2020/10/23 by Hamid Rahkooy, Rahkooy, Hamid, Cristian Vargas Montero +1
Biochemistry, Genetics and Molecular Biology · Chemistry · Computer Science · Engineering · #Analytical Chemistry and Chromatography #Commutative Algebra (math.AC) #Computational Drug Discovery Methods #DNA and Biological Computing #FOS: Computer and information sciences #FOS: Mathematics #Gene Regulatory Network Analysis #Mass Spectrometry Techniques and Applications #Slime Mold and Myxomycetes Research #Symbolic Computation (cs.SC)
paper · pdf · doi:10.48550/arxiv.2010.12615
openalex publication_date 2020/10/23 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
We study binomiality of the steady state ideals of chemical reaction networks. Considering rate constants as indeterminates, the concept of unconditional binomiality has been introduced and an algorithm based on linear algebra has been proposed in a recent work for reversible chemical reaction networks, which has a polynomial time complexity upper bound on the number of species and reactions. In this article, using a modified version of species--reaction graphs, we present an algorithm based on graph theory which performs by adding and deleting edges and changing the labels of the edges in order to test unconditional binomiality. We have implemented our graph theoretical algorithm as well as the linear algebra one in Maple and made experiments on biochemical models. Our experiments show that the performance of the graph theoretical approach is similar to or better than the linear algebra approach, while it is drastically faster than Groebner basis and quantifier elimination methods.