Kinetic properties of bio-molecules by different noises in the two-dimensional free-energy model
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...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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AIP Publishing LLC
2021-02-01
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| Series: | AIP Advances |
| Online Access: | http://dx.doi.org/10.1063/5.0039689 |
| _version_ | 1818677154287714304 |
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| author | Yue Zheng Junjun Xu |
| author_facet | Yue Zheng Junjun Xu |
| author_sort | Yue Zheng |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-17T08:54:51Z |
| format | Article |
| id | doaj.art-8606e28df90f43e791216d072e414ffb |
| institution | Directory Open Access Journal |
| issn | 2158-3226 |
| language | English |
| last_indexed | 2024-12-17T08:54:51Z |
| publishDate | 2021-02-01 |
| publisher | AIP Publishing LLC |
| record_format | Article |
| series | AIP Advances |
| spelling | doaj.art-8606e28df90f43e791216d072e414ffb2022-12-21T21:55:59ZengAIP Publishing LLCAIP Advances2158-32262021-02-01112025318025318-510.1063/5.0039689Kinetic properties of bio-molecules by different noises in the two-dimensional free-energy modelYue Zheng0Junjun Xu1College of Chemical and Environmental Engineering, Liaoning University of Technology, Jinzhou, Liaoning 121000, ChinaCollege of Chemistry and Materials Engineering, Bohai University, Jinzhou, Liaoning 121013, ChinaFluctuation 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.http://dx.doi.org/10.1063/5.0039689 |
| spellingShingle | Yue Zheng Junjun Xu Kinetic properties of bio-molecules by different noises in the two-dimensional free-energy model AIP Advances |
| title | Kinetic properties of bio-molecules by different noises in the two-dimensional free-energy model |
| title_full | Kinetic properties of bio-molecules by different noises in the two-dimensional free-energy model |
| title_fullStr | Kinetic properties of bio-molecules by different noises in the two-dimensional free-energy model |
| title_full_unstemmed | Kinetic properties of bio-molecules by different noises in the two-dimensional free-energy model |
| title_short | Kinetic properties of bio-molecules by different noises in the two-dimensional free-energy model |
| title_sort | kinetic properties of bio molecules by different noises in the two dimensional free energy model |
| url | http://dx.doi.org/10.1063/5.0039689 |
| work_keys_str_mv | AT yuezheng kineticpropertiesofbiomoleculesbydifferentnoisesinthetwodimensionalfreeenergymodel AT junjunxu kineticpropertiesofbiomoleculesbydifferentnoisesinthetwodimensionalfreeenergymodel |