arXiv subjects

Nicola Vassena

Publications and source records attributed to Nicola Vassena.

21 records · Page 2Linked to original sources

arXiv2021

Sign-sensitivity of metabolic networks: which structures determine the sign of the responses

Perturbations are ubiquitous in metabolism. A central tool to understand and control their influence on metabolic networks is sensitivity analysis, which investigates how the network responds to external perturbations. We follow here a structural approach: the analysis is based on the network stoichiometry only and it does not require any quantitative knowledge of the reaction rates. We consider perturbations of reaction rates and metabolite concentrations, at equilibrium, and we investigate the responses in the network. For general metabolic systems, this paper focuses on the sign of the responses, i.e. whether a response is positive, negative or whether its sign depends on the parameters of the system. In particular, we identify and describe the subnetworks that are the main players in the sign description. These subnetworks are associated to certain kernel vectors of the stoichiometric matrix and are thus independent from the chosen kinetics.

q-bio.MN↗

arXiv2020

Sensitivity of metabolic networks: perturbing metabolite concentrations

Sensitivity studies the network response to perturbations. We consider local perturbations of the concentrations of metabolites at an equilibrium. We investigate the responses in the network, both of the metabolite concentrations and of the reaction fluxes. Our approach is purely qualitative, rather than quantitative. In fact, our analysis is based, solely, on the stoichiometry of the reaction network and we do not require any quantitative information on the reaction rates. Instead, the description is done only in algebraic terms, and the only data required is the network structure. Biological applications include metabolic control and network reconstruction.

q-bio.MN↗

arXiv2020

Good and bad children in metabolic networks

Equilibrium bifurcations arise from sign changes of Jacobian determinants, as parameters are varied. Therefore we address the Jacobian determinant for metabolic networks with general reaction kinetics. Our approach is based on the concept of Child Selections: each (mother) metabolite is mapped, injectively, to one of those (child) reactions that it drives as an input. Our analysis distinguishes reaction network Jacobians with constant sign from the bifurcation case, where that sign depends on specific reaction rates. In particular we distinguish "good" Child Selections, which do not affect the sign, from more interesting and mischievous "bad" children, which gang up towards sign changes, instability, and bifurcation.

math.DS↗