As I understand it, Thunderbolt 3 and USB 3.1 use the exact same USB-C connectors. I am aware that Thunderbolt 3 is approximately quadruple the speed of USB 3.1. I had assumed that it was because TB ran on optical fiber, but apparently this is not true, according to https://en.wikipedia.org/wiki/Thunderbolt_(interface). I also know it's not a parallel interface.
In that case, why is TB3 faster than USB 3.1? Is it something to do with the controller, or the cable itself?