The researchers have revealed that this structure lies below the hypothalamus at the base of the brain.
According to them, one group is synchronized with deep sleep that results from physical fatigue, and the other controls the dream state of rapid eye movement (REM) sleep.
The bottom neurons receive light information directly from the eyes and govern rhythms in tune with periods of light and dark, while the top neurons do not receive direct light information and so govern rhythms as a more independent internal biological clock.
Horacio de la Iglesia, a UW associate professor of biology, points out that some of the body's rhythms seem to be "more loyal" to the bottom neurons, and others are much more in tune with the top neurons.
Normally the two neuron groups are synchronized with each other, but disruptions like jet travel across time zones or shift work can throw the cycles out of kilter.
Deep sleep is most closely tied to light-dark cycles, and typically adjusts to a new schedule in a couple of days. However, REM sleep is more tied to the light-insensitive dorsal neurons, and can be out of sync for a week or more.
"When we impose a 22-hour light-dark cycle on animals, the ventral center can catch up but the dorsal doesn't adapt and defaults to its own inner cycle," de la Iglesia said.
In the rats he tests while conducting lab experiments, that normal cycle is 25 hours.
Upon imposing the artificial 22-hour light-dark schedule, the researcher observed that the rats' deep sleep quickly adapted to the 22-hour cycle, but their REM sleep continued to follow a 25-hour cycle.
The researcher said that REM sleep, consequently, did not occur in a normal progression following deep sleep.
"We found that after exposing rats to a shift of the light-dark timing that simulates a trip from Paris to New York, REM sleep needed 6 to 8 days to catch up with non-REM, or deep, sleep, the sleep you usually experience in the first part of the night," de la Iglesia said.
The study showed that the two types of sleep overlap immediately after the simulated jet lag occurs, and that there is a greater likelihood of the animals entering REM sleep earlier than they should.
According to de la Iglesia, this may help understand why travellers and shift workers may take several days to adapt to their new schedules.
"It also could explain why jet lag is associated with lower learning performance. We think the disruption of the normal circadian sequence of sleep states is very detrimental to learning," he said.
"One of the problems is that you are doing things at times that your body isn't prepared to do them. One group of neurons tells your body it is Paris time and another says that it is New York time. You are internally desynchronized," he added.
The researcher believes that this study may be useful in fine-tuning pharmaceutical and other therapies.
"We can go back to the treatments that are believed to be effective and see where they might be acting in the circuitry of these neuron centres, then refine them to be more effective," he said.
A researcher article on the study has been published online in the journal Current Biology.