| The translocation of biomolecules (DNA, protien, etc) through membranes is a common and important process in biosystems. In the past two decades, becouse of the significant process achieved in nanotechnology, people could study this process experimentally at single-molecule level. A nanopore-based device provides applications for polymer detection, DNA separation, and DNA sequencing. As we know, sequencing the human genome has helped us to understand disease, inheritance and individuality. In the 21st Century, people pay more attention for DNA sequencing. The conventional Sanger method consumes a lot of resources and time. Inspired by the $1,000 genome challenge proposed by the National Institutes of Health in 2004, nanopore sensors which are label-free and low-cost have became the powerful candinates to meet this challenge. Although a lot of progress has been achieved, many question still unanswered. It stimulates the theorists and experimental scientists to study the mechanism behind the phenomena.In experiment, a voltage drives biomolecules through a nanopore in membrane. The membrane separates the aqueous solution into two compartments. The information of the biomolecules could be studied by reading the ionic current through the nanopore. While the translocation process can be affected by five main factors:(ⅰ) external driving fields, (ⅱ) polymer dynamics, (ⅲ) properties of pores/channels, (ⅳ) polymer-pore interactions, and (ⅴ) solution properties. In recent experiments, the interaction between polymer and α-HL pore can be tuned via protonation of charged amino acid residues of the α-HL pore. It was found that the translocation time is dependent on the value of the pH gradient by tuning the pH at the trans side. It could expect that the gradient in pH may result in a gradient in the polymer-pore interaction. We study the translocation of polymer through a gradient channel with a gradient polymer-channel interaction E=E0 +kx by using Fokker-Planck equation. Here E0 is the initial potential energy at the entrance, x is the position of the monomer inside the channel, and k is the energy gradient. We find that there is a minimum of τ at a proper set of the initial potential energy E0 and the energy gradient k.To check our theoretical approach, the off-lattice Monte Carlo simulations are emploied to study the same phenomena. Considering different boundary conditions, we calculate two time scales for polymer translocation, the first passage time τFP and translocation time τt. The results are consist with our our theoretical approach and we also find different proper energy gradient k for different time scales.Besides the biological nanopores, such as a-HL, solid-state nanopores which are more robust are often used for sequencing. In recent experimental work, ssDNA containing a single benzoimidazole (Bzim)-modified 5-hydroxymethylcytosine (5hmC) could be detected by using the CNT-based nanopore. To understand the mechanism, we use molecular dynamics simulations to study the responses of the configuration of single-strand DNA (ssDNA) within a carbon nanotube (CNT) and the concomitant ion flow to a single modified base, i.e., benzoimidazole (Bzim)-modified 5-hydroxymethyl cytosine (5hmC). Our simulation results show the Bzimmodified 5hmC can considerably increase the ion flow through a single-walled carbon nanotube (SWCNT), despite its larger size, which is consistent with prior experimental results. This phenomenon is attributed to enhanced adsorption of DNA to the interior wall of the CNT driven by the Bzim-modified 5hmC, leading to a reduced steric effect on ion transport through the CNT. As revealed in this work, the distribution of ssDNA can be affected by limited change in the interactions with the CNT surface. Such behavior of ssDNA within small-sized CNTs can be exploited to further improve the sensitivity of nanopore detection. |
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