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Monte Carlo Study on Spontaneous Recoil of Confined DNA Chain
Yong-jun Xie,Hong-tao Yu,Hai-yang Yang¤,Yao Wang,Xing-yuan Zhang,Qin-wei Shi¤
Author NameAffiliationE-mail
Yong-jun Xie Department of Polymer Science and Engineering, University of Science and Technology of China,Hefei 230026, China  
Hong-tao Yu Department of Polymer Science and Engineering, University of Science and Technology of China,Hefei 230026, China  
Hai-yang Yang¤ Department of Polymer Science and Engineering, University of Science and Technology of China,Hefei 230026, China yhy@ustc.edu.cn 
Yao Wang Department of Polymer Science and Engineering, University of Science and Technology of China,Hefei 230026, China  
Xing-yuan Zhang Department of Polymer Science and Engineering, University of Science and Technology of China,Hefei 230026, China  
Qin-wei Shi¤ Hefei National Laboratory for Physical Sciences at Microscales, University of Science and Technology of China, Hefei 230026, China phsqw@ustc.edu.cn 
Abstract:
A part of a long DNA chain was driven into a confined environment by an electric field, while the rest remains in the higher-entropy region. Upon removal of the field, the chain recoils to the higher-entropy region spontaneously. This dynamical process was investigated by Monte Carlo simulations. The simulation reproduces the experimentally-observed phenomenon that the recoil of the DNA chain is initially slow and gradually increases in speed due to the presence of the confinement-entropic force. The results show that with increasing the dimension or decreasing the spacing of the nanopillars the recoil velocity of the DNA chain will increase. Further analysis suggests that the characteristic entropy per monomer in the confinement is proportional to the area fraction of the free part in the confinement.
Key words:  DNA chain, Spontaneous recoil, Monte Carlo simulation, Effective entropy
FundProject:
Monte Carlo Study on Spontaneous Recoil of Confined DNA Chain
谢永军,于洪涛,杨海洋¤,王瑶,张兴元,石勤伟¤
摘要:
在外加电场作用下,长链DNA分子的一部分链段进入构象熵较小的受限区域,其余部分仍滞留在高熵区. 电场撤除后,位于受限区域的DNA链段将自发回弹到高熵区域. 采用键涨落算法对这一动力学过程进行了模拟研究. 链段的回弹速度逐渐增大,这与实验结果是一致的. 模拟结果揭显示,增加受限区域的障碍物的尺寸或缩小间距都会导致DNA链段回弹速度的增加. 进一步的分析表明链单元在受限区域内的有效熵正比于其在受限区所能到达部分占总受限区域面积的比例.
关键词:  DNA链,自发回弹,Monte Carlo模拟,有效熵
DOI:10.1088/1674-0068/21/03/281-285
分类号: