Frequency-domain identification of photosynthetic regulation under fluctuating light

Abstract

Plant photosynthesis operates under naturally fluctuating light, yet its dynamic responses across timescales remain incompletely understood. Here, we apply sinusoidal light modulation as a controlled periodic input and analyze the response in the frequency domain, enabling quantitative system identification of photosynthetic dynamics. Using a minimal biochemical model of photosynthetic electron transport and regulation, we show that photosynthetic performance under fluctuating light differs systematically from that under constant illumination, even when the mean photon flux density is identical. Large-amplitude oscillations generate higher harmonics and alter time-averaged chlorophyll fluorescence, oxygen evolution, and non-photochemical quenching (NPQ), demonstrating that fluctuating light acts not merely as a perturbation but as a distinct physiological regime. For sufficiently small perturbations, the system behaves approximately linearly and can be characterized by transfer functions and Bode plots. We identify two dynamic regimes separated by a characteristic timescale of approximately 10 s. In the high-frequency domain, the response is governed by constitutive photochemical processes and reflects local steady-state properties, including the redox state of the plastoquinone pool. In the low-frequency domain, adaptive regulatory feedback dominates, particularly NPQ, which reshapes both the amplitude and phase of the photosynthetic response. Characteristic frequency-response features, including gain transitions and phase extrema, provide direct information about physiologically relevant quantities such as effective relaxation times and regulatory coupling strengths. We further introduce the concept of regulation fingerprints, defined as ratios of transfer functions between regulated and unregulated systems. These fingerprints reveal distinct spectral signatures of fast PsbS-dependent and slower zeaxanthin-dependent NPQ, enabling their quantitative separation and providing experimentally testable predictions for regulatory dynamics. Together, these results establish frequency-domain analysis as a general framework for probing, identifying, and testing the dynamic regulation of photosynthesis under fluctuating light. More broadly, they suggest that fluctuating illumination, often regarded as experimental noise, can instead serve as a structured probe of photosynthetic function in both laboratory and field environments.

Code and data availability

The paper presents purely simulation-based frequency-domain analysis using the BDM model, whose code was published in prior work (Niu et al. 2025), not in this paper. No paper-specific public dataset, image, code repository, model checkpoint, or supplement with an authors' public URL is provided in the supplied blocks.

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