Dynamics of DNA translocation through an attractive nanopore

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dc.creatorLuo, Kaifu
dc.creatorAla-Nissila, Tapio
dc.creatorYing, See-Chen
dc.creatorBhattacharya, Aniket
dc.date2008-10-16
dc.date.accessioned2026-07-07T12:09:57Z
dc.date.available2026-07-07T12:09:57Z
dc.descriptionWe investigate the dynamics of DNA translocation through a nanopore driven by an external force using Langevin dynamics simulations in two dimensions (2D) to study how the translocation dynamics depend on the details of the DNA sequences. We consider a coarse-grained model of DNA built from two bases $A$ and $C$, having different base-pore interactions, {\textit e.g.}, a strong (weak) attractive force between the pore and the base $A$ ($C$) inside the pore. From a series of studies on hetero-DNAs with repeat units $A_mC_n$, we find that the translocation time decreases exponentially as a function of the volume fraction $f_C$ of the base $C$. %($ε_{pC} < ε_{pA}$). For longer $A$ sequences with $f_C \le 0.5$, the translocation time strongly depends on the orientation of DNA, namely which base enters the pore first. Our studies clearly demonstrate that for a DNA of certain length $N$ with repeat units $A_mC_n$, the pattern exhibited by the waiting times of the individual bases and their periodicity can unambiguously determine the values of $m$, $n$ and $N$ respectively. Therefore, a prospective experimental realization of this phenomenon may lead to fast and efficient sequence detection technic.
dc.description7 pages, 7 figures
dc.identifierhttps://arxiv.org/abs/0810.2907
dc.identifierhttp://arxiv.org/abs/0810.2907
dc.identifierPhysical Review E 78, 061911 (2008)
dc.identifierdoi:10.1103/PhysRevE.78.061911
dc.identifier.urihttp://salesiana.dossiersoluciones.com/handle/123456789/209804
dc.subjectSoft Condensed Matter
dc.subjectStatistical Mechanics
dc.titleDynamics of DNA translocation through an attractive nanopore
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