Yong-jun Xie, Hong-tao Yu, Hai-yang Yang¤, Yao Wang, Xing-yuan Zhang, Qin-wei Shi¤. Monte Carlo Study on Spontaneous Recoil of Confined DNA Chain[J]. Chinese Journal of Chemical Physics , 2008, 21(3): 281-285. doi: 10.1088/1674-0068/21/03/281-285
Citation: Yong-jun Xie, Hong-tao Yu, Hai-yang Yang¤, Yao Wang, Xing-yuan Zhang, Qin-wei Shi¤. Monte Carlo Study on Spontaneous Recoil of Confined DNA Chain[J]. Chinese Journal of Chemical Physics , 2008, 21(3): 281-285. doi: 10.1088/1674-0068/21/03/281-285

Monte Carlo Study on Spontaneous Recoil of Confined DNA Chain

doi: 10.1088/1674-0068/21/03/281-285
  • Received Date: 2007-09-12
  • Rev Recd Date: 2007-12-20
  • 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.
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Monte Carlo Study on Spontaneous Recoil of Confined DNA Chain

doi: 10.1088/1674-0068/21/03/281-285

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.

Yong-jun Xie, Hong-tao Yu, Hai-yang Yang¤, Yao Wang, Xing-yuan Zhang, Qin-wei Shi¤. Monte Carlo Study on Spontaneous Recoil of Confined DNA Chain[J]. Chinese Journal of Chemical Physics , 2008, 21(3): 281-285. doi: 10.1088/1674-0068/21/03/281-285
Citation: Yong-jun Xie, Hong-tao Yu, Hai-yang Yang¤, Yao Wang, Xing-yuan Zhang, Qin-wei Shi¤. Monte Carlo Study on Spontaneous Recoil of Confined DNA Chain[J]. Chinese Journal of Chemical Physics , 2008, 21(3): 281-285. doi: 10.1088/1674-0068/21/03/281-285

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