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Author

Lee, Chang Hyeong
Stochastic Analysis & Simulation(SAS) Lab
Research Interests
  • Stochastic analysis/computation, epidemic modeling, biological system simulation

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Fast Probability Generating Function Method for Stochastic Chemical Reaction Networks

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Title
Fast Probability Generating Function Method for Stochastic Chemical Reaction Networks
Author
Kim, PilwonLee, Chang Hyeong
Keywords
SIMULATION; KINETICS; SYSTEMS
Issue Date
201401
Publisher
UNIV KRAGUJEVAC
Citation
MATCH-COMMUNICATIONS IN MATHEMATICAL AND IN COMPUTER CHEMISTRY, v.71, no.1, pp.57 - 69
Abstract
Chemical master equations of the stochastic reaction network can be reformulated into a partial differential equation(PDE) of a probability generating function (PGF). Such PDEs are mostly hard to deal with due to variable coefficients and lack of proper boundary conditions. In this paper, we propose a way to reduce PGF-PDEs into a sparse linear system of coefficients of a power series solution. A power of such matrix gives a fast approximation of the solution. The process can be further accelerated by truncating high-order moments. The truncation also makes the method applicable to reaction networks with time-varying reaction rates. We show numerical accuracy of the method by simulating motivating biochemical examples including a viral infection model and G(2)/M model.
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ISSN
0340-6253
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