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

Abstract

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.

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

References in corpus (1)

• Conductivity of a suspension of nanowires in a weakly conducting medium

Cited by in corpus (3)

• Description of non-specific DNA-protein interaction and facilitated diffusion with a dynamical model
• Dynamical model of DNA-protein interaction: effect of protein charge distribution and mechanical properties
• Modelling diffusional transport in the interphase cell nucleus