5 papers
Bridging two theoretical frameworks of autocatalysis: RAF sets and stoichiometric autocatalysis
Richard Golnik, Thomas Gatter, Wim Hordijk +2
Autocatalysis lies at the heart of many (bio)chemical processes and is key to processes leading up to the origin of life. Two seemingly very different formalisms have emerged that…
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…
Autocatalytic Cores in Reaction Networks with Explicit Catalysis
Richard Golnik, Thomas Gatter, Peter F. Stadler +1
Autocatalytic cores are minimal units in reaction networks (RNs) responsible for the emergence of autocatalysis. In the absence of explicit catalysis, i.e., when an entity appears…
A Short Note on Relevant Cuts
Nico Domschke, Thomas Gatter, Richard Golnik +1
The set of relevant cuts in a graph is the union of all minimum weight bases of the cut space. A cut is relevant if and only if it is the a minimum weight cut between two distinct…
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…