The circadian rhythm is an internal biological clock that regulates roughly 24-hour cycles of physiology and behaviour — from sleep and wakefulness to hormone secretion, body temperature, and cell division. At the molecular level it is driven by a negative-feedback loop involving the transcription factors CLOCK/BMAL1, which activate the Period (PER) and Cryptochrome (CRY) genes; the resulting PER/CRY protein complex then inhibits CLOCK/BMAL1, suppressing its own production and creating an oscillation with a period close to 24 hours. This simulator models the core oscillator using a Goodwin-type ODE approximation, producing smooth rhythmic curves for melatonin, cortisol, and core body temperature.
Adjust wake time, sleep time, light intensity, chronotype offset (early bird vs. night owl), and jet-lag shift to see how the melatonin (indigo), cortisol (orange), core temperature (teal), and light exposure (yellow) curves shift and distort. The stats panel reports clock phase offset, estimated peak hormone times, the predicted sleep window, and your social jet lag — the difference between your biological mid-sleep and the social norm.
What exactly is the circadian rhythm and who has one?
Circadian rhythms (from Latin circa dies, "about a day") are self-sustaining biological oscillations with a period close to 24 hours. They are found in almost every living organism studied — bacteria, fungi, plants, insects, and all vertebrates. In isolation (constant dim light with no time cues), the human clock runs at about 24.2 hours on average, longer than a solar day. Zeitgebers ("time givers") such as light, meals, and exercise synchronise the internal clock to the exact 24-hour day.
How does light exposure reset the body clock?
Light detected by ipRGCs (intrinsically photosensitive retinal ganglion cells, containing the pigment melanopsin) travels via the retinohypothalamic tract to the suprachiasmatic nucleus (SCN) in the hypothalamus — the master pacemaker. Light in the evening delays the clock (makes it run later); light in the early morning advances it (makes it run earlier). This phase-shifting response follows a phase-response curve (PRC), which determines how much and in which direction a light pulse shifts the clock depending on when it occurs.
Why does melatonin peak in the middle of the night?
Melatonin is produced by the pineal gland under SCN control and is strongly suppressed by light. In a typical sleeper, melatonin secretion begins about 2 hours before habitual sleep time (dim-light melatonin onset, DLMO), peaks around 2–3 am, and is suppressed by morning light. Its primary role is not to induce sleep directly but to signal darkness duration to the circadian system — it is sometimes called the "hormone of darkness".
The cortisol awakening response is a sharp 50–100% rise in serum cortisol that occurs within 30–45 minutes of waking, peaking around 08:00 in a standard sleeper. The CAR is driven by the circadian clock and is distinct from the stress-induced HPA axis response. It prepares the body for the metabolic demands of the day — mobilising glucose, activating the immune system, and sharpening cognitive function. The simulator models this as an exponential peak above a declining baseline.
Social jet lag is the discrepancy between a person's biological sleep timing (driven by their chronotype) and the socially imposed schedule (work, school start times). It is measured as the difference in mid-sleep time between free days and work days. Chronic social jet lag of ≥2 hours is associated with increased risk of obesity, type 2 diabetes, cardiovascular disease, depression, and reduced cognitive performance — effects that mirror the health consequences of shift work and transatlantic jet lag.
A chronotype describes a person's natural preference for early or late sleep and activity timing. It is assessed using the Munich Chronotype Questionnaire (MCTQ), which measures the mid-sleep time on free days (MSF) corrected for sleep debt. Chronotypes follow a roughly normal distribution, with about 25% "morning types", 50% intermediate, and 25% "evening types". Chronotype is partly genetic (genes like PER3, CLOCK) and changes with age — teenagers shift toward evening types, then shift back toward morning types in adulthood.
Jet lag occurs when the internal clock is misaligned with the new local time after rapid long-distance travel. The SCN re-entrains to the new time zone at a rate of roughly 1–1.5 hours per day, so a 6-hour time difference takes about 4–6 days to recover from. Eastward travel (phase advance) is generally harder to adjust to than westward travel (phase delay) because the clock's natural period is slightly longer than 24 hours — it is easier to delay than to advance. Strategic light exposure and melatonin supplements can accelerate re-entrainment.
The Goodwin oscillator (1965) is a minimal model of biological negative feedback: a gene produces mRNA (X), which is translated to a protein (Y), which forms a repressor complex (Z) that inhibits the original gene. The system of ODEs dX/dt = v₁/(1+(Z/Ki)^n) − k₂X, dY/dt = k₃X − k₄Y, dZ/dt = k₅Y − k₆Z produces sustained oscillations when the Hill coefficient n ≥ 8. It is a simplified but instructive analogue of the actual PER/CRY/CLOCK/BMAL1 molecular feedback loop, which involves dozens of interacting proteins.
Core body temperature (CBT) follows a circadian rhythm with a minimum (Tmin) about 1–2 hours before habitual wake time and a peak in the late afternoon (~18:00–19:00). Sleep onset is most easily achieved when CBT is falling — a warm bath or exercise 1–2 hours before bed raises skin temperature, promotes heat dissipation, and lowers CBT faster, shortening sleep onset latency. This is why sleeping in a cool room (around 18°C) promotes better sleep quality.
Chronic circadian disruption — common in shift workers, frequent long-haul travellers, and people with irregular sleep schedules — is associated with significantly increased risks of metabolic syndrome, type 2 diabetes, cardiovascular disease, certain cancers (especially breast and prostate), depression, and impaired immune function. Night-shift workers have a 29% higher risk of obesity and a 40% higher risk of type 2 diabetes compared to day workers, according to large epidemiological studies.