Knowledge Management System of Institute of Theoretical Physics, CAS
Liu, F; Ou-Yang, ZC ; Liu, F , Tsing Hua Univ, Ctr Adv Study, Beijing 100084, Peoples R China.
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| Monte Carlo simulation for single RNA unfolding by force | |
| Source Publication | BIOPHYSICAL JOURNAL
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| Keyword | Mechanical Force Secondary Structure Kinetic-model Dna-molecules Stranded-dna Algorithm Information Pseudoknots Prediction Separation |
| Abstract | Using polymer elastic theory and known RNA free energies, we construct a Monte Carlo algorithm to simulate the single RNA folding and unfolding by mechanical force on the secondary structure level. For the constant force ensemble, we simulate the force-extension curves of the P5ab, P5abcDeltaA, and P5abc molecules in equilibrium. For the constant extension ensemble, we focus on the mechanical behaviors of the RNA P5ab molecule, which include the unfolding force dependence on the pulling speed, the force-hysteresis phenomenon, and the coincidence of stretching-relaxing force-curves in thermal equilibrium. We particularly simulate the time traces of the end-to-end distance of the P5ab under the constant force in equilibrium, which also have been recorded in the recent experiment. The reaction rate constants for the folding and unfolding are calculated. Our results show that the agreement between the simulation and the experimental measurements is satisfactory. |
| 2005 | |
| ISSN | 0006-3495 |
| Volume | 88Issue:1Pages:76-84 |
| Subject Area | Physics |
| Indexed By | SCI |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | http://ir.itp.ac.cn/handle/311006/13908 |
| Collection | SCI期刊论文 |
| Corresponding Author | Liu, F , Tsing Hua Univ, Ctr Adv Study, Beijing 100084, Peoples R China. |
| Recommended Citation GB/T 7714 | Liu, F,Ou-Yang, ZC,Liu, F , Tsing Hua Univ, Ctr Adv Study, Beijing 100084, Peoples R China.. Monte Carlo simulation for single RNA unfolding by force[J]. BIOPHYSICAL JOURNAL,2005,88(1):76-84. |
| APA | Liu, F,Ou-Yang, ZC,&Liu, F , Tsing Hua Univ, Ctr Adv Study, Beijing 100084, Peoples R China..(2005).Monte Carlo simulation for single RNA unfolding by force.BIOPHYSICAL JOURNAL,88(1),76-84. |
| MLA | Liu, F,et al."Monte Carlo simulation for single RNA unfolding by force".BIOPHYSICAL JOURNAL 88.1(2005):76-84. |
| Files in This Item: | ||||||
| File Name/Size | DocType | Version | Access | License | ||
| Monte Carlo Simulati（191KB） | 开放获取 | License | Application Full Text | |||
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