Stochastic simulation of biochemical reactions with partial-propensity and rejection-based approaches

DOI10.1016/J.MBS.2017.08.001MaRDI QIDQ1680723zbMATH OpenOpenAlexWikidataFDO

Authors Vo Hong Thanh

Publication date 16 November 2017

Published in Mathematical Biosciences (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.mbs.2017.08.001

zbMATH Keywords

computational biologystochastic simulationpartial-propensity rejection-based stochastic simulation algorithm

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Kinetics in biochemical problems (pharmacokinetics, enzyme kinetics, etc.) (92C45)

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Cites work

• Efficient kinetic Monte Carlo simulation
• Introduction to Interval Analysis
• Stochastic approaches for systems biology.
• The sorting direct method for stochastic simulation of biochemical systems with varying reaction execution behavior

Cited in

(7)

• A critical comparison of rejection-based algorithms for simulation of large biochemical reaction networks
• HRSSA - efficient hybrid stochastic simulation for spatially homogeneous biochemical reaction networks
• The Status of the QSSA Approximation in Stochastic Simulations of Reaction Networks
• The sorting direct method for stochastic simulation of biochemical systems with varying reaction execution behavior
• Push-forward method for piecewise deterministic biochemical simulations
• A first step to implement Gillespie's algorithm with rejection sampling
• Modelling biochemical reaction systems by stochastic differential equations with reflection

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