Efficient parameter sensitivity computation for spatially extended reaction networks

Author: 

Lester, C
Yates, C
Baker, R

Publication Date: 

28 January 2017

Journal: 

Journal of Chemical Physics

Last Updated: 

2019-04-26T16:22:16.647+01:00

Issue: 

4

Volume: 

146

DOI: 

10.1063/1.4973219

page: 

044106-044106

abstract: 

© 2017 Author(s).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 the 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.

Symplectic id: 

673953

Submitted to ORA: 

Submitted

Publication Type: 

Journal Article