M18: Software development for reaction-diffusion modelling

Background

Reaction-diffusion processes form an essential component of many problems in molecular and systems biology. Software tools to simulate these processes are becoming increasingly important as computational capability grows, allowing problems previously intractable (such as whole cell simulation) to become feasible. To enable these large-scale simulations, a multiscale description is necessary so that the software can accurately and efficiently use reaction-diffusion models with different levels of detail in different parts of the computational domain.

Techniques and Challenges

We will develop a collection of computer routines which are able to couple (i) molecular-based stochastic simulation algorithms (SSAs); (ii) compartment-based SSAs; and (iii) reaction-diffusion partial differential equations (PDEs). This hybrid software will have the accuracy of the most detailed modelling approach (in the region where it is required), but will benefit from the efficiency of less detailed (coarser) models in other parts of the computational domain. The boundary between different modelling regimes will be made both static (fixed) and dynamic (e.g. dependent on the number of molecules in the particular part of the computational domain).

The Future

The resulting software will implement multiscale methods which are currently under development in OCCAM (see, for example, M11 and BB25) and will utilise existing successful software packages already developed by the scientific community (e.g. Smoldyn and URDME).

References

[11/15] Flegg M. B., Chapman S. J., Erban R.: The two-regime method for optimizing stochastic reaction-diffusion simulations, J. R. Soc. Interface

Andrews S., Bray D.: Stochastic simulation of chemical reactions with spatial resolution and single molecule detail, Phys Biol. 1(3-4):137-51 (2004)

Erban R., Chapman S.J., Maini P.K.: A practical guide to stochastic simulations of reaction-diffusion processes, Lecture Notes (2007)