title: Facilitated diffusion of DNA-binding proteins: efficient simulation with the method of excess collisions.
abstract: 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.
authors.affiliation: Softmatter Laboratory, Department of Physics, Xiamen University, Xiamen 361005, People's Republic of China. merlitz@gmx.de
authors.forename: Holger
authors.initials: H
authors.lastname: Merlitz
authors.forename: Konstantin V
authors.initials: KV
authors.lastname: Klenin
authors.forename: Chen-Xu
authors.initials: CX
authors.lastname: Wu
authors.forename: Jörg
authors.initials: J
authors.lastname: Langowski
mesh_terms: D001665:Binding Sites; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D004058:Diffusion; D008954:Models, Biological; D009690:Nucleic Acid Conformation; D011487:Protein Conformation
chemical_list: D004268:DNA-Binding Proteins; D004247:DNA