A network dynamics approach to chemical reaction networks
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Publication:2807889
DOI10.1080/00207179.2015.1095353zbMATH Open1338.93042arXiv1502.02247OpenAlexW2594837916MaRDI QIDQ2807889FDOQ2807889
Shodhan Rao, Bayu Jayawardhana, Arjan van der Schaft
Publication date: 25 May 2016
Published in: International Journal of Control (Search for Journal in Brave)
Abstract: A crisp survey is given of chemical reaction networks from the perspective of general nonlinear network dynamics, in particular of consensus dynamics. It is shown how by starting from the complex-balanced assumption the reaction dynamics governed by mass action kinetics can be rewritten into a form which allows for a very simple derivation of a number of key results in chemical reaction network theory, and which directly relates to the thermodynamics of the system. Central in this formulation is the definition of a balanced Laplacian matrix on the graph of chemical complexes together with a resulting fundamental inequality. This directly leads to the characterization of the set of equilibria and their stability. Both the form of the dynamics and the deduced dynamical behavior are very similar to consensus dynamics. The assumption of complex-balancedness is revisited from the point of view of Kirchhoff's Matrix Tree theorem, providing a new perspective. Finally, using the classical idea of extending the graph of chemical complexes by an extra 'zero' complex, a complete steady-state stability analysis of mass action kinetics reaction networks with constant inflows and mass action outflows is given.
Full work available at URL: https://arxiv.org/abs/1502.02247
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Cites Work
- Port-Hamiltonian systems on graphs
- Distributed algorithms for reaching consensus on general functions
- The existence and uniqueness of steady states for a class of chemical reaction networks
- Structure and stability of certain chemical networks and applications to the kinetic proofreading model of T-cell receptor signal transduction
- On the mathematical structure of balanced chemical reaction networks governed by mass action kinetics
- Distributed Generator Coordination for Initialization and Anytime Optimization in Economic Dispatch
- Laplacian dynamics on general graphs
- Persistence Results for Chemical Reaction Networks with Time-Dependent Kinetics and No Global Conservation Laws
- A Proof of the Global Attractor Conjecture in the Single Linkage Class Case
- Characterization and partial synthesis of the behavior of resistive circuits at their terminals
- Multiple Equilibria in Complex Chemical Reaction Networks: Semiopen Mass Action Systems
- How far is complex balancing from detailed balancing?
- A tutorial on chemical reaction network dynamics
- Boundedness analysis for open chemical reaction networks with mass-action kinetics
- Input-to-State Stability of Rate-Controlled Biochemical Networks
- A graph-theoretical approach for the analysis and model reduction of complex-balanced chemical reaction networks
- Complex and detailed balancing of chemical reaction networks revisited
- Global stability of complex balanced mechanisms
- Stability of open pathways
- Title not available (Why is that?)
Cited In (36)
- Static and dynamic complex models: comparison and application to chemical systems
- Leaderless Deterministic Chemical Reaction Networks
- Integration of inventory control into the port-Hamiltonian framework for dissipative stabilization of chemical reactors
- Emulating cellular automata in chemical reaction-diffusion networks
- Nets with mana: a framework for chemical reaction modelling
- A Graphic Formulation of Nonisothermal Chemical Reaction Systems and the Analysis of Detailed Balanced Networks
- Reaction networks and kinetics of biochemical systems
- Structural analysis in biology: a control-theoretic approach
- The Gompertz model revisited and modified using reaction networks: Mathematical analysis
- Graph-theoretic characterizations of monotonicity of chemical networks in reaction coordinates
- Learning feedback Nash strategies for nonlinear port-Hamiltonian systems
- Adaptive aggregation of Markov chains: quantitative analysis of chemical reaction networks
- Stability of metabolic networks via linear-in-flux-expressions
- Complex dynamics and spatio-temporal patterns in a network of three distributed chemical reactors with periodical feed switching
- An algebraic characterization of self-generating chemical reaction networks using semigroup models
- Reaction networks and population dynamics. Abstracts from the workshop held June 18--24, 2017
- On the complexity of reconstructing chemical reaction networks
- Dynamical properties of discrete reaction networks
- Steady states and stability in metabolic networks without regulation
- Solving moment hierarchies for chemical reaction networks
- On the convergence of nonlinear averaging dynamics with three-body interactions on hypergraphs
- Delay stability of reaction systems
- Quasi-steady-state approximation for chemical reaction networks
- Optimal experimental design for linear time invariant state-space models
- Core-Periphery Detection in Hypergraphs
- Identifiability of chemical reaction networks
- Complex and detailed balancing of chemical reaction networks revisited
- Horizons of cybernetical physics
- Rate-based screening of pressure-dependent reaction networks
- Comparing Chemical Reaction Networks
- Chemical reaction-diffusion networks: convergence of the method of lines
- A Modular Criterion for Persistence of Chemical Reaction Networks
- A new decomposition of the graph Laplacian and the binomial structure of mass-action systems
- Network thermodynamics of biological systems: a bond graph approach
- Reactant subspaces and kinetics of chemical reaction networks
- Vector-Space Methods and Kirchhoff Graphs for Reaction Networks
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