Implementation of variable parameters in the Krylov-based finite state projection for solving the chemical master equation

DOI10.1016/J.AMC.2016.08.013MaRDI QIDQ1737166zbMATH OpenOpenAlexFDO

Authors H. D. Vo, Roger B. Sidje

Publication date 27 March 2019

Published in Applied Mathematics and Computation (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.amc.2016.08.013

zbMATH Keywords

matrix exponentialchemical master equationfinite state projectionadaptive Krylov method

Mathematics Subject Classification ID

Molecular structure (graph-theoretic methods, methods of differential topology, etc.) (92E10) Numerical methods for initial value problems involving ordinary differential equations (65L05) Numerical computation of matrix exponential and similar matrix functions (65F60)

Recommendations

• Solving the chemical master equation by a fast adaptive finite state projection based on the stochastic simulation algorithm
• A multiple time interval finite state projection algorithm for the solution to the chemical master equation
• An improved finite state projection algorithm for the numerical solution of the chemical master equation with applications
• Adaptive time-stepping using control theory for the chemical Langevin equation
• A modified uniformization method for the solution of the chemical master equation

Cites work

• A multiple time interval finite state projection algorithm for the solution to the chemical master equation
• A numerical study of large sparse matrix exponentials arising in Markov chains.
• Algorithm 919: A Krylov subspace algorithm for evaluating the \(\phi\)-functions appearing in exponential integrators
• Expokit
• Multiscale Modeling of Chemical Kinetics via the Master Equation
• Solving stochastic chemical kinetics by metropolis-Hastings sampling

Cited in

(2)

• A shift and invert reorthogonalization Arnoldi algorithm for solving the chemical master equation
• A multiple time interval finite state projection algorithm for the solution to the chemical master equation

Describes a project that uses

Uses Software

• Expokit
• Algorithm 919
• phipm

This page was built for publication: Implementation of variable parameters in the Krylov-based finite state projection for solving the chemical master equation

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q1737166)