I am trying to make a computer program that simulates another computer. I want to simulate something called the Scott CPU (from here). Could I change a small thing about it and not have to ask for permission to use it?
The copyright holder has the rights in whatever he created. If you have created something new based on his idea, the law will generally not be interested; but if your expression is recognisably a copy with a few changes, he can prevent publication or demand royalties. If you are uncertain which side of the line you fall, you should ask a lawyer (or, more cheaply, write to the author and ask if he objects).