2025/04/07 by Hadjar Rahou, Hulda S. Haraldsdóttir, Rahou, Hadjar +7
Biochemistry, Genetics and Molecular Biology · Mathematics · Physics and Astronomy · #FOS: Biological sciences #Gene Regulatory Network Analysis #Graph theory and applications #Molecular Networks (q-bio.MN) #Origins and Evolution of Life
paper · pdf · doi:10.48550/arxiv.2504.05085
openalex publication_date 2025/04/07 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/30
A detailed understanding of biochemical networks at the molecular level is essential for studying complex cellular processes. In this paper, we provide a comprehensive description of biochemical networks by considering individual atoms and chemical bonds. To address combinatorial complexity, we introduce a well-established approach to group similar types of information within biochemical networks. A conserved moiety is a set of atoms whose association is invariant across all reactions in a network. A reacting moiety is a set of bonds that are either broken, formed, or undergo a change in bond order in at least one reaction in the network. By mathematically identifying these moieties, we establish the biological significance of conserved and reacting moieties according to the mathematical properties of the stoichiometric matrix. We also present a novel decomposition of the stoichiometric matrix based on conserved moieties. This approach bridges the gap between graph theory, linear algebra, and biological interpretation, thus opening up new horizons in the study of chemical reaction networks.