Hybrid method for the chemical master equation

DOI10.1016/j.jcp.2007.07.020zbMath1126.80010OpenAlexW1991263093WikidataQ63407452 ScholiaQ63407452MaRDI QIDQ2462440

Andreas Hellander, Per Loetstedt

Publication date: 30 November 2007

Published in: Journal of Computational Physics (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1016/j.jcp.2007.07.020

zbMATH Keywords

Monte Carlo methodmaster equationquasi-Monte Carlo methodstochastic chemical kineticsstochastic simulation algorithmreaction rate equations

Mathematics Subject Classification ID

Monte Carlo methods (65C05) Numerical computation of solutions to systems of equations (65H10) Finite difference methods for initial value and initial-boundary value problems involving PDEs (65M06) Finite element, Rayleigh-Ritz and Galerkin methods for initial value and initial-boundary value problems involving PDEs (65M60) Chemically reacting flows (80A32) Error bounds for initial value and initial-boundary value problems involving PDEs (65M15) Method of lines for initial value and initial-boundary value problems involving PDEs (65M20)

Related Items (21)

Jump-Diffusion Approximation of Stochastic Reaction Dynamics: Error Bounds and Algorithms ⋮ Model Reduction for Stochastic Reaction Systems ⋮ Hybrid representation and simulation of stiff biochemical networks ⋮ Modeling of chemical reaction systems with detailed balance using gradient structures ⋮ Hybrid framework for the simulation of stochastic chemical kinetics ⋮ Efficient ensemble stochastic algorithms for agent-based models with spatial predator-prey dynamics ⋮ Simultaneous state-time approximation of the chemical master equation using tensor product formats ⋮ Hybrid master equation for jump-diffusion approximation of biomolecular reaction networks ⋮ Method of conditional moments (MCM) for the chemical master equation ⋮ Approximation and inference methods for stochastic biochemical kinetics—a tutorial review ⋮ Stochastic aspects of asymmetric autocatalysis and absolute asymmetric synthesis ⋮ Sparse grids and hybrid methods for the chemical master equation ⋮ Numerical method for coupling the macro and meso scales in stochastic chemical kinetics ⋮ Adaptive solution of the master equation in low dimensions ⋮ Hybrid simulation of autoregulation within transcription and translation ⋮ Solving chemical master equations by adaptive wavelet compression ⋮ A multi-time-scale analysis of chemical reaction networks. II: Stochastic systems ⋮ Multi-scenario modelling of uncertainty in stochastic chemical systems ⋮ Hybrid discrete/continuum algorithms for stochastic reaction networks ⋮ Markovian dynamics on complex reaction networks ⋮ Algebraic expressions of conditional expectations in gene regulatory networks

Uses Software

• Algorithm 823

Cites Work

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• Multiscale stochastic simulation algorithm with stochastic partial equilibrium assumption for chemically reacting systems
• Computing the moments of high dimensional solutions of the master equation
• Conservative solution of the Fokker-Planck equation for stochastic chemical reactions
• Nested stochastic simulation algorithms for chemical kinetic systems with multiple time scales
• A solver for the stochastic master equation applied to gene regulatory networks
• Implicit solution of hyerbolic equations with space-time adaptivity
• Smoothness and dimension reduction in quasi-Monte Carlo methods
• Solving Ordinary Differential Equations I
• Dimensional Reduction of the Fokker–Planck Equation for Stochastic Chemical Reactions
• Multiscale Modeling of Chemical Kinetics via the Master Equation
• Discrépance de suites associées à un système de numération (en dimension s)
• Monte Carlo Variance of Scrambled Net Quadrature
• Algorithm 823
• Handbook of stochastic methods for physics, chemistry and natural sciences.
• Fokker–Planck approximation of the master equation in molecular biology

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