Facilitated diffusion of DNA-binding proteins: Simulation of large systems

Details Facilitated diffusion of DNA-binding proteins: Simulation of large systems Facilitated diffusion of DNA-binding proteins: Simulation of large systems

2006-02-16

arxiv.org/abs/physics/0602113v1

Physics

Biological Physics

8 pages, 4 figures, submitted to J. Chem. Phys

Scientific paper

10.1063/1.2211614

The recently introduced method of excess collisions (MEC) is modified to estimate diffusion-controlled reaction times inside systems of arbitrary size. The resulting MEC-E equations contain a set of empirical parameters, which have to be calibrated in numerical simulations inside a test system of moderate size. Once this is done, reaction times of systems of arbitrary dimensions are derived by extrapolation, with an accuracy of 10 to 15 percent. The achieved speed up, when compared to explicit simulations of the reaction process, is increasing proportional to the extrapolated volume of the cell.

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