Foundations of chemical reaction network theory

M Feinberg - 2019 - Springer
When I am called upon to teach fluid mechanics, I always show students a copy of Newton's
Principia. I do this for a number of reasons, not least of which is the connection I hope they …

A compositional framework for reaction networks

JC Baez, BS Pollard - Reviews in Mathematical Physics, 2017 - World Scientific
Reaction networks, or equivalently Petri nets, are a general framework for describing
processes in which entities of various kinds interact and turn into other entities. In chemistry …

A survey of methods for deciding whether a reaction network is multistationary

B Joshi, A Shiu - Mathematical Modelling of Natural Phenomena, 2015 - mmnp-journal.org
Which reaction networks, when taken with mass-action kinetics, have the capacity for
multiple steady states? There is no complete answer to this question, but over the last 40 …

Identifying parameter regions for multistationarity

C Conradi, E Feliu, M Mincheva… - PLoS computational …, 2017 - journals.plos.org
Mathematical modelling has become an established tool for studying the dynamics of
biological systems. Current applications range from building models that reproduce …

Sign conditions for injectivity of generalized polynomial maps with applications to chemical reaction networks and real algebraic geometry

S Müller, E Feliu, G Regensburger, C Conradi… - Foundations of …, 2016 - Springer
We give necessary and sufficient conditions in terms of sign vectors for the injectivity of
families of polynomial maps with arbitrary real exponents defined on the positive orthant …

Generalized mass action systems: Complex balancing equilibria and sign vectors of the stoichiometric and kinetic-order subspaces

S Muller, G Regensburger - SIAM Journal on Applied Mathematics, 2012 - SIAM
Mass action systems capture chemical reaction networks in homogeneous and dilute
solutions. We suggest a notion of generalized mass action systems that admits arbitrary …

Unstable cores are the source of instability in chemical reaction networks

N Vassena, PF Stadler - Proceedings of the Royal …, 2024 - royalsocietypublishing.org
In biochemical networks, complex dynamical features such as superlinear growth and
oscillations are classically considered a consequence of autocatalysis. For the large class of …

Concordant chemical reaction networks

G Shinar, M Feinberg - Mathematical biosciences, 2012 - Elsevier
We describe a large class of chemical reaction networks, those endowed with a subtle
structural property called concordance. We show that the class of concordant networks …

On the persistence and global stability of mass-action systems

C Pantea - SIAM Journal on Mathematical Analysis, 2012 - SIAM
This paper concerns the long-term behavior of population systems, and in particular of
chemical reaction systems, modeled by deterministic mass-action kinetics. We approach two …

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 …