2023/08/24 by Dylan Antonio S. J. Talabis, Eduardo Mendoza, Talabis, Dylan Antonio +1
Agricultural and Biological Sciences · Biochemistry, Genetics and Molecular Biology · #65H10 #80A30 #92C45 #Dynamical Systems (math.DS) #FOS: Biological sciences #FOS: Mathematics #Fermentation and Sensory Analysis #Microbial Metabolic Engineering and Bioproduction #Molecular Networks (q-bio.MN) #Plant biochemistry and biosynthesis
paper · pdf · doi:10.48550/arxiv.2308.12586
openalex publication_date 2023/08/24 · openalex created_date 2023/08/26 · openalex updated_date 2026/07/28
A dynamical system obtains a wide variety of kinetic realizations, which is advantageous for the analysis of biochemical systems. A reaction network, derived from a dynamical system, may or may not possess some properties needed for a thorough analysis. We improve and extend the work of M. Johnston \citeJOHN2014 and Hong et al. \citeHONG2023 on network translations to network transformations, where the network is modified while preserving the dynamical system. These transformations can shrink, extend, or retain the stoichiometric subspace. Here, we show that positive dependent network can be translated to a weakly reversible network. Using the kinetic realizations of (1) calcium signaling in the olfactory system and (2) metabolic insulin signaling, we demonstrate the benefits of transformed systems with positive deficiency for analyzing biochemical systems. Furthermore, we present an algorithm for a network transformation of a weakly reversible non-complex factorizable kinetic (NFK) system to a weakly reversible complex factorizable kinetic (CFK) system, thereby enhancing the Subspace Coincidence Theorem for NFK systems of Nazareno et al. \citeNAZA2019. Finally, using the transformed kinetic realization of monolignol biosynthesis in Populus xylem, we study the structural and kinetic properties of transformed systems,including the invariance of concordance and variation of injectivity and mono-/multi-stationarity under network transformation.