicating with the computer through those slots is very complex (it would take a lot of code to do it, maybe so much that the microcontroller may not have enough built in memory to store all that code)
You could add a SPI/i2c/UART to USB chip (serial communication) on your custom arduino board and them connect the USB created by that chip to one of the USB 2.0 headers and then your arduino could talk to the computer using serial communication, so software on the computer could send and receive data from your custom arduino board
When you're ready to go a step above Arduino, there are microcontrollers like PIC18 and PIC32 which have USB functionality built in and which is fast enough (can do a few mbps in both directions) which makes it possible to do neat things with them.
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