4 papers
The blending region hybrid framework for the simulation of stochastic reaction-diffusion processes
Christian A. Yates, Adam George, Armand Jordana +3
The simulation of stochastic reaction-diffusion systems using fine-grained representations can become computationally prohibitive when particle numbers become large. If particle nu…
Efficiently simulating discrete-state models with binary decision trees
Christopher Lester, Ruth E. Baker, Christian A. Yates
Stochastic simulation algorithms (SSAs) are widely used to numerically investigate the properties of stochastic, discrete-state models. The Gillespie Direct Method is the pre-emine…
Unbiased on-lattice domain growth
Cameron A. Smith, Cécile Mailler, Christian A. Yates
Domain growth is a key process in many areas of biology, including embryonic development, the growth of tissue, and limb regeneration. As a result, mechanisms for incorporating it…
A hybrid algorithm for coupling PDE and compartment-based dynamics
Jonathan U. Harrison, Christian A. Yates
Stochastic simulation methods can be applied successfully to model exact spatio-temporally resolved reaction-diffusion systems. However, in many cases, these methods can quickly be…