SpatKin: Rule-based modeling of spatially extended systems on the membrane

I will present a rule-based algorithm and its implementation, SpatKin, designed for spatially-extended simulations of signaling on the plasma membrane. The software allows for the exact simulation of the time-continuous Markov process. Specific biochemical reactions and molecule movements are created on-the-fly based on rules defined by the user. In the limit of infinite diffusion, the method becomes equivalent to the NFsim algorithm. However, in realistic conditions the diffusion in the membrane is limited, and, as demonstrated with several examples, the diffusion coefficient qualitatively influences the dynamics of the signaling system.