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Mechanistic Models: Compartment Models in Individual and Population Analysis01:23

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Mapping CO2 fixation to two effective parameters: A framework toward data-informed species and model comparison.

Andreas Stillits1, Teresa E Knudsen1, Ala Trusina1

  • 1Biocomplexity, Niels Bohr Institute, University of Copenhagen, Copenhagen 2200, Denmark.

Proceedings of the National Academy of Sciences of the United States of America
|June 5, 2026
PubMed
Summary

Understanding plant carbon dioxide (CO2) assimilation is key to improving crop yields. This study simplifies CO2 uptake models, revealing dominant limitations and species-specific modeling needs for better crop resilience.

Keywords:
assimilation ratemesophyll conductancemodel selectionmodels of photosynthesisreaction–diffusion

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Area of Science:

  • Plant Physiology
  • Biophysics
  • Computational Biology

Background:

  • Improving crop yield and resilience requires understanding limitations in carbon dioxide (CO2) assimilation rate in plant leaves.
  • Mechanistic models integrating diffusion, biochemistry, and geometry can resolve the combined effects of multiple traits.
  • Existing models like simple serial resistance models neglect tissue geometry, while detailed anatomical models are computationally intensive and require hard-to-measure parameters.

Purpose of the Study:

  • To develop a framework for systematic comparison of species and models for CO2 assimilation.
  • To identify the essential level of model resolution for different plant species.
  • To simplify the understanding of CO2 fixation limitations in leaves.

Main Methods:

  • Developed a minimal reaction-diffusion model to reduce CO2 fixation in leaves to two key parameters.
  • Created a compact phase space based on these parameters to identify rate-limiting regimes.
  • Mapped diverse plant species onto this phase space to analyze limitations and model requirements.

Main Results:

  • Identified three naturally emerging rate-limiting regimes: stomatal uptake, intercellular diffusion, and intracellular processes.
  • Revealed dominant co-limitations by stomatal and intracellular processes across diverse species.
  • Found an equal partition between species requiring spatially resolved leaf-scale models and those adequately described by intracellular models.

Conclusions:

  • The study presents a scalable framework for interpreting complex trait data and bridging the gap between different modeling approaches.
  • Model resolution for CO2 assimilation is species-specific, necessitating tailored modeling strategies.
  • Understanding these limitations is crucial for enhancing crop yield and resilience through targeted trait improvement.