Plant cells can accumulate large quantities of storage polysaccharides as a result of photosynthesis. Such polysaccharides can be hydrolyzed, chemically or enzymatically, into sugars that can be fermented to biofuels. In order to identify experimentally manipulable parameters for optimization, and to understand better the system dynamics, we have developed a detailed ordinary differential equation model of key carbon and energy metabolic pathways relevant to biofuel production. Photosynthetic carbon metabolism has been incorporated as two modules; a model of the photosynthetic dark reactions, photorespiration and sucrose synthesis; and, a new model of starch degradation that to our knowledge is the most detailed such model to date. In this presentation, we demonstrate how we simulate photosynthetic carbon metabolite concentrations and fluxes, constrained by available literature data, using the High-Performance Systems Biology Toolkit developed by our group, with emphasis on exploring the dependence of photosynthetic carbon metabolism on boundary fluxes. We also describe the modeling of pathways for synthesis of nucleotide-sugars, key monomers for plant cell wall polysaccharide synthesis and potential targets for addressing lignocellulosic biomass recalcitrance to degradation.