Simulation of biochemical reactions with time-dependent rates by the rejection-based algorithm

V.H. Thanh, C. Priami

Research output: Contribution to journalArticleScientificpeer-review

Abstract

We address the problem of simulating biochemical reaction networks with time-dependent rates and propose a new algorithm based on our rejection-based stochastic simulation algorithm (RSSA) [Thanh et al., J. Chem. Phys. 141(13), 134116 (2014)]. The computation for selecting next reaction firings by our time-dependent RSSA (tRSSA) is computationally efficient. Furthermore, the generated trajectory is exact by exploiting the rejection-based mechanism. We benchmark tRSSA on different biological systems with varying forms of reaction rates to demonstrate its applicability and efficiency. We reveal that for nontrivial cases, the selection of reaction firings in existing algorithms introduces approximations because the integration of reaction rates is very computationally demanding and simplifying assumptions are introduced. The selection of the next reaction firing by our approach is easier while preserving the exactness. © 2015 AIP Publishing LLC.
Original languageEnglish
JournalJournal of Chemical Physics
Volume143
Issue number5
DOIs
Publication statusPublished - 2015
MoE publication typeA1 Journal article-refereed

Keywords

  • Algorithms
  • Approximation algorithms
  • Stochastic models
  • Stochastic systems, Biochemical reaction network
  • Biochemical reactions
  • Computationally efficient
  • Generated trajectories
  • Simplifying assumptions
  • Stochastic simulation algorithms
  • Time dependent, Reaction rates, algorithm
  • biological model
  • disease transmission
  • epidemic
  • gene expression regulation
  • genetic transcription
  • kinetics
  • markov chain, Algorithms
  • Disease Transmission, Infectious
  • Epidemics
  • Gene Expression Regulation
  • Kinetics
  • Models, Biological
  • Stochastic Processes
  • Transcription, Genetic

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