Efficient parameter sensitivity computation for spatially extended reaction networks

Christopher Lester, Christian Yates, Ruth E. Baker

Research output: Contribution to journalArticle

2 Citations (Scopus)
36 Downloads (Pure)

Abstract

Reaction-diffusion models are widely used to study spatially-extended chemical reaction systems. In order to understand how the dynamics of a reaction-diffusion model are affected by changes in its input parameters, efficient methods for computing parametric sensitivities are required. In this work, we focus on stochastic models of spatially-extended chemical reaction systems that involve partitioning the computational domain into voxels. Parametric sensitivities are often calculated using Monte Carlo techniques that are typically computationally expensive; however, variance reduction techniques can decrease the number of Monte Carlo simulations required. By exploiting the characteristic dynamics of spatially-extended reaction networks, we are able to adapt existing finite difference schemes to robustly estimate parametric sensitivities in a spatially-extended network. We show that algorithmic performance depends on the dynamics of the given network and the choice of summary statistics. We then describe a hybrid technique that dynamically chooses the most appropriate simulation method for the network of interest. Our method is tested for functionality and accuracy in a range of different scenarios.
Original languageEnglish
Article number044106
JournalJournal of Chemical Physics
Volume146
Issue number4
Early online date5 Jan 2017
DOIs
Publication statusPublished - 28 Jan 2017

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