Translocation of closed polymers through a nanopore under an applied external field

doi:10.1088/1674-1056/19/1/018106

Abstract The dynamic behaviours of the translocations of closed circular polymers and closed knotted polymers through a nanopore, under the driving of an applied field, are studied by three-dimensional Langevin dynamics simulations. The power-law scaling of the translocation time $\tau$ with the chain length N and the distribution of translocation time are investigated separately. For closed circular polymers, a crossover scaling of translocation time with chain length is found to be $\tau \sim N^{\alpha}$, with the exponent α varying from $\alpha =0.71$ for relatively short chains to $\alpha =1.29$ for longer chains under driving force $F=5$. The scaling behaviour for longer chains is in good agreement with experimental results, in which the exponent $\alpha =1.27$ for the translocation of double-strand DNA. The distribution of translocation time $D(\tau)$ is close to a Gaussian function for duration time $\tau <\tau _{\rm p}$ and follows a falling exponential function for duration time $\tau >\tau _{\rm p}$. For closed knotted polymers, the scaling exponent α is 1.27 for small field force ($F=5$) and 1.38 for large field force ($F=10$). The distribution of translocation time $D(\tau)$ remarkably features two peaks appearing in the case of large driving force. The interesting result of multiple peaks can conduce to the understanding of the influence of the number of strands of polymers in the pore at the same time on translocation dynamic process and scaling property.

Keywords: Langevin dynamics closed polymer scaling behaviour distribution of translocation time

Received: 11 February 2009
Revised: 29 April 2009
Accepted manuscript online:

PACS:	82.35.Pq	(Biopolymers, biopolymerization)
	87.14.G-	(Nucleic acids)

Fund: Project supported by the National Natural Science Foundation of China (Grant Nos. 20574052, 20774066, 20974081 and 20934004), the Program for New Century Excellent Talents in University, China (Grant No. NCET-05-0538), and the Natural Science Foundation of Zhejiang Province, China (Grant No. Y4090098).

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Jiang Shao-Chuan(江绍钏), Zhang Lin-Xi(章林溪), Xia A-Gen(夏阿根), Chen Hong-Ping(陈宏平), and Cheng Jun(成军) Translocation of closed polymers through a nanopore under an applied external field 2010 Chin. Phys. B 19 018106

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Translocation of closed polymers through a nanopore under an applied external field

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