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Determination of flux directions by thermodynamic network analysis: Computing informative metabolite pools. (English) Zbl 1243.80013

Summary: Network thermodynamics focuses on the energetic analysis of complex metabolic networks. The method connects free Gibbs energies, metabolite concentrations and flux directions by fundamental thermodynamic laws. Here, a new application of network thermodynamics is presented that identifies those metabolite pools that have to be measured in order to determine as many flux directions as possible. For a medium-scaled reaction network such informative metabolite pools are computed with an approach based on Monte Carlo sampling. It turns out that some reactions can be directed with only a few measurements whereas other reactions cannot be directed even with a complete data set. High connectivity in metabolic reaction networks in alliance with concentration ranges make it impossible to intuitively foresee such results. In particular, the impact of measurements of a special type of metabolites being involved in many reactions, so called energetic currency metabolites is investigated.

MSC:

80M25 Other numerical methods (thermodynamics) (MSC2010)
65C05 Monte Carlo methods

Software:

anNET
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References:

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