A hybrid algorithm for coupling partial differential equation and compartment-based dynamics

Jonathan Harrison, Christian Yates

Research output: Contribution to journalArticle

5 Citations (Scopus)
53 Downloads (Pure)

Abstract

Stochastic simulation methods can be applied successfully to model exact spatio-temporally resolved reaction-diffusion systems. However, in many cases, these methods can quickly become extremely computationally intensive with increasing particle numbers. An alternative description of many of these systems can be derived in the diffusive limit as a deterministic, continuum system of partial differential equations (PDEs). Although the numerical solution of such PDEs is, in general, much more efficient than the full stochastic simulation, the deterministic continuum description is generally not valid when copy numbers are low and stochastic effects dominate. Therefore, to take advantage of the benefits of both of these types of models, each of which may be appropriate in different parts of a spatial domain, we have developed an algorithm that can be used to couple these two types of model together. This hybrid coupling algorithm uses an overlap region between the two modelling regimes. By coupling fluxes at one end of the interface and using a concentration-matching condition at the other end, we ensure that mass is appropriately transferred between PDE- and compartment-based regimes. Our methodology gives notable reductions in simulation time in comparison with using a fully stochastic model, while maintaining the important stochastic features of the system and providing detail in appropriate areas of the domain. We test our hybrid methodology robustly by applying it to several biologically motivated problems including diffusion and morphogen gradient formation. Our analysis shows that the resulting error is small, unbiased and does not grow over time.

Original languageEnglish
Article number20160335
Number of pages11
JournalJournal of the Royal Society, Interface
Volume13
Issue number122
DOIs
Publication statusPublished - 14 Sep 2016

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Partial differential equations
Stochastic models
Fluxes

Keywords

  • Multiscale
  • hybrid algorithms
  • deterministic
  • stochastic
  • reaction-diffusion

Cite this

A hybrid algorithm for coupling partial differential equation and compartment-based dynamics. / Harrison, Jonathan; Yates, Christian.

In: Journal of the Royal Society, Interface, Vol. 13, No. 122, 20160335, 14.09.2016.

Research output: Contribution to journalArticle

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