Computing all possible graph structures describing linearly conjugate realizations of kinetic systems

Ács, Bernadett and Szederkényi, Gábor and Tuza, Zsolt and Tuza, Z. A. (2016) Computing all possible graph structures describing linearly conjugate realizations of kinetic systems. COMPUTER PHYSICS COMMUNICATIONS, 204. pp. 11-20. ISSN 0010-4655

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Abstract

In this paper an algorithm is given to determine all possible structurally different linearly conjugate realizations of a given kinetic polynomial system. The solution is based on the iterative search for constrained dense realizations using linear programming. Since there might exist exponentially many different reaction graph structures, we cannot expect to have a polynomial-time algorithm, but we can organize the computation in such a way that polynomial time is elapsed between displaying any two consecutive realizations. The correctness of the algorithm is proved, and possibilities of a parallel implementation are discussed. The operation of the method is shown on two illustrative examples.

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