Effects of activity distance on dynamics of bio-molecules in the multidimensional potential energy model

Abstract

Activity distance, which is commonly used to describe the transformation from a bound state to a transition state in the potential energy landscape model, is the key factor in the bio-molecular system to study dynamic properties. Adopted both in phenomenological theory and the statistical model, activity distance is the fundamental parameter to describe the kinetic characteristics of bio-molecules and is usually connected with the change in the pulling force F. The effects of activity distance Δx‡ are easy to be detected in a single dimensional landscape model because the force only expresses the mechanical work −Fx, which mainly overlaps with the fluctuation of the configuration of bio-molecules. However, as the force cannot affect the transformation directly in the multidimensional landscape model, the deflection angle φ is introduced in our work to discuss the pulling force, which has partial effects on the Q dimension. By comparing the mean waiting time ⟨t⟩ under the conditions of normal kinetics and dynamic disorder, in this study, we show the typical results from the effects of activity distance on the multidimensional potential energy model.