Model Reconstruction for Moment-Based Stochastic Chemical Kinetics

DOI10.1145/2699712zbMATH Open1384.92066arXiv1410.3177OpenAlexW2294445361MaRDI QIDQ4635227FDOQ4635227

Alexander Andreychenko, Linar Mikeev, Verena Wolf

Publication date: 16 April 2018

Published in: ACM Transactions on Modeling and Computer Simulation (Search for Journal in Brave)

Abstract: Based on the theory of stochastic chemical kinetics, the inherent randomness and stochasticity of biochemical reaction networks can be accurately described by discrete-state continuous-time Markov chains. The analysis of such processes is, however, computationally expensive and sophisticated numerical methods are required. Here, we propose an analysis framework in which we integrate a number of moments of the process instead of the state probabilities. This results in a very efficient simulation of the time evolution of the process. In order to regain the state probabilities from the moment representation, we combine the fast moment-based simulation with a maximum entropy approach for the reconstruction of the underlying probability distribution. We investigate the usefulness of this combined approach in the setting of stochastic chemical kinetics and present numerical results for three reaction networks showing its efficiency and accuracy. Besides a simple dimerization system, we study a bistable switch system and a multi-attractor network with complex dynamics.

Full work available at URL: https://arxiv.org/abs/1410.3177

zbMATH Keywords

maximum entropystochastic chemical kineticsmoment closurechemical master equation

Mathematics Subject Classification ID

Chemical kinetics in thermodynamics and heat transfer (80A30) Classical flows, reactions, etc. in chemistry (92E20)

Cited In (9)

• Approximation and inference methods for stochastic biochemical kinetics—a tutorial review
• Algebraic expressions of conditional expectations in gene regulatory networks
• Model checking Markov population models by stochastic approximations
• Revisiting moment-closure methods with heterogeneous multiscale population models
• Method of conditional moments (MCM) for the chemical master equation
• The application of theory of probability to the modelling of chemical kinetics systems
• Modeling backward chemical rate processes in the direct simulation Monte Carlo method
• Interval analysis of worst-case stationary moments for stochastic chemical reactions with uncertain parameters
• Hybrid master equation for jump-diffusion approximation of biomolecular reaction networks

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