Reverse engineering and identification in systems biology: strategies, perspectives and challenges
The interplay of mathematical modelling with experiments is one of the central elements in
systems biology. The aim of reverse engineering is to infer, analyse and understand …
systems biology. The aim of reverse engineering is to infer, analyse and understand …
A tutorial on Chemical Reaction Networks dynamics
D Angeli - 2009 European Control Conference (ECC), 2009 - ieeexplore.ieee.org
Chemical Reaction Networks (CRN for short) can be effectively modeled by means of
nonlinear, parameter-dependent systems of ordinary differential equations. The uncertain …
nonlinear, parameter-dependent systems of ordinary differential equations. The uncertain …
Inference of complex biological networks: distinguishability issues and optimization-based solutions
Background The inference of biological networks from high-throughput data has received
huge attention during the last decade and can be considered an important problem class in …
huge attention during the last decade and can be considered an important problem class in …
Finding complex balanced and detailed balanced realizations of chemical reaction networks
Reversibility, weak reversibility and deficiency, detailed and complex balancing are
generally not “encoded” in the kinetic differential equations but they are realization …
generally not “encoded” in the kinetic differential equations but they are realization …
Identifiability of large nonlinear biochemical networks
AF Villaverde, A Barreiro - 2016 - repositorium.uminho.pt
Dynamic models formulated as a set of ordinary differential equations provide a detailed
description of the time-evolution of a system. Such models of (bio) chemical reaction …
description of the time-evolution of a system. Such models of (bio) chemical reaction …
Rigorously proven chaos in chemical kinetics
M Susits, J Tóth - Chaos: An Interdisciplinary Journal of Nonlinear …, 2024 - pubs.aip.org
This study addresses a longstanding question regarding the mathematical proof of chaotic
behavior in kinetic differential equations. Following the numerous numerical and …
behavior in kinetic differential equations. Following the numerous numerical and …
Computing weakly reversible linearly conjugate chemical reaction networks with minimal deficiency
Mass-action kinetics is frequently used in systems biology to model the behavior of
interacting chemical species. Many important dynamical properties are known to hold for …
interacting chemical species. Many important dynamical properties are known to hold for …
Linear conjugacy of chemical reaction networks
MD Johnston, D Siegel - Journal of mathematical chemistry, 2011 - Springer
Under suitable assumptions, the dynamic behaviour of a chemical reaction network is
governed by an autonomous set of polynomial ordinary differential equations over …
governed by an autonomous set of polynomial ordinary differential equations over …
A linear programming approach to weak reversibility and linear conjugacy of chemical reaction networks
A numerically effective procedure for determining weakly reversible chemical reaction
networks that are linearly conjugate to a known reaction network is proposed in this paper …
networks that are linearly conjugate to a known reaction network is proposed in this paper …
Realizations of kinetic differential equations
The induced kinetic differential equation of a reaction network endowed with mass action
type kinetics is a system of polynomial differential equations. The problem studied here is …
type kinetics is a system of polynomial differential equations. The problem studied here is …