Photosynthesis Research

, Volume 93, Issue 1–3, pp 223–234 | Cite as

E-photosynthesis: a comprehensive modeling approach to understand chlorophyll fluorescence transients and other complex dynamic features of photosynthesis in fluctuating light

  • Ladislav Nedbal
  • Jan Červený
  • Uwe Rascher
  • Henning Schmidt
Research Article

Abstract

Plants are exposed to a temporally and spatially heterogeneous environment, and photosynthesis is well adapted to these fluctuations. Understanding of the complex, non-linear dynamics of photosynthesis in fluctuating light requires novel-modeling approaches that involve not only the primary light and dark biochemical reactions, but also networks of regulatory interactions. This requirement exceeds the capacity of the existing molecular models that are typically reduced to describe a partial process, dynamics of a specific complex or its particular dynamic feature. We propose a concept of comprehensive model that would represent an internally consistent, integral framework combining information on the reduced models that led to its construction. This review explores approaches and tools that exist in engineering, mathematics, and in other domains of biology that can be used to develop a comprehensive model of photosynthesis. Equally important, we investigated techniques by which one can rigorously reduce such a comprehensive model to models of low dimensionality, which preserve dynamic features of interest and, thus, contribute to a better understanding of photosynthesis under natural and thus fluctuating conditions. The web-based platform www.e-photosynthesis.org is introduced as an arena where these concepts and tools are being introduced and tested.

Keywords

Chlorophyll fluorescence emission Forced oscillations Non-linearity Photosystem II System biology System decomposition Model reduction 

Abbreviations

CAM

Crassulacean acid metabolism

Chl

Chlorophyll

Fm

Maximum fluorescence yield measured in light-adapted organism during saturating flash of light

ΔF

Difference between the maximum fluorescence F m′ and steady state fluorescence yields

ODE

Ordinary differential equations

PQ

Plastoquinone

PSI

Photosystem I

PSII

Photosystem II

QA

Primary quinone acceptor of Photosystem II

QSSA

Quasi steady-state approximation

SBML

Systems Biology Markup Language

Notes

Acknowledgments

LN was supported by the Czech Academy of Sciences Grant AV0Z60870520, by the Czech Ministry of Education, Sports and Youth Grant MSM6007665808, by the Grant Agency of the Czech Republic GACR 206/05/0894. JČ was supported in part by the grant 1M0567 of the Czech Ministry of Education. HS was supported by a grant from the Swedish Foundation for Strategic Research.

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Copyright information

© Springer Science+Business Media B.V. 2007

Authors and Affiliations

  • Ladislav Nedbal
    • 1
    • 2
  • Jan Červený
    • 1
    • 2
    • 3
  • Uwe Rascher
    • 4
  • Henning Schmidt
    • 5
  1. 1.Institute of Systems Biology and Ecology ASCRNove HradyCzech Republic
  2. 2.Institute of Physical Biology, University of South BohemiaNove HradyCzech Republic
  3. 3.Centre of Applied CyberneticsCzech Technical UniversityPrague 6Czech Republic
  4. 4.Institute of Chemistry and Dynamics of the Geosphere ICG-III: PhytosphereJuelichGermany
  5. 5.Fraunhofer-Chalmers Research CentreGothenborgSweden

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