Reservoir approach schematics and validation.
(A) Molecules can diffuse in and out of the reservoir. Although distinct molecules are shown for illustration, the reservoir is perfectly mixed. (B) Particles at a depth z must diffuse a distance of either zimpl—z to enter, or z–zimpl to exit, the explicit simulation domain. The integrals are solved numerically over discrete slices with thickness Δz. (C) Time courses of the number of molecules in the explicit domain, comparing our approach and a non-reactive Brownian dynamics simulation. The shaded regions represent the mean±1 S.D. over 5 realizations. (D) Time-averaged comparisons, mean±1 S.D. of fluctuations, over 500s, 1 realization.