We 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 $C$. %($epsilon_{pC} < epsilon_{pA}$). 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.
Using Langevin dynamics simulations, we investigate the influence of polymer-pore interactions on the dynamics of biopolymer translocation through nanopores. We find that an attractive interaction can significantly change the translocation dynamics.
This can be understood by examining the three components of the total translocation time $tau approx tau_1+tau_2+tau_3$ corresponding to the initial filling of the pore, transfer of polymer from the textit{cis} side to the textit{trans} side, and emptying of the pore, respectively. We find that the dynamics for the last process of emptying of the pore changes from non-activated to activated in nature as the strength of the attractive interaction increases, and $tau_3$ becomes the dominant contribution to the total translocation time for strong attraction. This leads to a new dependence of $tau$ as a function of driving force and chain length. Our results are in good agreement with recent experimental findings, and provide a possible explanation for the different scaling behavior observed in solid state nanopores {it vs.} that for the natural $alpha$-hemolysin channel.
We investigate the dynamics of DNA translocation through a nanopore using 2D Langevin dynamics simulations, focusing on the dependence of the translocation dynamics on the details of DNA sequences. The DNA molecules studied in this work are built fro
m two types of bases $A$ and $C$, which has been shown previously to have different interactions with the pore. We study DNA with repeating blocks $A_nC_n$ for various values of $n$, and find that the translocation time depends strongly on the {em block length} $2n$ as well as on the {em orientation} of which base entering the pore first. Thus, we demonstrate that the measurement of translocation dynamics of DNA through nanopore can yield detailed information about its structure. We have also found that the periodicity of the block sequences are contained in the periodicity of the residence time of the individual nucleotides inside the pore.
One of the most fundamental quantities associated with polymer translocation through a nanopore is the translocation time $tau$ and its dependence on the chain length $N$. Our simulation results based on both the bond fluctuation Monte Carlo and Mole
cular Dynamics methods confirm the original prediction $tausim N^{2 u+1}$, which scales in the same manner as the Rouse relaxation time of the chain except for a larger prefactor, and invalidates other scaling claims.
We investigate the influence of polymer-pore interactions on the translocation dynamics using Langevin dynamics simulations. An attractive interaction can greatly improve translocation probability. At the same time, it also increases translocation ti
me slowly for weak attraction while exponential dependence is observed for strong attraction. For fixed driving force and chain length the histogram of translocation time has a transition from Gaussian distribution to long-tailed distribution with increasing attraction. Under a weak driving force and a strong attractive force, both the translocation time and the residence time in the pore show a non-monotonic behavior as a function of the chain length. Our simulations results are in good agreement with recent experimental data.
