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تسجيل مستخدم جديدFacilitated diffusion of DNA-binding proteins: Efficient simulation with the method of excess collisions (MEC)
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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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The diffusion-controlled limit of reaction times for site-specific DNA-binding proteins is derived from first principles. We follow the generally accepted concept that a protein propagates via two competitive modes, a three-dimensional diffusion in s
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