Normally, internal clocks are dependent on light. Therefore, if a free-running animal is exposed to constant periods of light and dark, their circadian rhythm can be shifted. For example, a free-running hamster exposed to set periods of light and dark can adjust the hamster's cycle to do its wheel running in the dark period instead of the light period. The change in the circadian rhythm is called a phase shift and the process of synchronizing the rhythm to the environmental stimulus is called entrainment. Zeitgebers are any cues that animals use to synchronize their rhythm with the environment, and it is usually the light-dark cycle. Usually, the zeitgeber entrains circadian rhythms, which causes a phase shift.

Changes in circadian rhythm

A small subregion of the hypothalamus, the suprachiasmatic nucleus (SCN) is in charge of serving as the biological clock. Damage to the SCN affects circadian rhythms relating to drinking and locomotion. Transplant experiments by Ralph et al. showed that when nonmutant hamsters with damage to the SCN were placed in conditions with a constant level of light, their circadian rhythms were gone. However, after these hamsters received SCN transplants from fetal hamsters, the hamsters started showing free-running activity again.

- Pineal gland
- Retinohypothalamic pathway
- Molecular levels of circadian rhythm

Hypothalamus (suprachiasmatic nucleus) and circadian rhythm

When animals continue to maintain their own cycle even when they aren't provided external cues about time of day, it is called free-running. The cycle during free-running is not exactly 24 hours. 
- changes in circadian rhythm
- hypothalamus 

University of Rochester

An internal biological clock that allows animals to proceed with their circadian rhythms. Usually, the internal clock is dependent on light. However, animals will still continue their circadian rhythm even in the absence of external cues. For example, even if it is constantly light or dark, animals will proceed with their circadian rhythm. 
- free running

Endogenous clock and circadian rhythm

Breedlove, S. & Watson, N. (2017). Behavioral neuroscience, eighth edition. Oxford University Press.

Behavioral Neuroscience 8th Edition

Free running

The process by which circadian rhythms can be reset by light. 

* Phase delay: time of sleep and wake move to later in the day, due to light exposure in the first half of the night.
* Phase advance: time of sleep and wake move to earlier in the day, due to light exposure in the second half of the night..

Entrainment

The suprachiasmatic nucleus (SCN) of the hypothalamus regulates circadian rhythms. Light activates intrinsically photosensitive retinal ganglion cells, causing the release of glutamate onto SCN neurons. This eventually leads to the transcription of the circadian regulating genes Per1 and Per2. The SCN is referred to as the "circadian pacemaker" because it oscillates in a circadian fashion.

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