Markovian dynamics on complex reaction networks

DOI10.1016/J.PHYSREP.2013.03.004zbMATH Open1432.60075arXiv1205.5524OpenAlexW3104859924MaRDI QIDQ740680FDOQ740680

Authors: G. Jenkinson, John Goutsias 

Publication date: 9 September 2014

Published in: Physics Reports (Search for Journal in Brave)

Abstract: Complex networks, comprised of individual elements that interact with each other through reaction channels, are ubiquitous across many scientific and engineering disciplines. Examples include biochemical, pharmacokinetic, epidemiological, ecological, social, neural, and multi-agent networks. A common approach to modeling such networks is by a master equation that governs the dynamic evolution of the joint probability mass function of the underling population process and naturally leads to Markovian dynamics for such process. Due however to the nonlinear nature of most reactions, the computation and analysis of the resulting stochastic population dynamics is a difficult task. This review article provides a coherent and comprehensive coverage of recently developed approaches and methods to tackle this problem. After reviewing a general framework for modeling Markovian reaction networks and giving specific examples, the authors present numerical and computational techniques capable of evaluating or approximating the solution of the master equation, discuss a recently developed approach for studying the stationary behavior of Markovian reaction networks using a potential energy landscape perspective, and provide an introduction to the emerging theory of thermodynamic analysis of such networks. Three representative problems of opinion formation, transcription regulation, and neural network dynamics are used as illustrative examples.

Full work available at URL: https://arxiv.org/abs/1205.5524

Recommendations

• Examples of computation of exact moment dynamics for chemical reaction networks
• A network dynamics approach to chemical reaction networks
• The modeling and analysis of biochemical reaction systems
• Asymptotic analysis of multiscale approximations to reaction networks
• Sensitivity of Steady States in Networks with Application to Markov Chains and Chemical Reaction Networks

zbMATH Keywords

complex networksMarkovian dynamicsmaster equationpotential energy landscapestochastic nonlinear dynamicsthermodynamic analysis

Mathematics Subject Classification ID

Applications of continuous-time Markov processes on discrete state spaces (60J28) Applications of Brownian motions and diffusion theory (population genetics, absorption problems, etc.) (60J70) Systems biology, networks (92C42) Neural nets applied to problems in time-dependent statistical mechanics (82C32)

Cites Work

• The effects of stochastic population dynamics on food web structure
• Investigating the two-moment characterisation of subcellular biochemical networks
• New moment closures based on a priori distributions with applications to epidemic dynamics
• On the Gaussian approximation for master equations
• Stochastic modeling of nonlinear epidemiology
• The multivariate Langevin and Fokker–Planck equations
• Birth and death processes in large populations
• A general expression for the mean in a simple stochastic epidemic
• Applying the saddlepoint approximation to bivariate stochastic processes
• Efficient stochastic sensitivity analysis of discrete event systems
• Sensitivity summation theorems for stochastic biochemical reaction systems
• Expokit
• Title not available (Why is that?)
• Nineteen Dubious Ways to Compute the Exponential of a Matrix, Twenty-Five Years Later
• The Structure and Function of Complex Networks
• Monte Carlo strategies in scientific computing
• The mathematics of infectious diseases
• Numerical recipes. The art of scientific computing.
• Introduction to Stochastic Search and Optimization
• Stochastic Dynamics of a Finite-Size Spiking Neural Network
• Networks. An introduction.
• Novel moment closure approximations in stochastic epidemics
• Nonlinear dynamical systems and control. A Lyapunov-based approach
• Effects of a disease affecting a predator on the dynamics of a predator-prey system
• A hierarchy of approximations of the master equation scaled by a size parameter
• A stochastic analysis of first-order reaction networks
• Moment equations and dynamics of a household SIS epidemiological model
• An algorithmic introduction to numerical simulation of stochastic differential equations
• Stochastic neural field theory and the system-size expansion
• Title not available (Why is that?)
• A Master Equation Formalism for Macroscopic Modeling of Asynchronous Irregular Activity States
• A POWER SERIES EXPANSION OF THE MASTER EQUATION
• Title not available (Why is that?)
• Title not available (Why is that?)
• Title not available (Why is that?)
• Title not available (Why is that?)
• Global sensitivity analysis: The primer
• Limit theorems for sequences of jump Markov processes approximating ordinary differential processes
• Bayesian Inference for Stochastic Kinetic Models Using a Diffusion Approximation
• Formal methods for computational systems biology. 8th international school on formal methods for the design of computer, communication, and software systems, SFM 2008 Bertinoro, Italy, June 2--7, 2008. Advanced lectures
• Asymptotic analysis of multiscale approximations to reaction networks
• Matrix Riccati equations in control and systems theory
• Separation of time-scales and model reduction for stochastic reaction networks
• Title not available (Why is that?)
• Amplified biochemical oscillations in cellular systems
• Title not available (Why is that?)
• Stochastic Petri Nets
• Systematic Fluctuation Expansion for Neural Network Activity Equations
• Title not available (Why is that?)
• Sparse grids and hybrid methods for the chemical master equation
• Disentangling the web of life
• Distributions for negative-feedback-regulated stochastic gene expression: dimension reduction and numerical solution of the chemical master equation
• Multivariate analysis of noise in genetic regulatory networks
• Approximate Moment Dynamics for Chemically Reacting Systems
• Using gene expression noise to understand gene regulation
• Stochastic approach to chemical kinetics
• Stochastic thermodynamics: principles and perspectives
• Mathematical theory of nonequilibrium steady states. On the frontier of probability and dynamical systems.
• An individual-based approach to SIR epidemics in contact networks
• On moment closures for population dynamics in continuous space
• Synchrony and asynchrony in a fully stochastic neural network
• A quasistationary analysis of a stochastic chemical reaction: Keizer's paradox
• A multiple time interval finite state projection algorithm for the solution to the chemical master equation
• Petri nets. Fundamental models, verification and applications.
• Multiscale Modeling of Chemical Kinetics via the Master Equation
• Adaptive Discrete Galerkin Methods Applied to the Chemical Master Equation
• Potential in stochastic differential equations: novel construction
• Concepts and models of a quantitative sociology. The dynamics of interacting populations
• Nonlinear stochastic dynamics of mesoscopic homogeneous biochemical reaction systems - an analytical theory
• The simple stochastic epidemic: a complete solution in terms of known functions
• Modeling in biopharmaceutics, pharmacokinetics, and pharmacodynamics. Homogeneous and heterogeneous approaches.
• Opinion spreading and agent segregation on evolving networks
• Solving the chemical master equation for monomolecular reaction systems analytically
• Representations of Markov processes as multiparameter time changes
• The sorting direct method for stochastic simulation of biochemical systems with varying reaction execution behavior
• A dynamical low-rank approach to the chemical master equation
• Solving chemical master equations by adaptive wavelet compression
• The multidimensional maximum entropy moment problem: a review on numerical methods
• Hybrid method for the chemical master equation
• A SIMPLE STOCHASTIC EPIDEMIC
• Markov chains with almost exponential hitting times
• An extension of the moment closure method
• Nested stochastic simulation algorithms for chemical kinetic systems with multiple time scales
• Reversible-equivalent-monomolecular tau: a leaping method for ``small number and stiff stochastic chemical systems
• Effects of immigration on some stochastic logistic models: A cumulant truncation analysis
• Title not available (Why is that?)
• Estimations of intrinsic and extrinsic noise in models of nonlinear genetic networks
• Computing the moments of high dimensional solutions of the master equation
• A modified uniformization method for the solution of the chemical master equation
• Title not available (Why is that?)
• Moment closure and the stochastic logistic model
• Stochastic reduction method for biological chemical kinetics using time-scale separation
• Cellular biology in terms of stochastic nonlinear biochemical dynamics: Emergent properties, isogenetic variations and chemical system inheritability
• Fluctuation theorem for currents and Schnakenberg network theory
• A jump-growth model for predator-prey dynamics: derivation and application to marine ecosystems
• A derivative matching approach to moment closure for the stochastic logistic model
• An adaptive wavelet method for the chemical master equation
• A numerical study of large sparse matrix exponentials arising in Markov chains.
• Novel bivariate moment-closure approximations
• Moment closure approximations for stochastic kinetic models with rational rate laws
• Efficient methods for studying stochastic disease and population dynamics
• Social balance on networks: the dynamics of friendship and enmity
• Modeling epidemics dynamics on heterogenous networks
• Title not available (Why is that?)
• Gibbs sampler-based coordination of autonomous swarms
• Nonequilibrium thermodynamics modeling of coupled biochemical cycles in living cells
• A solver for the stochastic master equation applied to gene regulatory networks
• Physics and social science -- the approach of synergetics
• An efficient finite difference method for parameter sensitivities of continuous time Markov chains
• Title not available (Why is that?)
• Asymptotic properties of Markovian master equations

Cited In (19)

• Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks
• The linear noise approximation for spatially dependent biochemical networks
• Information dimension of stochastic processes on networks: relating entropy production to spectral properties
• A multilevel adaptive reaction-splitting simulation method for stochastic reaction networks
• A multi-time-scale analysis of chemical reaction networks. II: Stochastic systems
• Approximation and inference methods for stochastic biochemical kinetics -- a tutorial review
• Adaptive aggregation of Markov chains: quantitative analysis of chemical reaction networks
• Multiscale Simulation of Stochastic Reaction-Diffusion Networks
• Stationary distributions of continuous-time Markov chains: a review of theory and truncation-based approximations
• Low-dimensional SIR epidemic models with demographics on heterogeneous networks
• Lumping the Approximate Master Equation for Multistate Processes on Complex Networks
• Dynamical properties of discrete reaction networks
• Stationary distributions via decomposition of stochastic reaction networks
• The theory of individual based discrete-time processes
• Fragility in Dynamic Networks: Application to Neural Networks in the Epileptic Cortex
• An algebraic approach to product-form stationary distributions for some reaction networks
• Ergodicity analysis and antithetic integral control of a class of stochastic reaction networks with delays
• Multiple-scale stochastic processes: decimation, averaging and beyond
• A detailed balanced reaction network is sufficient but not necessary for its Markov chain to be detailed balanced

This page was built for publication: Markovian dynamics on complex reaction networks

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q740680)