A shift and invert reorthogonalization Arnoldi algorithm for solving the chemical master equation

DOI10.1016/j.amc.2018.12.021zbMath1428.92007OpenAlexW2907014257WikidataQ128691041 ScholiaQ128691041MaRDI QIDQ2008892

Yong Liu, Chuanqing Gu

Publication date: 26 November 2019

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

Full work available at URL: https://doi.org/10.1016/j.amc.2018.12.021

zbMATH Keywords

chemical master equationreorthogonalizationtheoretical error estimatesKrylov FSP algorithmshift and invert Arnoldi method

Mathematics Subject Classification ID

Kinetics in biochemical problems (pharmacokinetics, enzyme kinetics, etc.) (92C45) Computational methods for problems pertaining to biology (92-08) Numerical linear algebra (65F99) Numerical computation of matrix exponential and similar matrix functions (65F60)

Related Items (1)

A conjugate-gradient-type rational Krylov subspace method for ill-posed problems

Uses Software

• Expokit
• MATLAB expm

Cites Work

• Unnamed Item
• Solving the chemical master equation by a fast adaptive finite state projection based on the stochastic simulation algorithm
• Implementation of variable parameters in the Krylov-based finite state projection for solving the chemical master equation
• RD-rational approximations of the matrix exponential
• Analysis of inexact Krylov subspace methods for approximating the matrix exponential
• A multiple time interval finite state projection algorithm for the solution to the chemical master equation
• Residual, Restarting, and Richardson Iteration for the Matrix Exponential
• An Inner-Outer Iteration for Computing PageRank
• Shift-Invert Arnoldi Approximation to the Toeplitz Matrix Exponential
• An inexact shift‐and‐invert Arnoldi algorithm for Toeplitz matrix exponential
• Multiscale Modeling of Chemical Kinetics via the Master Equation
• The Scaling and Squaring Method for the Matrix Exponential Revisited
• Analysis of Some Krylov Subspace Approximations to the Matrix Exponential Operator
• Expokit
• Preconditioning Lanczos Approximations to the Matrix Exponential

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