Model schematic. From genes to ecosystems. a Cell with basic intracellular mechanisms including (A1) photosynthesis system, (A2) glycogen metabolism, and (A3) Posttranslational oscillator (PTO). I irradiance, PSU photosynthetic unit (a = open, b = closed, c = damaged), D1′ free photosystem II reaction center protein, G3P internal stored energy, m = cell size/mass, and GLG glycogen. Gene/protein: rpoMH/RNAP RNA polymerase, rptMH/RPT ribosome, psuMH/PSU photosynthetic unit, psbAI/D1 PSII reaction center, luxAB/Lux luciferase, polMH/Pol DNA polymerase, ftsMH/Fts cell division, dumMH/−, dummy (accounts for genes not explicitly considered), kaiA/KaiA, kaiB/KaiB, kaiC/KaiC (UKaiC unphosphorylated, SKaiC phosphorylated only on serine 431, TKaiC phosphorylated only on threonine 432, DKaiC phosphorylated on both sites), circadian clock, and glgC/GlgC glycogen synthesis. glgP/GlgP glycogen degradation. Schematic is simplified and not all processes are shown for clarity (see Section S1, Figs. S1–S14, Tables S1–24 for model details). b Population. An agent-based approach is used to scale up from individual cells to the population. c Light regime. Diel light pattern based on sunset/sunrise calculations, seasonal, and horizontal based on monthly MODIS photosynthetically available radiation (PAR) and vertical attenuation based on MODIS Chlorophyll a. d Circulation model grid. 2° × 2° resolution in the horizontal, 22 layers in the vertical, transport based on OFES model [20]. Green points marked O13 is Lagrangian track of transcriptomics survey off Californian coast from ref. [32], see Fig. 3c. e Global scale
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