Efficient rejection-based simulation of biochemical reactions with stochastic noise and delays

V.H. Thanh, C. Priami, R. Zunino

Research output: Contribution to journalArticleScientificpeer-review

Abstract

We propose a new exact stochastic rejection-based simulation algorithm for biochemical reactions and extend it to systems with delays. Our algorithm accelerates the simulation by pre-computing reaction propensity bounds to select the next reaction to perform. Exploiting such bounds, we are able to avoid recomputing propensities every time a (delayed) reaction is initiated or finished, as is typically necessary in standard approaches. Propensity updates in our approach are still performed, but only infrequently and limited for a small number of reactions, saving computation time and without sacrificing exactness. We evaluate the performance improvement of our algorithm by experimenting with concrete biological models. © 2014 AIP Publishing LLC.
Original languageEnglish
JournalJournal of Chemical Physics
Volume141
Issue number13
DOIs
Publication statusPublished - 2014
MoE publication typeA1 Journal article-refereed

Keywords

  • Biochemical reactions
  • Stochastic noise, folic acid, algorithm
  • biochemistry
  • biological model
  • chemical model
  • computer simulation
  • human
  • metabolism
  • neoplasm
  • signal transduction
  • statistics, Algorithms
  • Biochemical Processes
  • Computer Simulation
  • Folic Acid
  • Humans
  • MAP Kinase Signaling System
  • Models, Biological
  • Models, Chemical
  • Neoplasms
  • Stochastic Processes

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