Core pathways for photosynthesis, biopolymer storage and mobilization, functional biomass synthesis and maintenance, and catabolism and oxidative phosphorylation followed the same approach as in the PPM. Briefly, under photoautotrophic conditions, the microalgal cell uses sunlight (hv) to produce oxygen and convert carbon dioxide into glyceraldehyde-3phosphate (G3P) (R1) via the Calvin cycle. Under nutrient-deplete conditions, microalgae store carbon in the cell as carbohydrate and lipid biopolymers. The carbohydrates are assumed to be stored in the form of polyglucose (starch or glycogen; XPG), produced via gluconeogenesis (R8, R9) and broken down to glucose-6-phosphate (G6P; R10) and then G3P via glycolysis (R6) or glycolysis with the pentose phosphate pathway (R7; new to PM 2 ; additional details in the next paragraph). The lipid biopolymers are assumed to be in the form of triacylglycerol (TAG; XTAG), which are synthesized via acetyl-CoA to palmitic acid (C16:0) and then TAG (R12) and, when consumed, TAG is hydrolyzed and palmitate is activated to palmitoyl-CoA and degraded to acetyl-CoA (R13). Processes for functional biomass (XALG) production are lumped into two reaction equations: (i) the synthesis of biomass precursors (protein, DNA, RNA) from acetyl-CoA and nutrients (nitrogen, phosphorus) (R3); and (ii) the polymerization of precursors into functional biomass and cell maintenance (R4). The elemental composition of XALG is fixed as CH1.8O0.5N0.2P0.018, where phosphorus was not included in the PPM but has been added here based on a N:P mass ratio of 5:1. Finally, catabolism of acetyl-CoA proceeds via the tricarboxylic acid (TCA) cycle to yield NADH (R14) and ATP can be produced via oxidative phosphorylation (R15). The efficiency of oxidative phosphorylation (P/O ratio) in mitochondria (δ PO ) determines how much ATP is produced per mole of NADH oxidized and, consistent with past lumped pathway metabolic models, is assumed to remain the same regardless of growth conditions (e.g., carbon source). Additional details about these metabolic pathways are described in previous work. New reactions were added to support the heterotrophic growth of microalgae on two extracellular organic carbon sources: glucose and acetate. Glucose is transported into the cell and then converted to G6P via hexokinase (R5), and acetate is converted into acetyl-CoA by acetyl-CoA synthetase (R11). R6 represents the first five steps of glycolysis and is active under photoautotrophic conditions, whereas R7 also includes the pentose phosphate pathway and is active under heterotrophic growth and nitrogen limited conditions.