Dynamics of posttranslational modification systems: Recent progress and future directions

C Conradi, A Shiu - Biophysical journal, 2018 - cell.com
Posttranslational modification of proteins is important for signal transduction, and hence
significant effort has gone toward understanding how posttranslational modification …

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 …

Multistationarity in structured reaction networks

A Dickenstein, MP Millan, A Shiu, X Tang - Bulletin of Mathematical …, 2019 - Springer
Many dynamical systems arising in biology and other areas exhibit multistationarity (two or
more positive steady states with the same conserved quantities). Although deciding …

Robustness and parameter geography in post-translational modification systems

KM Nam, BM Gyori, SV Amethyst… - PLoS computational …, 2020 - journals.plos.org
Biological systems are acknowledged to be robust to perturbations but a rigorous
understanding of this has been elusive. In a mathematical model, perturbations often exert …

[HTML][HTML] Lower bounds for positive roots and regions of multistationarity in chemical reaction networks

F Bihan, A Dickenstein, M Giaroli - Journal of Algebra, 2020 - Elsevier
Given a real sparse polynomial system, we present a general framework to find explicit
coefficients for which the system has more than one positive solution. Our approach is based …

Translated chemical reaction networks

MD Johnston - Bulletin of mathematical biology, 2014 - Springer
Many biochemical and industrial applications involve complicated networks of
simultaneously occurring chemical reactions. Under the assumption of mass action kinetics …

A global convergence result for processive multisite phosphorylation systems

C Conradi, A Shiu - Bulletin of mathematical biology, 2015 - Springer
Multisite phosphorylation plays an important role in intracellular signaling. There has been
much recent work aimed at understanding the dynamics of such systems when the …

A deficiency-based approach to parametrizing positive equilibria of biochemical reaction systems

MD Johnston, S Müller, C Pantea - Bulletin of Mathematical Biology, 2019 - Springer
We present conditions which guarantee a parametrization of the set of positive equilibria of a
generalized mass-action system. Our main results state that (1) if the underlying generalized …

Multistationarity in the space of total concentrations for systems that admit a monomial parametrization

C Conradi, A Iosif, T Kahle - Bulletin of Mathematical Biology, 2019 - Springer
We apply tools from real algebraic geometry to the problem of multistationarity of chemical
reaction networks. A particular focus is on the case of reaction networks whose steady states …

Parameter regions that give rise to 2 [n/2]+ 1 positive steady states in the n-site phosphorylation system

M Giaroli, R Rischter, MP Millán… - arXiv preprint arXiv …, 2019 - arxiv.org
The distributive sequential n-site phosphorylation/dephosphorylation system is an important
building block in networks of chemical reactions arising in molecular biology, which has …