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Monte Carlo simulation for single RNA unfolding by force
Liu, F; Ou-Yang, ZC; Liu, F , Tsing Hua Univ, Ctr Adv Study, Beijing 100084, Peoples R China.
2005
发表期刊BIOPHYSICAL JOURNAL
ISSN0006-3495
卷号88期号:1页码:76-84
摘要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.
部门归属Tsing Hua Univ, Ctr Adv Study, Beijing 100084, Peoples R China; Chinese Acad Sci, Inst Theoret Phys, Beijing 100080, Peoples R China
关键词Mechanical Force Secondary Structure Kinetic-model Dna-molecules Stranded-dna Algorithm Information Pseudoknots Prediction Separation
学科领域Physics
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收录类别SCI
WOS记录号WOS:000226090900010
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被引频次:9[WOS]   [WOS记录]     [WOS相关记录]
文献类型期刊论文
条目标识符http://ir.itp.ac.cn/handle/311006/13908
专题理论物理所1978-2010年知识产出
通讯作者Liu, F , Tsing Hua Univ, Ctr Adv Study, Beijing 100084, Peoples R China.
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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.
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