Supplement: Rule-based spatial modeling with diffusing, geometrically constrained molecules

When assuming a well stirred reactor and known macroscopic kinetic rates for mass action kinetics, microscopic rate constants for SRSim can be calculated. Prerequisite is knowing the characteristic geometric tolerances for the formation of bonds. In many cases, there will be no values available from biophysical or theoretical experiments yet. Even having generated a certain macroscopic behavior with fitted parameters in a simulation experiment does not prove that the physically correct parameters are found. There might still be various microscopic parameter combinations that would generate this effect. Nonetheless, no hypothesis can be verified until it is formulated. So different parameters can still be tested for their influence on the model and various scenarios about possible microscopic explanations for a macroscopic effect can be evaluated. Beginning with monomolecular reactions like A v1,k1 −→ B, a macroscopic rate constant k1mac, given in s−1, is translated to k1mic by expressing the reaction rate in terms of the expected number of particles E(Nreacting in dt) undergoing the reaction in an infinitesimal time step dt. Then, the reaction rate v1 equals