BiRNe: Symbolic bifurcation analysis of reaction networks with Python
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| Format: | Preprint |
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2025
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| _version_ | 1866918208210993152 |
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| author | Golnik, Richard Gatter, Thomas Stadler, Peter F. Vassena, Nicola |
| author_facet | Golnik, Richard Gatter, Thomas Stadler, Peter F. Vassena, Nicola |
| contents | 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 to techniques such as Gröbner basis computation and related algebraic tools. However, these methods face significant computational complexity, limiting their applicability to relatively small networks involving only a handful of species. In contrast, building on recent theoretical advances, we introduce here \textsc{BiRNe} (BIfurcations in Reaction NEtworks) Python module, which relies on a symbolic approach designed to detect bifurcations in larger reaction networks (up to 10-20 species, depending on the network's connectivity) equipped with parameter-rich kinetics. This class includes enzymatic kinetics such as Michaelis--Menten, ligand-binding kinetics like Hill functions, and generalized mass-action kinetics. For a given network, the current algorithm identifies all minimal autocatalytic subnetworks and fully characterizes the presence of bifurcations associated with zero eigenvalues, thus determining whether the network admits multistationarity. It also detects oscillatory bifurcations arising from positive-feedback structures, capturing a significant class of possible oscillations. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2511_14431 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | BiRNe: Symbolic bifurcation analysis of reaction networks with Python Golnik, Richard Gatter, Thomas Stadler, Peter F. Vassena, Nicola Molecular Networks Dynamical Systems 05C92, 37G10, 37N25, 92C40, 92C42, 37-04, 68-06 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 to techniques such as Gröbner basis computation and related algebraic tools. However, these methods face significant computational complexity, limiting their applicability to relatively small networks involving only a handful of species. In contrast, building on recent theoretical advances, we introduce here \textsc{BiRNe} (BIfurcations in Reaction NEtworks) Python module, which relies on a symbolic approach designed to detect bifurcations in larger reaction networks (up to 10-20 species, depending on the network's connectivity) equipped with parameter-rich kinetics. This class includes enzymatic kinetics such as Michaelis--Menten, ligand-binding kinetics like Hill functions, and generalized mass-action kinetics. For a given network, the current algorithm identifies all minimal autocatalytic subnetworks and fully characterizes the presence of bifurcations associated with zero eigenvalues, thus determining whether the network admits multistationarity. It also detects oscillatory bifurcations arising from positive-feedback structures, capturing a significant class of possible oscillations. |
| title | BiRNe: Symbolic bifurcation analysis of reaction networks with Python |
| topic | Molecular Networks Dynamical Systems 05C92, 37G10, 37N25, 92C40, 92C42, 37-04, 68-06 |
| url | https://arxiv.org/abs/2511.14431 |