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Awake brain dynamics are maintained by various wake-promoting mechanisms, particularly the neuromodulators Acetylcholine (ACh) and Noradrenaline (NA), whose levels naturally decrease during the transition to sleep. The combined influence of these neurotransmitters on brain connectivity during sleep remains unclear, as previous models have examined them mostly in isolation or only in deep sleep. In this study, we analyze fMRI data obtained from healthy individuals and employ a whole-brain model to investigate how changes in brain neurochemistry during NREM sleep, specifically involving ACh and NA, affect the Functional Connectivity (FC) of the brain. FC analysis reveals distinct connectivity changes: a decrease in Locus Coeruleus (LC) connectivity with the cortex during N2 and N3, and a decrease in Basal Forebrain (BF) connectivity with the cortex during N3. Additionally, compared to Wakefulness (W), there is a transition to a more integrated state in N1 and a more segregated state in N3. Using a Wilson-Cowan whole-brain model, informed by an empirical connectome and a heterogeneous receptivity map of neuromodulators, we explored possible mechanisms underlying these dynamics. We fit the model adjusting the coupling and input-output slope of the whole-brain model to account for ACh and NA, respectively, and show that region-specific neurotransmitter effect is key to explain their effects on FC. This work enhances our understanding of neurotransmitters\u2019 roles in modulating sleep stages and their significant contribution to brain state transitions between different states of consciousness, both in health and disease.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1012852","type":"journal-article","created":{"date-parts":[[2025,10,28]],"date-time":"2025-10-28T17:34:29Z","timestamp":1761672869000},"page":"e1012852","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":2,"title":["Noradrenaline and acetylcholine shape functional connectivity organization of NREM substages: An empirical and simulation 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