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Monte Carlo Simulation on Stretching of Single DNA Molecules in Confined Environments
Zhang Huming,Xie Yongjun,He Xiujuan,Shi Qinwei,Zhu Pingping,Yang Haiyang*
Author NameAffiliationE-mail
Zhang Huming College of Chenistry and Material Science, University of Science and Technology of China, Hefei 230026  
Xie Yongjun College of Chenistry and Material Science, University of Science and Technology of China, Hefei 230026  
He Xiujuan College of Mechanics and Car Engineering, Hefei University of Technology, Hefei 230009  
Shi Qinwei College of Chenistry and Material Science, University of Science and Technology of China, Hefei 230026  
Zhu Pingping College of Chenistry and Material Science, University of Science and Technology of China, Hefei 230026  
Yang Haiyang* College of Chenistry and Material Science, University of Science and Technology of China, Hefei 230026 yhy@ustc.edu.cn  
Abstract:
Stretching and relaxation of a single DNA molecule tethered in a specially designed thin slit were studied using Monte Carlo simulation combined with bond fluctuation method. It was found that the extension and relaxation of the single DNA molecule are greatly affected by the confined environment. If the extent of the confined environment is increased by decreasing the distance between the two planar surfaces of the slit, the extension of the single DNA molecule increases, due to the screening of the hydrodynamic interaction of DNA segments by the planar surfaces of the slit. The relaxation of the single DNA molecule in different confined environments verifies this assumption completely. The correlation between the end-to-end separation and flow velocity obtained by Monte Carlo simulation is in good agreement with either the experimental results or theoretical consideration reported previously.
Key words:  Monte Carlo simulation, Bond-fluctuation method, DNA molecules, Degree of confinement, Polymer conformation
FundProject:
单链DNA在受限环境中伸展的Monte Carlo模拟
张胡铭,谢永军,何秀娟,石勤伟,朱平平,杨海洋*
摘要:
将Monte Carlo方法和键长涨落算法相结合,模拟了受限于两平行平面间的单链DNA分子在外力作用下的伸展以及撤除外力以后弛豫的动力学过程,研究了受限程度对DNA分子的伸展长度及弛豫过程的影响.结果表明,随着受限程度的增加, DNA分子链的构象更加伸展,这主要是由于随着平面间距的减少, DNA分子不同链段之间流体力学相互作用将会被平面屏蔽所致,受限程度不同时DNA分子的弛豫过程进一步证实了这一点.DNA分子的伸展长度(即末端距)随着流速的变化关系与文献给出的实验结果及其对此所做的理论分析是基本一致的.
关键词:  Monte Carlo模拟  键长涨落算法  DNA分子  受限程度  高分子链构象
DOI:10.1088/1674-0068/18/6/1005-1009
分类号: