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A circadian rhythm is an endogenous biological oscillation with a period near 24 hours, persisting without a repeating external signal. A circadian clock times biological activities and anticipates daily changes without continual external instructions. A free-running circadian rhythm reveals its intrinsic period; entrainment of circadian rhythm coordinates it with an external cycle.^[ref]

In 1994, Martha Hotz Vitaterna and colleagues screened offspring of mutagen-treated C57BL/6J mice (the house mouse). Each mouse lived in a cage with a running wheel, inside a ventilated, light-tight chamber with timer-controlled lighting. Wheel revolutions were recorded electronically or on an event recorder. The initial screen used 14:10 LD for the first 41 animals and 12:12 LD thereafter; LD denotes hours of light and darkness. Transfer to constant darkness, DD, omitted the next scheduled lights-on; recording continued for at least three weeks. The first 41 animals also received brief light pulses, so those records were not uninterrupted DD.^[ref]

The subsequent-generation comparison in Figure 2 used 12:12 LD before DD. Animals without the Clock mutation and with mutant genotypes supplied the comparison: the B6 examples in panels A–C had initial DD periods of 23.6, 24.8 and 27.1 hours, respectively; the homozygote later lost its sustained circadian rhythm. Total activity remained comparable across genotypes in the interstrain comparison. The mutation therefore altered timing, beyond merely reducing running. Wheel activity is a behavioral readout; it does not directly measure every circadian clock or establish a human period.^[ref]

Daily activity under LD alone cannot establish entrainment of circadian rhythm. Light can directly change activity without resetting the circadian clock: masking of circadian rhythm. Removing the light cycle helps distinguish these effects; they can coexist.^[ref] In an experiment, other repeating inputs must also be controlled: a nominally dark room with daily handling is not automatically an environment without timing cues.

Entrainment of circadian rhythm synchronizes a circadian clock to a repeating cue, a zeitgeber. One-to-one entrainment of circadian rhythm gives one cycle per environmental cycle with a stable relative circadian phase.^[ref] The stable relation need not put an activity onset exactly at lights-off: a constant offset also expresses phase locking.

For an original local model, let $x_n$ be the activity-onset offset from lights-off on environmental cycle $n$, with a negative value meaning an earlier onset. Choose an intrinsic period $\tau =23.5\mathrm{h}$ and environmental period $T=24\mathrm{h}$. Let $D(x)$ be a stipulated daily delay, measured in hours; positive $D$ moves the next onset later. The recurrence relation isA fixed phase relationship $x_{\ast }$ requires $D(x_{\ast })=T-\tau$: here a half-hour delay balances the half-hour intrinsic advance each cycle. This equality alone describes balance; restoration after a small disturbance also requires fixed point stability for an iteration.

Choose the illustrative local law $D(x)=0.5\mathrm{h}-0.4x$. Thenfor the chosen starting offset $x_0=-3\mathrm{h}$. The error shrinks by a factor of $0.6$ each cycle, proving fixed point stability for an iteration in this model. After five cycles $x_5=-0.23328\mathrm{h}$, about fourteen minutes early. At the fixed point, the imposed delay is $0.5\mathrm{h}$ and the corrected onset interval is $\tau +D(x_{\ast })=24\mathrm{h}$, although the uncoupled period remains $23.5\mathrm{h}$.

The uncorrected comparison has $D=0$ and $x_n=-3\mathrm{h}+n(\tau -T)$, so after five cycles it is $5.5$ hours early. The two traces separate ongoing timekeeping from adjustment to a zeitgeber. The chosen linear delay law is only a local teaching construction: it is not a measured response to light, does not account for wrapping of circadian phase, and does not predict an organism's entrainment range. Nor does it include masking of circadian rhythm. In a real study, tracking several cycles after removal of the cue or after a timed perturbation supplies information that a single activity value under illumination cannot provide.

In masking of circadian rhythm, an external condition changes the observed output without necessarily changing the underlying circadian clock.