Accurate Chemical Master Equation Solution Using Multi-Finite Buffers

DOI10.1137/15M1034180zbMath1354.92033arXiv1707.08233WikidataQ28821892 ScholiaQ28821892MaRDI QIDQ5298146

Jie Liang, Youfang Cao, Anna Terebus

Publication date: 13 December 2016

Published in: Multiscale Modeling & Simulation (Search for Journal in Brave)

Full work available at URL: https://arxiv.org/abs/1707.08233

zbMATH Keywords

first passage time distributionstate space truncationstochastic biological networkschemical master equationsteady state probability landscapetime-evolving probability landscapes

Mathematics Subject Classification ID

Kinetics in biochemical problems (pharmacokinetics, enzyme kinetics, etc.) (92C45) Biochemistry, molecular biology (92C40) Computational methods for problems pertaining to biology (92-08)

Related Items (6)

Conditional Monte Carlo for Reaction Networks ⋮ The Exit Time Finite State Projection Scheme: Bounding Exit Distributions and Occupation Measures of Continuous-Time Markov Chains ⋮ Stationary Distributions of Continuous-Time Markov Chains: A Review of Theory and Truncation-Based Approximations ⋮ Generalizing Gillespie's direct method to enable network-free simulations ⋮ Finite state projection for approximating the stationary solution to the chemical master equation using reaction rate equations ⋮ Accuracy of Multiscale Reduction for Stochastic Reaction Systems

Uses Software

• Expokit
• ARPACK

Cites Work

• State space truncation with quantified errors for accurate solutions to discrete chemical master equation
• Relation of a new interpretation of stochastic differential equations to Itô process
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• Adaptive Discrete Galerkin Methods Applied to the Chemical Master Equation
• GMRES: A Generalized Minimal Residual Algorithm for Solving Nonsymmetric Linear Systems
• A POWER SERIES EXPANSION OF THE MASTER EQUATION
• Expokit
• Near Complete Decomposability: Bounding the Error by a Stochastic Comparison Method
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• Stochastic ordering for continuous-time processes
• The Finite State Projection Approach for the Analysis of Stochastic Noise in Gene Networks
• Stochastic approach to chemical kinetics
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• Fokker–Planck approximation of the master equation in molecular biology
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