Application perspective of particle-particle potentials in reaction-diffusion dynamics. The incorporation of inter-particle potentials introduces several fields of applications. (A) Bond potentials allow the building of particle groups to form more realistic representations of proteins or other complexes of molecules (i: crystal structure of four Syntaxin-1a proteins (syx), ii: 11-particle representations of syx). iii: specific attraction potentials allow the study of self-organized syx cluster formation through weak homophilic interactions (dotted circles enclose individual syx). (B) The use of repulsive and weakly attractive potentials allows the study of reactions in highly crowded systems such as the cytosol. Depicted is a 100 nm cube of cytosol in which tRNAs (blue) and ribosomes (yellow) diffuse and react, together with all other molecules (green). (C) Groups of repulsive particles can be used to model the specific architecture , of rhodopsin (purple) in the rod cell visual cascade. Photon activated rhodopsin (yellow) diffuses through the architecture (black line) and activates G proteins (blue). The depicted systems were modeled in ReaDDy  and visualized with VMD .