Related papers: ssDNA sequencing by rectification
DNA unzipping by nanopore translocation has implications in diverse contexts, from polymer physics to single-molecule manipulation to DNA-enzyme interactions in biological systems. Here we use molecular dynamics simulations and a…
Rotary motors play key roles in energy transduction, from macroscale windmills to nanoscale turbines such as ATP synthase in cells. Despite our capabilities to construct engines at many scales, developing functional synthetic turbines at…
We investigate the electron (hole) transport through short double-stranded DNA wires in which the electrons are strongly coupled to the specific vibrational modes (vibrons) of the DNA. We analyze the problem starting from a tight-binding…
Extracting the sequence information of DNA from the blocked ionic current is the crucial step of the ionic current-based nanopore sequencing approaches. The thinnest graphene nanopore, which contained only one layer of carbon atoms,…
DNA has been considered a promising medium for storing digital information. As an essential step in the DNA-based data storage workflow, coding algorithms are responsible to implement functions including bit-to-base transcoding, error…
We develop revised theoretical ideas on the mechanism by which the transcription factor proteins locate their specific binding sites on DNA faster than the three-dimensional (3D) diffusion controlled rate limit. We demonstrate that the…
Brownian motion provides access to hydrodynamic properties of nanoscale objects independent of their optical resolvability. Here, we present a diffusion-based approach to infer effective particle size distributions of DNA-functionalized…
The dielectrophoresis method for trapping and attaching nanoscale double-stranded DNA between nanoelectrodes was developed. The method gives a high yield of trapping single or a few molecules only which enables transport measurements at the…
By resorting to a model inspired to the standard Davydov and Holstein-Fr\"ohlich models, in the present paper we study the motion of an electron along a chain of heavy particles modelling a sequence of nucleotides proper to a DNA fragment.…
Low-energy electrons offer a unique possibility for long exposure imaging of individual biomolecules without significant radiation damage. In addition, low-energy electrons exhibit high sensitivity to local potentials and thus can be…
The measured electric resistance of carbon nanotubes wrapped with DNA molecules depends strongly on the spin of the injected electrons. Motivated by these experiments, we study the effect of helix-shaped potentials on the electronic…
We have micromachined a silicon-chip device that transports DNA with a Brownian ratchet that rectifies the Brownian motion of microscopic particles. Transport properties for a DNA 50mer agree with theoretical predictions, and the DNA…
Owing to its several merits over other DNA sequencing technologies, nanopore sequencers hold an immense potential to revolutionize the efficiency of DNA storage systems. However, their higher error rates necessitate further research to…
RNA sequencing (RNA-seq) is the conventional genome-scale approach used to capture the expression levels of all detectable genes in a biological sample. This is now regularly used for population-based studies designed to identify genetic…
The errors occurring in DNA-based storage are correlated in nature, which is a direct consequence of the synthesis and sequencing processes. In this paper, we consider the memory-$k$ nanopore channel model recently introduced by Hamoum et…
To increase the information capacity of DNA storage, composite DNA letters were introduced. We propose a novel channel model for composite DNA in which composite sequences are decomposed into ordered standard non-composite sequences. The…
Synthetic DNA approaches 227.5 exabytes per gram of storage density with stability over millennial timescales. Realising this capacity requires error-correction codes that recover data from substantial synthesis and sequencing errors.…
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…
This paper presents a novel DNA sequences alignment method based on inverted index. Now most large scale information retrieval system are all use inverted index as the basic data structure. But its application in DNA sequence alignment is…
The effect of sequence heterogeneity on polynucleotide translocation across a pore and on simple models of molecular motors such as helicases, DNA polymerase/exonuclease and RNA polymerase is studied in detail. Pore translocation of RNA or…