Related papers: DNA Barcodes using a Cylindrical Nanopore
We consider error-correcting coding for deoxyribonucleic acid (DNA)-based storage using nanopore sequencing. We model the DNA storage channel as a sampling noise channel where the input data is chunked into $M$ short DNA strands, which are…
We propose using graphene electrodes with hydrogenated edges for solid-state nanopore-based DNA sequencing, and perform molecular dynamics simulations in conjunction with electronic transport calculations to explore the potential merits of…
We propose two-terminal devices for DNA sequencing which consist of a metallic graphene nanoribbon with zigzag edges (ZGNR) and a nanopore in its interior through which the DNA molecule is translocated. Using the nonequilibrium Green…
Solid-state nanopore and nanopipette sensors are powerful devices for the detection, quantification and structural analysis of biopolymers such as DNA and proteins, especially in carrier-enhanced resistive-pulse sensing. However, hundreds…
A multiscale approach is used to simulate the translocation of DNA through a nanopore. Within this scheme, the interactions of the molecule with the surrounding fluid (solvent) are explicitly taken into account. By generating polymers of…
We propose a DNA sequencing scheme based on silicene nanopores. Using first principles theory, we compute the electrical properties of such pores in the absence and presence of nucleobases. Within a two-terminal geometry, we analyze the…
We demonstrate simultaneous measurements of DNA translocation into glass nanopores using ionic current detection and fluorescent imaging. We verify the correspondence between the passage of a single DNA molecule through the nanopore and the…
Dielectrophoresis can potentially be used as an efficient trapping tool in the fabrication of molecular devices. For nanoscale objects, however, the Brownian motion poses a challenge. We show that the use of carbon nanotube electrodes makes…
The determination of a patient's DNA sequence can, in principle, reveal an increased risk to fall ill with particular diseases [1,2] and help to design "personalized medicine" [3]. Moreover, statistical studies and comparison of genomes [4]…
We report translocation experiments on double-strand DNA through a silicon oxide nanopore. Samples containing DNA fragments with seven different lengths between 2000 to 96000 basepairs have been electrophoretically driven through a 10 nm…
We investigate theoretically the translocation of structured RNA/DNA molecules through narrow pores which allow single but not double strands to pass. The unzipping of basepaired regions within the molecules presents significant kinetic…
Solid state nanopores have emerged as powerful tools for single-molecule sensing, yet the rapid uncontrolled translocation of the molecule through the pore remains a key limitation. We have previously demonstrated that an active…
We study theoretically the feasibility of using transverse electronic transport within a nanopore for rapid DNA sequencing. Specifically, we examine the effects of the environment and detection probes on the distinguishability of the DNA…
Fast, reliable and inexpensive DNA sequencing is an important pursuit in healthcare, especially in personalized medicine with possible deep societal impacts. Despite significant progress of various nanopore-based sequencing configurations,…
Nanopore sequencing is an emerging new technology for sequencing DNA, which can read long fragments of DNA (~50,000 bases) in contrast to most current short-read sequencing technologies which can only read hundreds of bases. While nanopore…
We study escape dynamics of a double-stranded DNA (dsDNA) through an idealized double nanopore (DNP) geometry subject to two equal and opposite forces (tug-of-war) using Brownian dynamics (BD) simulation. In addition to the geometrical…
Longitudinal resolution and lateral sensitivity are decisive characteristics that determine the suitability of a nanopore sensor for sequencing a strand of DNA as well as other important polymers. Previous modeling of DNA induced ionic…
We report current blockade (CB) characteristics of molecular motifs residing on a model dsDNA using electrokinetic Brownian dynamics (EKBD) and study the role of the valence of the counterions as the dsDNA translocates through a solitary…
Expanding genetic codes from natural standard nucleotides to artificial non-standard nucleotides marks a significant advancement in synthetic biology, with profound implications for biotechnology and medicine. Decoding the biological…
With the continued improvement of sequencing technologies, the prospect of genome-based medicine is now at the forefront of scientific research. To realize this potential, however, we need a revolutionary sequencing method for the…