Frequency spectra and the color of cellular noise

• Published in: Nature communications Vol. 13; no. 1; pp. 4305 - 18
• Main Authors: Gupta, Ankit, Khammash, Mustafa
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 25.07.2022; Nature Publishing Group; Nature Portfolio
• Subjects: 19th century; 631/114/2390; 631/553/2713; 631/61/338/552; Computer applications; Decomposition; Frequency analysis; Frequency spectrum; Humanities and Social Sciences; Intracellular; multidisciplinary; Networks; Noise; Oscillators; Reaction mechanisms; Science; Science (multidisciplinary); Signal processing; Spectra; Spectral analysis; Spectral theory; Spectrum analysis
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-022-31263-x

The invention of the Fourier integral in the 19th century laid the foundation for modern spectral analysis methods. This integral decomposes a temporal signal into its frequency components, providing deep insights into its generating process. While this idea has precipitated several scientific and technological advances, its impact has been fairly limited in cell biology, largely due to the difficulties in connecting the underlying noisy intracellular networks to the frequency content of observed single-cell trajectories. Here we develop a spectral theory and computational methodologies tailored specifically to the computation and analysis of frequency spectra of noisy intracellular networks. Specifically, we develop a method to compute the frequency spectrum for general nonlinear networks, and for linear networks we present a decomposition that expresses the frequency spectrum in terms of its sources. Several examples are presented to illustrate how our results provide frequency-based methods for the design and analysis of noisy intracellular networks. The invention of the Fourier integral in the 19th century laid the foundation for modern spectral analysis methods. Here the authors develop frequency-based methods for analyzing the reaction mechanisms within living cells from distinctively noisy single-cell output trajectories and present forward engineering of synthetic oscillators and controllers.