Numerical Approach to Spatial Deterministic-Stochastic Models Arising in Cell Biology.

ABSTRACT: Hybrid deterministic-stochastic methods provide an efficient alternative to a fully stochastic treatment of models which include components with disparate levels of stochasticity. However, general-purpose hybrid solvers for spatially resolved simulations of reaction-diffusion systems are not widely available. Here we describe fundamentals of a general-purpose spatial hybrid method. The method generates realizations of a spatially inhomogeneous hybrid system by appropriately integrating capabilities of a deterministic partial differential equation solver with a popular particle-based stochastic simulator, Smoldyn. Rigorous validation of the algorithm is detailed, using a simple model of calcium 'sparks' as a testbed. The solver is then applied to a deterministic-stochastic model of spontane

SUBMITTER: Schaff JC 

PROVIDER: S-EPMC5154471 | biostudies-literature | 2016 Dec

REPOSITORIES: biostudies-literature