Thermodynamics And Kinetics Properties Of A DNA Hairpin Under A Pulling Force

In this dissertation,we have investigated the phase transition of a DNA hairpin under a pulling force using the two-dimensional(2D)Langevin dynamics simulations.We have found that the unfolded probability is related to the pulling force.The DNA hairpin almost always keeps in the folded state and the unzipping event occurs occasionally at a small pulling force f=1.5.With an increase in f,the force induced unzipping frequency gets higher and a DNA hairpin nearly stays in unfolded states at a large pulling force f=2.0,We have found that the unfolded probability could be quantitatively expressed as a function of the pulling force,which is interpreted from the perspective of statistical mechanics.Then,by performing vast simulations with different parameter sets,the force-intensity of base pairing and the force-temperature phase diagram is plotted,respectively.It is shown that the increasing intensity of base pairing and the decreasing temperature are in favor of the folded states.The DNA hairpin under a pulling force is not always in entirely folded or unfolded states.In the intermediate regime plotted,the breaking of one or more base pairings is possible.These half-open states are metastable states and correspond to a plenty of local minima of the free energy landscape.The phase diagrams obtained in the present work are very helpful to deepen our understanding of the thermodynamic properties of a DNA hairpin under a pulling force.In addition,we got the relationship between the force and the pilling force rate and the relationship between opening time and the pulling force.Besides,we studied the relationship between opening probability and time,It's very helpful to deepen our understanding of the kinetics properties of a DNA hairpin under a pulling force.