Quantifying stochastic effects in biochemical reaction networks using partitioned leaping.

Harris LA, Piccirilli AM, Majusiak ER, Clancy P
Phys Rev E Stat Nonlin Soft Matter Phys. 2009 79 (5 Pt 1): 051906

PMID: 19518479 · DOI:10.1103/PhysRevE.79.051906

"Leaping" methods show great promise for significantly accelerating stochastic simulations of complex biochemical reaction networks. However, few practical applications of leaping have appeared in the literature to date. Here, we address this issue using the "partitioned leaping algorithm" (PLA) [L. A. Harris and P. Clancy, J. Chem. Phys. 125, 144107 (2006)], a recently introduced multiscale leaping approach. We use the PLA to investigate stochastic effects in two model biochemical reaction networks. The networks that we consider are simple enough so as to be accessible to our intuition but sufficiently complex so as to be generally representative of real biological systems. We demonstrate how the PLA allows us to quantify subtle effects of stochasticity in these systems that would be difficult to ascertain otherwise as well as not-so-subtle behaviors that would strain commonly used "exact" stochastic methods. We also illustrate bottlenecks that can hinder the approach and exemplify and discuss possible strategies for overcoming them. Overall, our aim is to aid and motivate future applications of leaping by providing stark illustrations of the benefits of the method while at the same time elucidating obstacles that are often encountered in practice.

MeSH Terms (8)

Algorithms Biopolymers Calcium Signaling Computer Simulation Models, Biological Models, Statistical Signal Transduction Stochastic Processes

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