Nitrogen doping of carbon nanoelectrodes for enhanced control of DNA translocation dynamics

Controlling the dynamics of DNA translocation is a central issue in the emerging nanopore-based DNA sequencing. To address the potential of heteroatom doping of carbon nanostructures to achieve this goal, herein we carry out atomistic molecular dynamics simulations for single-stranded DNAs translocating between two pristine or doped carbon nanotube (CNT) electrodes. Specifically, we consider the substitutional nitrogen doping of capped CNT (capCNT) electrodes and perform two types of molecular dynamics simulations for the entrapped and translocating single-stranded DNAs. We find that the substitutional nitrogen doping of capCNTs stabilizes the edge-on nucleobase configurations rather than the original face-on ones and slows down the DNA translocation speed by establishing hydrogen bonds between the N dopant atoms and nucleobases. Due to the enhanced interactions between DNAs and N-doped capCNTs, the duration time of nucleobases within the nanogap was extended by up to ~ 290 % and the fluctuation of the nucleobases was reduced by up to ~ 70 %. Given the possibility to be combined with extrinsic light or gate voltage modulation methods, the current work demonstrates that the substitutional nitrogen doping is a promising direction for the control of DNA translocation dynamics through a nanopore or nanogap based of carbon nanomaterials.Comment: 11 pages, 4 figure

Odd-odd continued fraction algorithm

By using a jump transformation associated to the Romik map, we define a new continued fraction algorithm called odd-odd continued fraction, whose principal convergents are rational numbers of odd denominators and odd numerators. Among others, it is proved that all the best approximating rationals of odd denominators and odd numerators of an irrational number are given by the principal convergents of the odd-odd continued fraction algorithm and vice versa.Comment: 17 pages, 4 figure

Quasi-Sturmian colorings on regular trees

Quasi-Sturmian words, which are infinite words with factor complexity eventually $n+c$ share many properties with Sturmian words. In this paper, we study the quasi-Sturmian colorings on regular trees. There are two different types, bounded and unbounded, of quasi-Sturmian colorings. We obtain an induction algorithm similar to Sturmian colorings. We distinguish them by the recurrence function.Comment: 22 pages, 6 figure