A Petri net approach to the study of persistence in chemical reaction networks
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Publication:2480002
Applications of graph theory (05C90) Directed graphs (digraphs), tournaments (05C20) Dynamical systems in biology (37N25) Kinetics in biochemical problems (pharmacokinetics, enzyme kinetics, etc.) (92C45) Models and methods for concurrent and distributed computing (process algebras, bisimulation, transition nets, etc.) (68Q85) Classical flows, reactions, etc. in chemistry (92E20)
Abstract: Persistency is the property, for differential equations in , that solutions starting in the positive orthant do not approach the boundary. For chemical reactions and population models, this translates into the non-extinction property: provided that every species is present at the start of the reaction, no species will tend to be eliminated in the course of the reaction. This paper provides checkable conditions for persistence of chemical species in reaction networks, using concepts and tools from Petri net theory. Nontrivial examples are provided to illustrate the theory.
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Cites work
- scientific article; zbMATH DE number 3855514 (Why is no real title available?)
- scientific article; zbMATH DE number 3722109 (Why is no real title available?)
- scientific article; zbMATH DE number 1182386 (Why is no real title available?)
- scientific article; zbMATH DE number 758785 (Why is no real title available?)
- scientific article; zbMATH DE number 814403 (Why is no real title available?)
- scientific article; zbMATH DE number 2247510 (Why is no real title available?)
- Applications and Theory of Petri Nets 2005
- Discrete, Continuous, and Hybrid Petri Nets
- Executable Petri net models for the analysis of metabolic pathways
- From Petri Nets to Differential Equations – An Integrative Approach for Biochemical Network Analysis
- Monotone chemical reaction networks
- Monotone control systems
- Multiple Equilibria in Complex Chemical Reaction Networks: II. The Species-Reaction Graph
- Persistence in dynamical systems
- Persistence in food chains with general interactions
- Steady-states of receptor-ligand dynamics: a theoretical framework
- Structure and stability of certain chemical networks and applications to the kinetic proofreading model of T-cell receptor signal transduction
- The existence and uniqueness of steady states for a class of chemical reaction networks
- Understanding bistability in complex enzyme-driven reaction networks
- Uniform Persistence and Repellors for Maps
- Uniform persistence and permanence for non-autonomous semiflows in population biology
- Uniformly Persistent Systems
Cited in
(84)- Lyapunov function partial differential equations for chemical reaction networks: some special cases
- From science to management: using Bayesian networks to learn about \textit{Lyngbya}
- Complex Balancing Reconstructed to the Asymptotic Stability of Mass-Action Chemical Reaction Networks with Conservation Laws
- Flatness and Complexity of Immediate Observation Petri Nets
- Endotactic Networks and Toric Differential Inclusions
- Deficiency Zero Petri Nets and Product Form
- Chemical reaction systems with toric steady states
- On the existence of the positive steady states of weakly reversible deficiency-one mass action systems
- Some consequences of thermodynamic feasibility for chemical reaction networks. Considering thermodynamic feasibility in current CRN research
- First-order chemical reaction networks. I: Theoretical considerations
- On necessary and sufficient conditions for proto-cell stationary growth
- Engineering model reduction and entropy-based Lyapunov functions in chemical reaction kinetics
- A global convergence result for processive multisite phosphorylation systems
- Minimal trap spaces of logical models are maximal siphons of their Petri net encoding
- Siphons in chemical reaction networks
- Some results on injectivity and multistationarity in chemical reaction networks
- The inheritance of nondegenerate multistationarity in chemical reaction networks
- Catalysis in reaction networks
- Persistence Results for Chemical Reaction Networks with Time-Dependent Kinetics and No Global Conservation Laws
- A scheme for molecular computation of maximum likelihood estimators for log-linear models
- Graph-theoretic characterizations of monotonicity of chemical networks in reaction coordinates
- Conditions for extinction events in chemical reaction networks with discrete state spaces
- Structural analysis in biology: a control-theoretic approach
- Endotactic and strongly endotactic networks with infinitely many positive steady states
- Some network conditions for positive recurrence of stochastically modeled reaction networks
- Synchronous balanced analysis
- Parameterized Analysis of Immediate Observation Petri Nets
- Reachability, persistence, and constructive chemical reaction networks. I: Reachability approach to the persistence of chemical reaction networks
- Directed reachability for infinite-state systems
- Stochastic switching in biology: from genotype to phenotype
- Source-Only Realizations, Weakly Reversible Deficiency One Networks, and Dynamical Equivalence
- Reachability, persistence, and constructive chemical reaction networks. II: A formalism for species composition in chemical reaction network theory and application to persistence
- On the Liouville integrability of Edelstein's reaction system in R^3
- Graphical methods for analysing feedback in biological networks -- a survey
- Algebra and geometry in the study of enzymatic cascades
- Persistent Subspaces of Reaction-Based Dynamical Systems
- An all-encompassing global convergence result for processive multisite phosphorylation systems
- Conservation laws in biochemical reaction networks
- Weak dynamical nonemptiability and persistence of chemical kinetics systems
- Oscillations and bistability in a model of ERK regulation
- Robust persistence and permanence of polynomial and power law dynamical systems
- Persistence and stability of a class of kinetic compartmental models
- A stratum approach to global stability of complex balanced systems
- Dynamical properties of discrete reaction networks
- Homotopy methods for counting reaction network equilibria
- Individuals, populations and fluid approximations: a Petri net based perspective
- Quasi-toric differential inclusions
- Translated chemical reaction networks
- Linking network structure and dynamics to describe the set of persistent species in reaction diffusion systems
- Permanence of sparse catalytic networks
- How far is complex balancing from detailed balancing?
- Dominance and T-Invariants for Petri Nets and Chemical Reaction Networks
- Persistence in chemical reaction networks with arbitrary time delays
- Exact analysis of intrinsic qualitative features of phosphorelays using mathematical models
- How Petri nets might enhance your systems biology toolkit
- Dual perspectives of equilibrium throughput properties of continuous mono-T-semiflow Petri nets: firing rate and initial marking variations
- Forward-invariant peeling in chemical dynamics: a simple case study
- A tutorial on chemical reaction network dynamics
- Boundedness analysis for open chemical reaction networks with mass-action kinetics
- Necessary and sufficient conditions for protocell growth
- Linear conjugacy in biochemical reaction networks with rational reaction rates
- A linear programming approach to weak reversibility and linear conjugacy of chemical reaction networks
- Inheritance of oscillation in chemical reaction networks
- Linear conjugacy of chemical reaction networks
- Autocatalysis in reaction networks
- On the relation between \(\omega \)-limit set and boundaries of mass-action chemical reaction networks
- Boundedness of trajectories for weakly reversible, single linkage class reaction systems
- A computational approach to persistence, permanence, and endotacticity of biochemical reaction systems
- Oscillations in three-reaction quadratic mass-action systems
- Asymptotic stability of delayed complex balanced reaction networks with non-mass action kinetics
- On the number of steady states in a multiple futile cycle
- Intermediates and generic convergence to equilibria
- Computing weakly reversible deficiency zero network translations using elementary flux modes
- The deficiency zero theorem and global asymptotic stability for a class of chemical reaction networks with arbitrary time delays
- Chemical reaction-diffusion networks: convergence of the method of lines
- Problematic configurations and choice-join pairs on Mono-T-Semiflow nets: towards the characterization of behavior-structural properties
- A Modular Criterion for Persistence of Chemical Reaction Networks
- Dominance and deficiency for Petri nets and chemical reaction networks
- Graphical characterizations of robust stability in biological interaction networks
- Intermediates, catalysts, persistence, and boundary steady states
- Charlie -- an extensible Petri net analysis tool
- Product-form stationary distributions for deficiency zero chemical reaction networks
- Reachability, persistence, and constructive chemical reaction networks. III: A mathematical formalism for binary enzymatic networks and application to persistence
- A computational approach to extinction events in chemical reaction networks with discrete state spaces
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