13 citations · 24 across the 9 of their papers we have counts for
12 papers
Layered mixed matrices and reaction networks
Arne Kuhrs, Máté L. Telek, Nicola Vassena
The purpose of this work is twofold. In the first part, we consider layered mixed matrices introduced by Murota, relate them to existing notions in combinatorial commutative algebr…
Sequential and distributive dual futile cycle: Hopf bifurcation can occur under parameter-rich kinetics but cannot occur under mass action kinetics
Nicola Vassena
This paper establishes that the system of ordinary differential equations arising from the sequential and distributive dual futile cycle has the structural capacity for Hopf bifurc…
BiRNe: Symbolic bifurcation analysis of reaction networks with Python
Richard Golnik, Thomas Gatter, Peter F. Stadler +1
Computer algebra methods for analyzing reaction networks often rely on the assumption of mass-action kinetics, which transform the governing ODEs into polynomial systems amenable t…
Enumeration of Autocatalytic Subsystems in Large Chemical Reaction Networks
Richard Golnik, Thomas Gatter, Peter F. Stadler +1
Autocatalysis is an important feature of metabolic networks, contributing crucially to the self-maintenance of organisms. Autocatalytic subsystems of chemical reaction networks (CR…
Stoichiometric recipes for periodic oscillations in reaction networks
Alexander Blokhuis, Peter F. Stadler, Nicola Vassena
Oscillatory chemical reactions are functional components in a variety of biological contexts. In chemistry, the construction and identification of even rudimentary oscillators rema…
Mass action systems: two criteria for Hopf bifurcation without Hurwitz
Nicola Vassena
We state two sufficient criteria for periodic oscillations in mass action systems. Neither criterion requires a computation of the Hurwitz determinants. Instead, both criteria expl…
Unstable Cores are the source of instability in chemical reaction networks
Nicola Vassena, Peter F. Stadler
In biochemical networks, complex dynamical features such as superlinear growth and oscillations are classically considered a consequence of autocatalysis. For the large class of pa…
Symbolic hunt of instabilities and bifurcations in reaction networks
Nicola Vassena
The localization of bifurcations in large parametric systems is still a challenge where the combination of rigorous criteria and informal intuition is often needed. With this motiv…
Structural conditions for saddle-node bifurcations in chemical reaction networks
Nicola Vassena
Motivated by investigating multistationarity in biochemical systems, we address saddle-node bifurcations for chemical reaction networks endowed with general kinetics. At positive e…
Structural obstruction to the simplicity of the eigenvalue zero in chemical reaction networks
Nicola Vassena
Multistationarity is the property of a system to exhibit two distinct equilibria (steady-states) under otherwise identical conditions, and it is a phenomenon of recognized importan…
Sign-sensitivity of metabolic networks: which structures determine the sign of the responses
Nicola Vassena
Perturbations are ubiquitous in metabolism. A central tool to understand and control their influence on metabolic networks is sensitivity analysis, which investigates how the netwo…
Sensitivity of metabolic networks: perturbing metabolite concentrations
Nicola Vassena
Sensitivity studies the network response to perturbations. We consider local perturbations of the concentrations of metabolites at an equilibrium. We investigate the responses in t…