Engine Collection

Available in the “strengths.engine_collection” module. This module proposes an engine implementing different methods.

strengths.engine_collection.euler_engine()

Engine using a simple Euler method with a static time step. Diffusion is treated as a first order reaction according to Bernstein’s method (Bernstein, 2005) [1].

strengths.engine_collection.gillespie_engine()

Engine using the original Gillespie algorithm (Gillespie, 1977) [3]. Diffusion is treated as a first order reaction according to Bernstein’s method (Bernstein, 2005) [1].

strengths.engine_collection.tauleap_engine()

Engine using the Gillespie tau leap method (Gillespie, 2001) [2] with a static time step. Diffusion is treated as a first order reaction according to Bernstein’s method (Bernstein, 2005) [1].

References

[1] (1,2,3)

Bernstein, D. (2005). Simulating mesoscopic reaction-diffusion systems using the Gillespie algorithm. Physical Review E, 71(4), Article 041103. https://doi.org/10.1103/PhysRevE.71.041103

[2]

Gillespie, D. T. (2001). Approximate accelerated stochastic simulation of chemically reacting systems. The Journal of Chemical Physics, 115(4), 1716-1733. https://doi.org/10.1063/1.1378322

[3]

Gillespie, D. T. (1977). Exact stochastic simulation of coupled chemical reactions. The Journal of Physical Chemistry, 81(25), 2340-2361. https://doi.org/10.1021/j100540a008