Comparison of scalability between NeuroRD and Smoldyn.

Time and memory allocation were measured for several sets of simulations (see section Validation in the text for details). All simulations were run for 3000 msecs and the total volume of the system was 110 µm3. The simulation Diffusion includes one molecular species and no reactions while all the remaining simulations have 4 molecular species and 2 reversible bimolecular reactions. The simulation labeled Reaction starts out of biochemical equilibrium albeit the distribution of molecules in space is homogeneous. Reaction & Diffusion (I and II), start in equilibrium but molecules are injected after 100 msecs disturbing both the homogeneous distributions of molecules and their biochemical equilibrium. Concentrations in simulation Reaction & Diffusion II are well within the physiological range (highest molecular species (A) concentration: ∼400 nM).