Chemical reaction network theory elucidates sources of multistability in interferon signaling

I Otero-Muras, P Yordanov… - PLoS computational …, 2017 - journals.plos.org
Bistability has important implications in signaling pathways, since it indicates a potential cell
decision between alternative outcomes. We present two approaches developed in the …

Positive equilibria of Hill-type kinetic systems

BS Hernandez, ER Mendoza - Journal of Mathematical Chemistry, 2021 - Springer
This work introduces a novel approach to study properties of positive equilibria of a chemical
reaction network NN endowed with Hill-type kinetics K, called a Hill-type kinetic (HTK) …

Graphical reduction of reaction networks by linear elimination of species

M Sáez, C Wiuf, E Feliu - Journal of mathematical biology, 2017 - Springer
The quasi-steady state approximation and time-scale separation are commonly applied
methods to simplify models of biochemical reaction networks based on ordinary differential …

A fast and convergent combined Newton and gradient descent method for computing steady states of chemical reaction networks

S Berra, A La Torraca, F Benvenuto… - arXiv preprint arXiv …, 2022 - arxiv.org
In this work we present a fast, globally convergent, iterative algorithm for computing the
asymptotically stable states of nonlinear large--scale systems of quadratic autonomous …

Linear conjugacy of chemical kinetic systems

AL Nazareno, RPL Eclarin, ER Mendoza… - arXiv preprint arXiv …, 2019 - arxiv.org
Two networks are said to be linearly conjugate if the solution of their dynamic equations can
be transformed into each other by a positive linear transformation. The study on dynamical …

Multi-objective optimization of experiments using curvature and fisher information matrix

E Manesso, S Sridharan, R Gunawan - Processes, 2017 - mdpi.com
The bottleneck in creating dynamic models of biological networks and processes often lies
in estimating unknown kinetic model parameters from experimental data. In this regard …

Combined Newton-Gradient Method for Constrained Root-Finding in Chemical Reaction Networks

S Berra, A La Torraca, F Benvenuto… - Journal of Optimization …, 2024 - Springer
In this work, we present a fast, globally convergent, iterative algorithm for computing the
asymptotically stable states of nonlinear large-scale systems of quadratic autonomous …

A computational approach to multistationarity in poly-PL kinetic systems

DM Magpantay, BS Hernandez, AA Reyes V… - arXiv preprint arXiv …, 2020 - arxiv.org
One important question that interests those who work in chemical reaction network theory
(CRNT) is this: Does the system obtained from a reaction network admit a positive …

A computational approach to extinction events in chemical reaction networks with discrete state spaces

MD Johnston - Mathematical Biosciences, 2017 - Elsevier
Recent work of Johnston et al. has produced sufficient conditions on the structure of a
chemical reaction network which guarantee that the corresponding discrete state space …

Linear conjugacy in biochemical reaction networks with rational reaction rates

A Gábor, KM Hangos, G Szederkényi - Journal of Mathematical Chemistry, 2016 - Springer
In this paper we show that the model form of a wide class of kinetic systems with rational
terms in the reaction rates is invariant under a positive linear diagonal transformation. Thus …