Graphical reduction of reaction networks by linear elimination of species
From MaRDI portal
(Redirected from Publication:504070)
Abstract: The quasi-steady state approximation and time-scale separation are commonly applied methods to simplify models of biochemical reaction networks based on ordinary differential equations (ODEs). The concentrations of the "fast" species are assumed effectively to be at steady state with respect to the "slow" species. Under this assumption the steady state equations can be used to eliminate the "fast" variables and a new ODE system with only the slow species can be obtained. We interpret a reduced system obtained by time-scale separation as the ODE system arising from a unique reaction network, by identification of a set of reactions and the corresponding rate functions. The procedure is graphically based and can easily be worked out by hand for small networks. For larger networks, we provide a pseudo-algorithm. We study properties of the reduced network, its kinetics and conservation laws, and show that the kinetics of the reduced network fulfil realistic assumptions, provided the original network does. We illustrate our results using biological examples such as substrate mechanisms, post-translational modification systems and networks with intermediates (transient) steps.
Recommendations
- Quasi-steady-state and singular perturbation reduction for reaction networks with noninteracting species
- Uniform approximation of solutions by elimination of intermediate species in deterministic reaction networks
- A constructive approach to quasi-steady state reductions
- A multi-time-scale analysis of chemical reaction networks. I: Deterministic systems
- Model reduction of chemical reaction systems using elimination
Cites work
- scientific article; zbMATH DE number 3878852 (Why is no real title available?)
- scientific article; zbMATH DE number 3902654 (Why is no real title available?)
- scientific article; zbMATH DE number 3075094 (Why is no real title available?)
- Atoms of multistationarity in chemical reaction networks
- On the origin of Turing instability
- Quasi-steady state -- intuition, perturbation theory and algorithmic algebra
- Reaction network realizations of rational biochemical systems and their structural properties
- The QSSA in chemical kinetics: as taught and as practiced
- The rational parameterisation theorem for multisite post-translational modification systems
- Variable elimination in chemical reaction networks with mass-action kinetics
- Variable elimination in post-translational modification reaction networks with mass-action kinetics
Cited in
(38)- Numerical methods for the dynamical reduction of the complexity of biochemical reaction processes
- Transactions on Computational Systems Biology I
- LNetReduce: tool for reducing linear dynamic networks with separated timescales
- Variable elimination in post-translational modification reaction networks with mass-action kinetics
- Layered decomposition for the model order reduction of timescale separated biochemical reaction networks
- A unified framework for limit results in chemical reaction networks on multiple time-scales
- A multi-time-scale analysis of chemical reaction networks. I: Deterministic systems
- A multi-time-scale analysis of chemical reaction networks. II: Stochastic systems
- Algebra and geometry in the study of enzymatic cascades
- Algorithmic reduction of biological networks with multiple time scales
- Reduction of Chemical Reaction Networks with Approximate Conservation Laws
- Reduced models of networks of coupled enzymatic reactions
- Tropical abstraction of biochemical reaction networks with guarantees
- Graph-based, dynamics-preserving reduction of (bio)chemical systems
- Uniform approximation of solutions by elimination of intermediate species in deterministic reaction networks
- Elimination of intermediate species in multiscale stochastic reaction networks
- Model reduction of chemical reaction systems using elimination
- Approaches for the estimation of timescales in nonlinear dynamical systems: timescale separation in enzyme kinetics as a case study
- Partial equilibrium approximations in apoptosis. I: The intracellular-signaling subsystem
- Nonnegative Linear Elimination for Chemical Reaction Networks
- A large-scale assessment of exact lumping of quantitative models in the biomodels repository
- A proof of unlimited multistability for phosphorylation cycles
- Normalizing chemical reaction networks by confluent structural simplification
- Stochastic reduction method for biological chemical kinetics using time-scale separation
- Joining and decomposing reaction networks
- A reduction method for multiple time scale stochastic reaction networks with non-unique equilibrium probability
- Fast reactions with non-interacting species in stochastic reaction networks
- A large-scale assessment of exact model reduction in the biomodels repository
- Analytical reduction of nonlinear metabolic networks accounting for dynamics in enzymatic reactions
- On the sum of chemical reactions
- Singular perturbations and scaling
- Quasi-steady-state and singular perturbation reduction for reaction networks with noninteracting species
- Simplification of reversible Markov chains by removal of states with low equilibrium occupancy
- Targeted reduction of complex models with time scale hierarchy -- a case study
- Variable elimination in chemical reaction networks with mass-action kinetics
- Graphical criteria for positive solutions to linear systems
- The multistationarity structure of networks with intermediates and a binomial core network
- Intermediates and generic convergence to equilibria
This page was built for publication: Graphical reduction of reaction networks by linear elimination of species
Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q504070)
