Spatio-temporal dynamics within cells can now be recorded on film at appropriate resolutions thanks to advances made in florescence microscopy technologies. Even the single-particle tracking technique is now being applied to observations of biological molecules. Conversely, little is known about how reaction diffusion at the molecular level affects properties at the cellular level. Therefore, we propose an algorithm designed for the three-dimensional simulation of the reaction-diffusion dynamics of molecules, based on a particle model. Chemical reactions proceed through the interactions of particles in space. The activation energy determines the rate of these chemical reactions at each interaction. This energy-based model allows incorporating of the cellular membrane, membranes of other organelles, and cytoskeletons. The simulation algorithm was tested for a reversible enzyme reaction model and its validity verified . A snapshot image taken from simulated molecular interactions on the cellular membrane was shown to yield a clustering pattern associated with raft.