A novel Monte Carlo simulation for molecular interactions and diffusion in postsynaptic spines

We developed a new Monte Carlo simulator that can incorporate anomalous diffusion and chemical kinetics of intracellular signaling molecules in the dendritic spine. The simulator is based on two well-established Monte Carlo approaches, namely the Kopelman algorithm and the Kinetic Monte Carlo algorithm. This paper describes the basic features of the simulator and compares its performance for the general case of elementary chemical reactions. We then explore anomalous diffusion of calmodulin (CaM) in the dendrite. The simulations suggest that the CaM-binding protein RC3 plays a significant role in determining the spatio-temporal dynamics of CaM-target interaction.