Fig. 1. Schematic of metabolic and physiological acclimation processes simulated by MSE.

A single cell is shown at the center with several membrane transporters (colored rectangles) and macromolecular pools (graded circles). Four key modules are shown in expanded detail, described clockwise. (Top left) Metabolic networks differ for each of the 69 strains simulated. A multipartite graph of genes, reactions, and metabolites is shown for a particular strain, SS120. (Top right) Transporter abundances (n) are optimized according to a mechanistic model of substrate transport that resolves several different limitation regimes (diffusion limitation, growth limitation, porter limitation, and surface area limitation). Competition for resources between transporters results in deviations from the optimum n^* across the range of ambient substrate concentrations S_∞. (Bottom right) The downwelling irradiance spectrum selects the optimal distribution of pigments on the basis of absorption (Abs) spectra and the cellular energy demand, within experimental constraints. Excitons are shuttled to photosystems I and II from each electronic state of each light-harvesting pigment [divinylchlorophyll a (DV-Chl a), divinylchlorophyll b (DV-Chl b), and α-carotene (α-Car)]. Under excess light conditions, the photoprotective pigment zeaxanthin (Zeax) acts both to dissipate excess photons from light-harvesting pigments to heat and to quench singlet oxygen generated by the relaxation of triply excited chlorophylls a and b. (Bottom left) Macromolecular compositions are optimized within experimental constraints to maximize growth given the availability of nutrient and energy resources. Differences between environments in the size of each graded circle are intended to reflect changes in the levels of each macromolecular pool. Carbs, carbohydrates; dMets, dissolved (free) metabolites.