Approximate exponential algorithms to solve the chemical master equation

DOI10.3846/13926292.2015.1048760MaRDI QIDQ5011245zbMATH OpenOpenAlexFDO

Authors Azam Mooasvi, Adrian Sandu

Publication date 27 August 2021

Published in Mathematical Modelling and Analysis (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1410.1934

zbMATH Keywords

chemical master equationexact solutionstochastic chemical kineticsstochastic simulation algorithmtau-leap

Mathematics Subject Classification ID

Dynamical systems in biology (37N25) Applications of stochastic analysis (to PDEs, etc.) (60H30) Kinetics in biochemical problems (pharmacokinetics, enzyme kinetics, etc.) (92C45)

Abstract: This paper discusses new simulation algorithms for stochastic chemical kinetics that exploit the linearity of the chemical master equation and its matrix exponential exact solution. These algorithms make use of various approximations of the matrix exponential to evolve probability densities in time. A sampling of the approximate solutions of the chemical master equation is used to derive accelerated stochastic simulation algorithms. Numerical experiments compare the new methods with the established stochastic simulation algorithm and the tau-leaping method.

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Cites work

• A new look at the chemical master equation
• Computing the moments of high dimensional solutions of the master equation
• Consistency and Stability of Tau-Leaping Schemes for Chemical Reaction Systems
• IMPLICIT SIMULATION METHODS FOR STOCHASTIC CHEMICAL KINETICS
• Multiscale Modeling of Chemical Kinetics via the Master Equation
• Multiscale stochastic simulation algorithm with stochastic partial equilibrium assumption for chemically reacting systems
• On the Construction and Comparison of Difference Schemes

Cited in

(9)

• Spectral approximation of solutions to the chemical master equation
• A shift and invert reorthogonalization Arnoldi algorithm for solving the chemical master equation
• A new look at the chemical master equation
• A multiple time interval finite state projection algorithm for the solution to the chemical master equation
• A Linear Programming Approach to Parameter Fitting for the Master Equation
• Solving stochastic chemical kinetics by metropolis-Hastings sampling
• scientific article; zbMATH DE number 6733754 (Why is no real title available?)
• An Adaptive Method for Solving Chemical Master Equations using a Sparse Wavelet Basis
• Solving the master equation for extremely long time scale calculations

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