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I'm interested in which biological systems or hormones are involved in the following phenomenon:

Before sleep it may be difficult to find a comfortable position, and muscular aches and pains are more evident.

After 8 hours of sleep, many more positions are comfortable, and muscle aches/tension are non-existent. Some time after awakening, the feeling disappears.

What causes the difference in feeling between prior to falling asleep and after? Are there some hormones involved? Is it caused by some form of thought/feeling inhibition (e.g., part of a brain "falls asleep")?

If I remember correctly, after long running muscles accumulate some compound that is a result of metabolizing energy without enough oxygen, which causes muscles to ache. Could a similar process be involved?

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The compound you're thinking about is lactic acid. When oxygen is low, pyruvate is reduced to lactic acid to regenerate NAD+. It might have something to do with the aching related to sleep, but I'm not sure. –  jello Jul 27 '12 at 12:40
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