Event-driven simulation of reaction-diffusion processes with exact leaps over fast re-bindings

by Zahedeh Bashardanesh (Uppsala University)

Tuesday 3 Jun 2014, 13:30 → 14:30 Europe/Stockholm

122:026

Biochemical networks can be seen as an ensemble of diffusing molecules of different species and their chemical reactions. Green's Function Reaction Dynamics (ten Wolde et al) (GFRD) is using analytical solution to Smoluchowski equation to drive next event time. In order to derive a solvable Smoluchowski equation for the system of N particles, GFRD algorithm partitions the N-body system into singles and pairs. The next tentative time for both types of monomolecular reaction and bimolecular reaction can be sampled from the Green's function solution of the corresponding diffusion equation together with reactions incorporated as the boundary conditions. For simulating systems subject to diffusion limited biochemical reactions, GFRD will be expensive due to putting particles adjacent of each other after the dissociation event which leads to next event be chosen for their re-binding. In order to correctly integrate over all fast re-bindings, in our algorithm reversibleGFRD (rGFRD) we found the Green's function solution for reversible dissociation which put the particles at certain distance apart after the dissociation event.