Monte Carlo simulation for single RNA unfolding by force

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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.
刊名	BIOPHYSICAL JOURNAL
	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
ISSN号	0006-3495
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.
学科主题	Physics
URL标识	查看原文
WOS记录号	WOS:000226090900010
公开日期	2012-08-30
内容类型	期刊论文
源URL	[http://ir.itp.ac.cn/handle/311006/13908]
专题	理论物理研究所_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.
推荐引用方式 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.