is hybrid of
Gibson-Bruck next reaction algorithm
explicit fourth-order Runge-Kutta method
Pahle hybrid method
Pahle hybrid Gibson-Bruck Next Reaction method/Runge-Kutta method
2020-10-29
http://identifiers.org/biosimulators/copasi
http://identifiers.org/doi/10.1007/978-1-59745-525-1_2
http://identifiers.org/doi/10.1016/j.jbiotec.2017.06.1200
http://identifiers.org/doi/10.1093/bioinformatics/btl485
http://identifiers.org/doi/10.5555/1218112.1218421
Combines a deterministic numerical integration of ODEs with a stochastic simulation algorithm. The whole biochemical network is partitioned into a deterministic and a stochastic subnet internally. The deterministic subnet contains all reactions in which only species with high particle numbers take part. All reactions with at least one low-numbered species are in the stochastic subnet. The partitioning of the biochemical network can change dynamically during the simulation. The reaction probabilities of the stochastic subnet are approximated as constant during one stochastic step. A 4th-order Runge-Kutta method is used to numerically integrate the deterministic part of the system. The stochastic subnet is simulated by the Gibson-Bruck Next Reaction Method.
JRK