dorsal/arxiv
View SchemaFacilitated diffusion of DNA-binding proteins: Efficient simulation with the method of excess collisions (MEC)
| Authors | Holger Merlitz, Konstantin V. Klenin, Chen-Xu Wu, Jörg Langowski |
|---|---|
| Categories | |
| ArXiv ID | physics/0510146 |
| URL | https://arxiv.org/abs/physics/0510146 |
| DOI | 10.1063/1.2178806 |
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.
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"abstract": "In this paper, a new method to efficiently simulate diffusion controlled\nsecond order chemical reactions is derived and applied to site-specific\nDNA-binding proteins. The protein enters a spherical cell and propagates via\ntwo competing modes, a free diffusion and a DNA-sliding mode, to search for its\nspecific binding site in the center of the cell. There is no need for a\nstraightforward simulation of this process. Instead, an alternative and exact\napproach is shown to be essentially faster than explicit random-walk\nsimulations. The speed-up of this novel simulation technique is rapidly growing\nwith system size.",
"arxiv_id": "physics/0510146",
"authors": [
"Holger Merlitz",
"Konstantin V. Klenin",
"Chen-Xu Wu",
"J\u00f6rg Langowski"
],
"categories": [
"physics.bio-ph"
],
"doi": "10.1063/1.2178806",
"title": "Facilitated diffusion of DNA-binding proteins: Efficient simulation with the method of excess collisions (MEC)",
"url": "https://arxiv.org/abs/physics/0510146"
},
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