Figure 9.

Validation of reaction–diffusion. A. Lack of effect of diffusion in STEPS (points with error bars showing the sd) on first-order irreversible reaction (analytical solution, full line) with uniform initial concentration. Setting the diffusion constant to zero did not change the simulation results (not shown). B. Diffusion does not significantly affect stationary distribution of molecule that undergoes a zero-order production reaction and second order reaction with clamped species when tetrahedron size is larger than acceptable minimum. STEPS simulation (histogram) compared to analytical solution to chemical master equation (open circles).

Hepburn et al. BMC Systems Biology 2012 6:36   doi:10.1186/1752-0509-6-36
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