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 (4)

• How do proteins search for their specific sites on coiled or globular DNA
• Facilitated diffusion of DNA-binding proteins
• Conductivity of a suspension of nanowires in a weakly conducting medium
• Facilitated diffusion of DNA-binding proteins: Efficient simulation with the method of excess collisions (MEC)

Cited by in corpus (6)

• Facilitated diffusion on mobile DNA: configurational traps and sequence heterogeneity
• Description of non-specific DNA-protein interaction and facilitated diffusion with a dynamical model
• Comparison of kinetic and dynamical models of DNA-protein interaction and facilitated diffusion
• Dynamical model of DNA-protein interaction: effect of protein charge distribution and mechanical properties
• Facilitated diffusion on confined DNA
• Modelling diffusional transport in the interphase cell nucleus