Affections of dynamic ductility and molecular friction for kinetic properties of bio-molecules in multidimensional landscape model

Abstract

Because of affections from fluctuation, the migration or reaction rate of bio-molecules is mainly related to the time-memory effect. This kinetic phenomenon is primarily dominated by dynamic ductility and molecular crowding in the solvent. These two important elements directly connect with the affections of the random force and systematic friction (ζ) in a real solvent. They can affect fluctuation characteristics of bio-molecules. Properties of bio-molecular kinetics are mainly submitted to the configuration quality and random collision. The multidimensional landscape must be needed in typical research processes for kinetics of bio-molecules. The random collision affection in the x dimension and the typical ductility for the free-energy surface in the Q dimension have been abstracted in our work. The two-dimensional generalized Langevin equation including fractional Gaussian noise or white noise is used to study the migration rate or the mean waiting time. The essential quality of the bio-molecules’ kinetic properties can be revealed by the comparative study between dynamic disorder (DD) and common diffusion. We have found that there are sharp dynamic differences between DD and normal kinetics. Moreover, dynamic ductility and solvent friction can lead to great affections to the bio-molecular dynamics.