Publication Date




Embargo Period


Degree Type


Degree Name

Doctor of Philosophy (PHD)


Physics (Arts and Sciences)

Date of Defense


First Committee Member

Sheyum Syed

Second Committee Member

Mason Klein

Third Committee Member

Chaoming Song

Fourth Committee Member

James Baker


Sleep is an ancient behavior that is observed in nearly all organisms. Animals typically spend a significant part of their life sleeping, and prolonged sleep deprivation leads to serious physiological changes, signifying the importance of sleep. However, little is known about the regulation of sleep. Sleep is thought to be controlled by two mechanisms: the circadian clock, a biological oscillator that controls daily activity, and the sleep homeostat that tracks organism’s sleep need and controls the duration of sleep. While the circuit of the circadian clock is well studied, almost nothing is known about the structure of the sleep homeostat. Since sleep in flies is very similar to mammalian sleep, we use the fruit fly Drosophila melanogaster as a model organism to understand the homeostat. Since activity and sleep are tightly connected, the first part of this dissertation focuses on activity rhythms. In fruit flies, daily locomotor activity recordings are widely used to study the circadian clock, an endogenous biochemical oscillator with a period of 24 hours that helps to synchronize an organism’s internal processes and behavioral outputs with daily cycles in the environment. Drosophila is a crepuscular animal, meaning it is most active during dusk and dawn. Typical fly locomotor recordings in light/dark conditions show two peaks of activity: a morning peak (M) that happens when the light turns on, and an evening peak (E) that happens when the light turns off. Despite decades of study, a quantitative understanding of the temporal shape of Drosophila locomotor rhythms is missing. Locomotor recordings have been used mostly to extract the period of the circadian clock, leaving these data-rich time series largely underutilized. We propose a mathematical model with four exponential terms and a single period of oscillation that closely reproduces the shape of the locomotor data in both time and frequency domains. In frequency space, our model produces multiple spectral peaks that account for nearly all periodicities seen in fly locomotion power spectra. We show that the proposed single-period waveform is sufficient to explain the position and height of >88 % of spectral peaks in the locomotion of wild-type and circadian mutants of Drosophila. Our results indicate that multiple spectral peaks from fly locomotion are simply harmonics of the circadian period rather than independent ultradian oscillators as previously reported. In the time domain, our model provides a quantitative description of M and E peaks of activity. From timescales of the exponentials, we hypothesize that model rates reflect the activity of neuropeptides that likely transduce signals of the circadian clock and the sleep-wake homeostat to shape behavioral outputs. Next, we focus on the structure of the sleep homeostat in flies. In Drosophila, sleep is typically studied using behavioral metrics, such as average daily sleep amount or average sleep bout duration. The homeostatic sleep regulation is investigated using deprivation experiments, where flies ability to recoup sleep loss is analyzed. These measures have helped to identify multiple substrates and distinct groups of neurons that regulate sleep or wakefulness. Although these findings provide important information about sleep regulation, the functional structure of the homeostat remains largely unknown. Here we propose a new approach to study sleep homeostat in fruit flies. To access the structure of the homeostat, we investigate fly sleep architecture at the level of individual bouts. We find that the distribution of sleep bout lengths in wild type flies is best described by a sum of 4 exponential terms. Analysis of bout distributions in sleep and homeostat mutants show that while flies with altered sleep duration still retain the 4 exponential functional form, ablation of the homeostat leads to the collapse of the multiexponential distribution. These results suggest that the sleep homeostat regulates durations of sleep episodes through 4 independent regulatory pathways. Investigation of sleep bout distribution in clock mutants reveals a link between the circadian clock and the homeostat, giving rise to the possibility that the output of the clock regulates one of the pathways. We further demonstrate that another pathway might be regulated by light and that this interaction is mediated through the blue-sensing photo-pigment CRYPTOCHROME.


Drosophila melanogaster; sleep; homeostat; circadian clock; locomotion; mathematical model