Solving the chemical master equation by a fast adaptive finite state projection based on the stochastic simulation algorithm

DOI10.1016/J.MBS.2015.08.010MaRDI QIDQ900714zbMATH OpenOpenAlexWikidataFDO

Authors Roger B. Sidje, H. D. Vo

Publication date 22 December 2015

Published in Mathematical Biosciences (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.mbs.2015.08.010

zbMATH Keywords

model reductionmatrix exponentialstochastic simulation algorithmchemical master equationfinite state projection

Mathematics Subject Classification ID

Applications of Markov chains and discrete-time Markov processes on general state spaces (social mobility, learning theory, industrial processes, etc.) (60J20) Kinetics in biochemical problems (pharmacokinetics, enzyme kinetics, etc.) (92C45)

Recommendations

• Block-tridiagonal state-space realization of chemical master equations: a tool to compute explicit solutions
• Finite state projection for approximating the stationary solution to the chemical master equation using reaction rate equations
• A multiple time interval finite state projection algorithm for the solution to the chemical master equation
• A modified uniformization method for the solution of the chemical master equation
• Multiscale Modeling of Chemical Kinetics via the Master Equation

Cites work

• A multiple time interval finite state projection algorithm for the solution to the chemical master equation
• Expokit
• Modeling and Simulating Chemical Reactions
• Multiscale Modeling of Chemical Kinetics via the Master Equation
• Solving the chemical master equation by a fast adaptive finite state projection based on the stochastic simulation algorithm

Cited in

(17)

• Data-driven method for efficient characterization of rare event probabilities in biochemical systems
• Implementation of variable parameters in the Krylov-based finite state projection for solving the chemical master equation
• A review of stochastic and delay simulation approaches in both time and space in computational cell biology
• A dynamical low-rank approach to solve the chemical master equation for biological reaction networks
• An Adaptive Method for Solving Chemical Master Equations using a Sparse Wavelet Basis
• Conditional Monte Carlo for reaction networks
• A shift and invert reorthogonalization Arnoldi algorithm for solving the chemical master equation
• Solving the chemical master equation by a fast adaptive finite state projection based on the stochastic simulation algorithm
• The exit time finite state projection scheme: bounding exit distributions and occupation measures of continuous-time Markov chains
• Block-tridiagonal state-space realization of chemical master equations: a tool to compute explicit solutions
• Finite state projection for approximating the stationary solution to the chemical master equation using reaction rate equations
• Solving stochastic chemical kinetics by metropolis-Hastings sampling
• Radial basis function collocation for the chemical master equation
• A multiple time interval finite state projection algorithm for the solution to the chemical master equation
• The high-dimensional matrix equation for biochemical reaction systems
• Accurate chemical master equation solution using multi-finite buffers
• An improved finite state projection algorithm for the numerical solution of the chemical master equation with applications

Describes a project that uses

Uses Software

• Expokit

This page was built for publication: Solving the chemical master equation by a fast adaptive finite state projection based on the stochastic simulation algorithm

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q900714)