Detailed explanation of the model and further analysis.

<p>Contains lists of all parameter values used in the model (Table A), all modeled reactions (Table B), initial conditions (Table C), parameters used to model light-adapted cells (Table D), and ranges of parameter variation during state transition model analysis (Table E). We also include explanations of the reaction kinetics and Gibbs energy calculations used, as well as further analyses of the model.</p> <p>(PDF)</p>