Facilitated diffusion of DNA-binding proteins:Efficient simulation with the method of excess collisions

摘要

In this paper,a new method to efficiently simulate diffusion controlled second order chemical reactions is derived and applied to site-specific DNA-binding proteins.The protein enters a spherical cell and propagates via two competing modes,a free diffusion and a DNA-sliding mode,to search for its specific binding site in the center of the cell.There is no need for a straightforward simulation of this process.Instead,an alternative and exact approach is shown to be essentially faster than explicit random walk simulations.The speed-up of this novel simulation technique is rapidly growing with system size.