Polymer translocation through a nanopore under an applied external field

• Published in: The Journal of chemical physics 2006-03, Vol.124 (11), p.114704-114704-7
• Main Authors: Luo, Kaifu, Huopaniemi, Ilkka, Ala-Nissila, Tapio, Ying, See-Chen
• Format: Article
• Language: English
• Subjects: Electromagnetic Fields; Models, Chemical; Nanostructures - chemistry; Nucleic Acids - chemistry; Polymers - chemistry; Proteins - chemistry
• ISSN: 0021-9606; 1089-7690
• DOI: 10.1063/1.2179792

We investigate the dynamics of polymer translocation through a nanopore under an externally applied field using the two-dimensional fluctuating bond model with single-segment Monte Carlo moves. We concentrate on the influence of the field strength E , length of the chain N , and length of the pore L on forced translocation. As our main result, we find a crossover scaling for the translocation time τ with the chain length from τ ∼ N 2 ν for relatively short polymers to τ ∼ N 1 + ν for longer chains, where ν is the Flory exponent. We demonstrate that this crossover is due to the change in the dependence of the translocation velocity v on the chain length. For relatively short chains v ∼ N − ν , which crosses over to v ∼ N − 1 for long polymers. The reason for this is that with increasing N there is a high density of segments near the exit of the pore, which slows down the translocation process due to slow relaxation of the chain. For the case of a long nanopore for which R || , the radius of gyration R g along the pore, is smaller than the pore length, we find no clear scaling of the translocation time with the chain length. For large N , however, the asymptotic scaling τ ∼ N 1 + ν is recovered. In this regime, τ is almost independent of L . We have previously found that for a polymer, which is initially placed in the middle of the pore, there is a minimum in the escape time for R || ≈ L . We show here that this minimum persists for weak fields E such that E L is less than some critical value, but vanishes for large values of E L .