Abstract
Fluctuation characteristics of a migration rate constant can mainly dominate kinetic properties of bio-molecules, and these characteristics are usually submitted to surroundings and the configuration qualities of bio-molecules themselves. The two-dimensional (2D) free-energy landscape including the extension coordinate and conformational variable is needed to study the migration rate of bio-molecules in our work. We adopted the 2D generalized Langevin equation to reveal the key nature of the bio-molecules’ kinetic properties during the turnover processes by using fractional Gaussian noise (fGn) and white noise (WN). Specifically, the dependence of mean waiting time under external force on both intrinsic energy height and noise strength ratio has been extensively analyzed. Particular attention in this work is paid to distinguish the important discrepancies among the normal diffusion, sub-diffusion, and mixed kinetics. Our results suggest that the unsymmetrical kernel matrix formed by fGn and WN is a significant factor to reveal the key information of the bio-molecules in the complex system. Moreover, mixed kinetic behavior is also an important phenomenon, which cannot be neglected.
Highlights
Kinetic properties of the macromolecules during bio-chemical reaction processes1–3 in complex surrounding conditions become more and more important to research, and key information from such reactions can guide new ways for medical and bio-scientific fields
The white noise (WN) condition dependent on the normal diffusion situation is applied to the x coordinate and no time-memory features can be found in this condition
Because of the remarkable effect from both changing of angles and extension, it is necessary to establish the 2D free-energy landscape model
Summary
Kinetic properties of the macromolecules during bio-chemical reaction processes in complex surrounding conditions become more and more important to research, and key information from such reactions can guide new ways for medical and bio-scientific fields. The direction x can express features of the white noise (WN), and the Q coordinate can be given the expression of fGn. So we use the twodimensional (2D) free-energy landscape G(x, Q) and an unsymmetrical kernel matrix with two different kinds of noises to analyze the dynamics of the unfolding processes of bio-molecules. It is very interesting to investigate the situation if two different kinds of noises would be applied to analyze the dynamics of the system Because of these serious considerations, it is essential to establish a model based on the 2D energy profile with WN and fGn characteristics.. The migration rate under the pulling force condition will be analyzed, and we will investigate affections from barrier height ∆G‡ and noise strength ratio α Both δ(t) and timedependent functions will be introduced to form the matrix expressing properties of two coordinate noises.. IV, and the dynamics of the bio-molecules will be elucidated
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