HRSSA - Efficient hybrid stochastic simulation for spatially homogeneous biochemical reaction networks

Tutkimustuotos: Lehtiartikkelivertaisarvioitu

Tutkijat

Organisaatiot

  • University of Trento

Kuvaus

This paper introduces HRSSA (Hybrid Rejection-based Stochastic Simulation Algorithm), a new efficient hybrid stochastic simulation algorithm for spatially homogeneous biochemical reaction networks. HRSSA is built on top of RSSA, an exact stochastic simulation algorithm which relies on propensity bounds to select next reaction firings and to reduce the average number of reaction propensity updates needed during the simulation. HRSSA exploits the computational advantage of propensity bounds to manage time-varying transition propensities and to apply dynamic partitioning of reactions, which constitute the two most significant bottlenecks of hybrid simulation. A comprehensive set of simulation benchmarks is provided for evaluating performance and accuracy of HRSSA against other state of the art algorithms.

Yksityiskohdat

AlkuperäiskieliEnglanti
Sivut301-317
Sivumäärä17
JulkaisuJournal of Computational Physics
Vuosikerta317
TilaJulkaistu - 2016
OKM-julkaisutyyppiA1 Julkaistu artikkeli, soviteltu

ID: 27839823