title: Force unfolding single RNAs.
abstract: We develop a continue time Monte Carlo algorithm to simulate single RNAs unfolded by a time-dependent external force on the secondary structure level. Two recent unfolding RNA experiments carried out by Bustamante group are mainly investigated. We find that, in contrast to popular two-state assumption about the RNAs free energy landscape along the molecular extension, the molecules used in the experiments do not present apparent energy barriers. The strong cooperative folding and unfolding transitions of the RNAs observed in the experiments and in our simulations arise from the interaction of the molecules and the light trap. In addition, we also investigate the properties of Jarzynski's remarkable equality, whose experimental test has received considerable attention.
authors.affiliation: Center for Advanced Study, Tsinghua University, Beijing 100084, China. liufei@tsinghua.edu.cn
authors.forename: Fei
authors.initials: F
authors.lastname: Liu
authors.forename: Huan
authors.initials: H
authors.lastname: Tong
authors.forename: Zhong-Can
authors.initials: ZC
authors.lastname: Ou-Yang
mesh_terms: D003198:Computer Simulation; D004548:Elasticity; D008846:Micromanipulation / Q000379:methods*; D008956:Models, Chemical; D008958:Models, Molecular; D015233:Models, Statistical; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D012313:RNA / Q000737:chemistry*; D013269:Stochastic Processes; D013314:Stress, Mechanical
chemical_list: D012313:RNA