Exploiting stoichiometric redundancies for computational efficiency and network reduction Academic Article uri icon

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abstract

  • Analysis of metabolic networks typically begins with construction of the stoichiometry matrix, which characterizes the network topology. This matrix provides, via the balance equation, a description of the potential steady-state flow distribution. This paper begins with the observation that the balance equation depends only on the structure of linear redundancies in the network, and so can be stated in a succinct manner, leading to computational efficiencies in steady-state analysis. This alternative description of steady-state behaviour is then used to provide a novel method for network reduction, which complements existing algorithms for describing intracellular networks in terms of input-output macro-reactions (to facilitate bioprocess optimization and control). Finally, it is demonstrated that this novel reduction method can be used to address elementary mode analysis of large networks: the modes supported by a reduced network can capture the input-output modes of a metabolic module with significantly reduced computational effort.

publication date

  • July 3, 2015