Algorithm for perturbing thermodynamically infeasible metabolic networks.
Networks of reactions inside the cell are constrained by the laws of mass and energy balance. The second law of thermodynamics further constrains the topology of the metabolic network, by disallowing interactions that can sustain themselves when they are isolated from the rest of the network. We present an algorithm that identifies such subnetworks and makes them feasible by deleting reactions. This perturbs the network topology, but preserves the optimality of the mass balance solutions. This method has been applied to a full network of Escherichia coli.
Nigam
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W.W. Hansen Experimental Physics Laboratory, Stanford University, Stanford, CA 94305-4085, USA. rakesh@quake.stanford.edu
Liang
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D000465:Algorithms; D008660:Metabolism; D008962:Models, Theoretical; D013816:Thermodynamics