The regular daily fluctuation in temperature and wakefulness is called:

I believe the most appropriate answer would be biological clock. Biological clocks are organism's innate timing device that is composed of molecules that interact throughout the body. They are found almost in every tissue and organ. 
It is an inherent timing mechanism in a living system that is inferred to exist in order to explain the timing or periodicity of behaviors and physiological states and processes, such as temperatures, wakefulness among others