Factorial Knockouts Distinguish Physical Necessity from Numerical Compensation in a PSI–LHCI Transport Model
Year: 2026
Type: preprint
Abstract: Mechanistic interpretation of photosynthetic energy-transfer models requires more than reproduction of experimental observables: a model intended to support mechanistic claims should also respond consistently when its proposed functional organizations are removed. Here, we evaluate whether a calibrated PSI–LHCI transport surrogate encodes physically meaningful principles by applying a 2 × 2 factorial knockout framework that independently removes site-energy heterogeneity and coupling-strength heterogeneity in a 155-pigment network. All perturbations were evaluated using the same Full-model calibration without parameter refitting. Although the calibrated model reproduced a high excitation-trapping yield, eliminating either energetic or coupling heterogeneity unexpectedly improved its apparent transport performance. A strict zero-coupling control confirmed that coupling itself remained necessary for network-mediated reaction-center access, whereas the supplied organization of coupling strengths was not supported by the surrogate. An audit of the model inputs further identified peripheral localization of all lowest-energy states and effective coupling scales far above those used in structure-based chlorophyll Hamiltonians. These findings do not imply that native PSI favors flat energy landscapes or uniform couplings. Instead, they show that endpoint agreement alone does not validate a mechanistic interpretation of a pigment-network model. Factorial knockout analysis provides a falsification-oriented framework for separating physical necessity from proposed organization, diagnosing numerical compensation, and identifying the constraints required for more predictive models of PSI–LHCI energy transfer. Significance Statement Photosynthetic energy-transfer models are often judged by whether they reproduce a measured efficiency or lifetime. A successful fit, however, can hide incorrect internal physics when several parameters compensate for one another. We introduce a factorial knockout test that asks two separate questions: must pigment coupling exist, and does the modeled organization of pigment energies and coupling strengths actually improve transport? Applied to a calibrated PSI–LHCI surrogate, the test confirms that coupling is essential but shows that removing either modeled organization improves the fitted performance. Targeted controls trace this failure to peripheral low-energy assignments and an unrealistically large coupling scale. The framework turns an apparently successful simulation into a falsifiable mechanistic model and identifies which physical constraints must be repaired before biological design principles can be inferred.
Authors: Hai Zhang, Boyi Feng, Huan Tan, Yuqi Wang, Haoming Luo
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
Funder: Westlake University
OpenAlex ID: W7204498593