Metabolic model, structured

Models for batch culture can be constructed by assuming mechanisms for each phase of the cycle. These mechanisms must be reasonably comph-cated to account for a lag phase and for a prolonged stationary phase. Unstructured models treat the cells as a chemical entity that reacts with its environment. Structured models include some representation of the internal cell chemistry. Metabolic models focus on the energy-producing mechanisms within the cells. 

Within this contribution, our aim was to summarize and describe the ways and means of modelmaking. In our opinion, and reflecting the structure of this contribution, the construction and analysis of metabolic models rests upon five main pillars (i) The expertise and knowledge of classic biochemistry, defining the building blocks and their interactions (as described in Section III). 

R. Heinrich and S. Schuster, The modeling of metabolic systems, structure, control and optimality. BioSystems 47, 61 77 (1998). 

While there are numerous PBPK and TK approaches to chemical mixtures, these representative examples demonstrate a spectrum of approaches, from simple binary mixtures to complex, often uncharacterized mixtures. The underlying commonality is the need for a validated TK model structure, the inclusion of defensible parameter values, and some external measure of metabolic interaction that can serve as the basis for starting values for model parameters. Within a mixture, PBPK modeling approaches are most valid for the chemical of concern when that chemical is specifically addressed by the model. 

Another two key concepts in metabolic engineering are metabolic pathway analysis and metabolic pathway modeling. The former is used for assessing inherent network properties in the complete biochemical reaction networks. It involves identification of the metabolic network structure (or pathway topology), quantification of the fluxes through the branches of the metabolic network, and identification of the control structures within the metabolic network. 

---