Fig 14. Validation of MCell4 simulation against BioNetGen/NFsim and MCell3R using a model of CaMKII.
The input BNGL model for NFsim was obtained by automatic BNGL export of BNGL from the MCell4 model. The simulation ran for 100000 iterations (0.1 s). Lines in the graphs are averages from 256 runs with different random seeds, and bands represent one standard deviation. Molecules in MCell3R and MCell4 use diffusion constant of 10−3cm2/s to emulate a well-mixed solution (the usual value is around 10−6cm2/s). The names of the observed species are indicated in the graph titles: A) Ca is unbound calcium ions; B) CaM1C is CaM(C∼1, N∼0, camkii); C) CaM1N is CaM(C∼0, N∼1, camkii); D) KCaM2N is CaMKII(T286∼U, cam!1).CaM(C∼0, N∼2, camkii!1). The simulation was initiated far from equilibrium; therefore there was an initial jump in the molecule numbers. The molecule names are explained in [40].