Markovian dynamics on complex reaction networks
From MaRDI portal
Publication:740680
DOI10.1016/j.physrep.2013.03.004zbMath1432.60075arXiv1205.5524OpenAlexW3104859924MaRDI QIDQ740680
Publication date: 9 September 2014
Published in: Physics Reports (Search for Journal in Brave)
Full work available at URL: https://arxiv.org/abs/1205.5524
master equationcomplex networksMarkovian dynamicspotential energy landscapestochastic nonlinear dynamicsthermodynamic analysis
Neural nets applied to problems in time-dependent statistical mechanics (82C32) Applications of Brownian motions and diffusion theory (population genetics, absorption problems, etc.) (60J70) Systems biology, networks (92C42) Applications of continuous-time Markov processes on discrete state spaces (60J28)
Related Items (15)
Multiscale Simulation of Stochastic Reaction-Diffusion Networks ⋮ An Algebraic Approach to Product-form Stationary Distributions for Some Reaction Networks ⋮ Information dimension of stochastic processes on networks: relating entropy production to spectral properties ⋮ Approximation and inference methods for stochastic biochemical kinetics—a tutorial review ⋮ The theory of individual based discrete-time processes ⋮ Stationary Distributions of Continuous-Time Markov Chains: A Review of Theory and Truncation-Based Approximations ⋮ Multiple-scale stochastic processes: decimation, averaging and beyond ⋮ Low-dimensional SIR epidemic models with demographics on heterogeneous networks ⋮ A Multilevel Adaptive Reaction-splitting Simulation Method for Stochastic Reaction Networks ⋮ Fragility in Dynamic Networks: Application to Neural Networks in the Epileptic Cortex ⋮ A multi-time-scale analysis of chemical reaction networks. II: Stochastic systems ⋮ Stationary distributions via decomposition of stochastic reaction networks ⋮ Ergodicity Analysis and Antithetic Integral Control of a Class of Stochastic Reaction Networks with Delays ⋮ The linear noise approximation for spatially dependent biochemical networks ⋮ Moment-Based Methods for Parameter Inference and Experiment Design for Stochastic Biochemical Reaction Networks
Cites Work
- Bayesian Inference for Stochastic Kinetic Models Using a Diffusion Approximation
- The simple stochastic epidemic: a complete solution in terms of known functions
- A SIMPLE STOCHASTIC EPIDEMIC
- A general expression for the mean in a simple stochastic epidemic
- Networks
- Applying the saddlepoint approximation to bivariate stochastic processes
- Physics and social science -- the approach of synergetics
- Monte Carlo strategies in scientific computing
- Unnamed Item
- Unnamed Item
- Unnamed Item
- Unnamed Item
- Unnamed Item
- Unnamed Item
- Unnamed Item
- Unnamed Item
- Unnamed Item
- Unnamed Item
- Unnamed Item
- Unnamed Item
- Unnamed Item
- Unnamed Item
- Unnamed Item
- Unnamed Item
- Unnamed Item
- Novel moment closure approximations in stochastic epidemics
- A stochastic analysis of first-order reaction networks
- Moment equations and dynamics of a household SIS epidemiological model
- Moment closure approximations for stochastic kinetic models with rational rate laws
- Efficient methods for studying stochastic disease and population dynamics
- Cellular biology in terms of stochastic nonlinear biochemical dynamics: Emergent properties, isogenetic variations and chemical system inheritability
- A jump-growth model for predator-prey dynamics: derivation and application to marine ecosystems
- Modeling in biopharmaceutics, pharmacokinetics, and pharmacodynamics. Homogeneous and heterogeneous approaches.
- A dynamical low-rank approach to the chemical master equation
- Moment closure and the stochastic logistic model
- Computing the moments of high dimensional solutions of the master equation
- Gibbs sampler-based coordination of autonomous swarms
- Social balance on networks: the dynamics of friendship and enmity
- Opinion spreading and agent segregation on evolving networks
- Nested stochastic simulation algorithms for chemical kinetic systems with multiple time scales
- Efficient stochastic sensitivity analysis of discrete event systems
- Solving the chemical master equation for monomolecular reaction systems analytically
- A solver for the stochastic master equation applied to gene regulatory networks
- Reversible-equivalent-monomolecular tau: a leaping method for ``small number and stiff stochastic chemical systems
- 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
- Sparse grids and hybrid methods for the chemical master equation
- Stochastic thermodynamics: principles and perspectives
- A modified uniformization method for the solution of the chemical master equation
- Solving chemical master equations by adaptive wavelet compression
- The multidimensional maximum entropy moment problem: a review on numerical methods
- Sensitivity summation theorems for stochastic biochemical reaction systems
- Fluctuation theorem for currents and Schnakenberg network theory
- Asymptotic analysis of multiscale approximations to reaction networks
- Representations of Markov processes as multiparameter time changes
- Asymptotic properties of Markovian master equations
- Markov chains with almost exponential hitting times
- A numerical study of large sparse matrix exponentials arising in Markov chains.
- Matrix Riccati equations in control and systems theory
- Mathematical theory of nonequilibrium steady states. On the frontier of probability and dynamical systems.
- Effects of immigration on some stochastic logistic models: A cumulant truncation analysis
- The effects of stochastic population dynamics on food web structure
- Effects of a disease affecting a predator on the dynamics of a predator-prey system
- Investigating the two-moment characterisation of subcellular biochemical networks
- Stochastic reduction method for biological chemical kinetics using time-scale separation
- Modeling epidemics dynamics on heterogenous networks
- Distributions for negative-feedback-regulated stochastic gene expression: dimension reduction and numerical solution of the chemical master equation
- New moment closures based on a priori distributions with applications to epidemic dynamics
- An individual-based approach to SIR epidemics in contact networks
- Concepts and models of a quantitative sociology. The dynamics of interacting populations
- Separation of time-scales and model reduction for stochastic reaction networks
- On the Gaussian approximation for master equations
- On moment closures for population dynamics in continuous space
- Multivariate analysis of noise in genetic regulatory networks
- Stochastic modeling of nonlinear epidemiology
- Synchrony and asynchrony in a fully stochastic neural network
- Novel bivariate moment-closure approximations
- A quasistationary analysis of a stochastic chemical reaction: Keizer's paradox
- A derivative matching approach to moment closure for the stochastic logistic model
- An extension of the moment closure method
- A multiple time interval finite state projection algorithm for the solution to the chemical master equation
- Hybrid method for the chemical master equation
- A hierarchy of approximations of the master equation scaled by a size parameter
- The sorting direct method for stochastic simulation of biochemical systems with varying reaction execution behavior
- Nonequilibrium thermodynamics modeling of coupled biochemical cycles in living cells
- Amplified biochemical oscillations in cellular systems
- The Mathematics of Infectious Diseases
- An Algorithmic Introduction to Numerical Simulation of Stochastic Differential Equations
- Using Gene Expression Noise to Understand Gene Regulation
- Nonlinear stochastic dynamics of mesoscopic homogeneous biochemical reaction systems—an analytical theory
- Stochastic Neural Field Theory and the System-Size Expansion
- An Adaptive Wavelet Method for the Chemical Master Equation
- The multivariate Langevin and Fokker–Planck equations
- Disentangling the Web of Life
- Estimations of intrinsic and extrinsic noise in models of nonlinear genetic networks
- Multiscale Modeling of Chemical Kinetics via the Master Equation
- A Master Equation Formalism for Macroscopic Modeling of Asynchronous Irregular Activity States
- Adaptive Discrete Galerkin Methods Applied to the Chemical Master Equation
- A POWER SERIES EXPANSION OF THE MASTER EQUATION
- Expokit
- Introduction to Stochastic Search and Optimization
- Nineteen Dubious Ways to Compute the Exponential of a Matrix, Twenty-Five Years Later
- The Structure and Function of Complex Networks
- Potential in stochastic differential equations: novel construction
- Stochastic Petri Nets
- An Efficient Finite Difference Method for Parameter Sensitivities of Continuous Time Markov Chains
- Systematic Fluctuation Expansion for Neural Network Activity Equations
- Approximate Moment Dynamics for Chemically Reacting Systems
- Stochastic Dynamics of a Finite-Size Spiking Neural Network
- Limit theorems for sequences of jump Markov processes approximating ordinary differential processes
- Stochastic approach to chemical kinetics
- Birth and death processes in large populations
This page was built for publication: Markovian dynamics on complex reaction networks
