Cellular growth and division in the Gillespie algorithm.
Recent experimental studies elucidating the importance of noise in gene regulation have ignited widespread interest in Gillespie's stochastic simulation technique for biochemical networks. We formulate modifications to the Gillespie algorithm which are necessary to correctly simulate chemical reactions with time-dependent reaction rates. We concentrate on time dependence of kinetic rates arising from the periodic process of growth and division of the cellular volume, and demonstrate that a careful re-derivation of the Gillespie algorithm is important when all stochastically simulated reactions have rates slower or comparable to the cellular growth rate. For an unregulated single-gene system, we illustrate our findings using recently proposed hybrid simulation techniques, and systematically compare our algorithm with analytic results obtained from the chemical master equation.
Lu
T
T
Department of Physics, University of California, San Diego, USA.
Volfson
D
D
Tsimring
L
L
Hasty
J
J
D000465:Algorithms; D000818:Animals; D018797:Cell Cycle Proteins / Q000378:metabolism*; D002455:Cell Division / Q000502:physiology*; D049108:Cell Enlargement; D049109:Cell Proliferation; D003198:Computer Simulation; D006801:Humans; D008954:Models, Biological; D014157:Transcription Factors / Q000378:metabolism*
D018797:Cell Cycle Proteins; D014157:Transcription Factors