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题名: Monte Carlo simulation for single RNA unfolding by force
作者: Liu, F ;  Ou-Yang, ZC
刊名: BIOPHYSICAL JOURNAL
出版日期: 2005
卷号: 88, 期号:1, 页码:76-84
关键词: MECHANICAL FORCE ;  SECONDARY STRUCTURE ;  KINETIC-MODEL ;  DNA-MOLECULES ;  STRANDED-DNA ;  ALGORITHM ;  INFORMATION ;  PSEUDOKNOTS ;  PREDICTION ;  SEPARATION
学科分类: Physics
通讯作者: Liu, F , Tsing Hua Univ, Ctr Adv Study, Beijing 100084, Peoples R China.
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
英文摘要: 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.
收录类别: SCI
原文出处: 查看原文
WOS记录号: WOS:000226090900010
Citation statistics: 
内容类型: 期刊论文
URI标识: http://ir.itp.ac.cn/handle/311006/13908
Appears in Collections:理论物理所1978-2010年知识产出_期刊论文

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Recommended Citation:
Liu, F,Ou-Yang, ZC. Monte Carlo simulation for single RNA unfolding by force[J]. BIOPHYSICAL JOURNAL,2005,88(1):76-84.
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