Facilitated Protein-DNA Binding: Theory and Monte Carlo Simulation

Abstract

The facilitated diffusion effect on protein-DNA binding is studied. A rigorous theoretical approach is presented to deal with the coupling between one-dimensional and three-dimensional diffusive motions. For a simplified model, the present approach can provide numerically exact results, which are confirmed by the lattice-based Monte Carlo simulations.

Monte Carlo Simulation Methods for External Field Effects on Diffusion-Influenced Reactions

“…[12][13][14][15][16][17] To study the field effects on diffusionreaction systems, one should make the simulation methods produce consistent results with the known analytical ones of diffusion-reaction equations. The relation between the magnitude of the external field and the hopping probability can be found to utilize the energy difference between lattice points as in the conventional Metropolis method.…”

Fundamental Function for the Random Walk Simulation with a Perfect Mirror in One Dimension

“…The solutions for the reflecting boundary condition are of importance as the analytic solution for a variety of diffusion-influenced systems can be constructed by using them. [3][4][5][6][7][8][9][10][11] The rigorous proof for the fundamental solutions with the Smoluchowski and reflecting boundary conditions is also presented by the mathematical induction.…”