Related papers: Improving sequencing by tunneling with multiplexin…
DNA sequencing has faced a huge demand since it was first introduced as a service to the public. This service is often offloaded to the sequencing companies who will have access to full knowledge of individuals' sequences, a major violation…
In order to overcome the limitations imposed by DNA barcoding when multiplexing a large number of samples in the current generation of high-throughput sequencing instruments, we have recently proposed a new protocol that leverages advances…
Single-stranded libraries generated from ancient DNA extracts have specific sequencing requirements. The short library molecules typically associated with ancient DNA templates are expected to behave differently during the annealing to the…
The formation of polaron and its migration in a DNA chain are studied within a semiclassical Peyrard-Biship-Holstein polaron model. Comparing the energetics of the polaron system found from the quantum chemical and semiclassical…
DNA sequencing is revolutionising the field of medicine. DNA sequencers, the machines which perform DNA sequencing, have evolved from the size of a fridge to that of a mobile phone over the last two decades. The cost of sequencing a human…
Detecting Domain Name System (DNS) tunneling is a significant challenge in security due to its capacity to hide harmful actions within DNS traffic that appears to be normal and legitimate. Traditional detection methods are based on…
DNA has immense potential as an emerging data storage medium. The principle of DNA storage is the conversion and flow of digital information between binary code stream, quaternary base, and actual DNA fragments. This process will inevitably…
We consider the problem of storing and retrieving information from synthetic DNA media. The mathematical basis of the problem is the construction and design of sequences that may be discriminated based on their collection of substrings…
Deep shotgun sequencing and analysis of genomes, transcriptomes, amplified single-cell genomes, and metagenomes has enabled investigation of a wide range of organisms and ecosystems. However, sampling variation in short-read data sets and…
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.…
Genetic information is stored in a linear sequence of base-pairs; however, thermal fluctuations and complex DNA conformations such as folds and loops make it challenging to order genomic material for in vitro analysis. In this work, we…
Gene annotation has traditionally required direct comparison of DNA sequences between an unknown gene and a database of known ones using string comparison methods. However, these methods do not provide useful information when a gene does…
Single-electron circuits of the future, consisting of a network of quantum dots, will require a mechanism to transport electrons from one functional part to another. For example, in a quantum computer[1] decoherence and circuit complexity…
DNA is a promising medium for digital information storage for its exceptional density and durability. While prior studies advanced coding theory, workflow design, and simulation tools, challenges such as synthesis costs, sequencing errors,…
We have applied the Numerical Renormalization Group method to study a mesoscopic system consisting of two samples of metal separated by an insulating barrier, with nanometer dimensions, which allows the tunnelling of a single electron from…
At low temperatures, the transport through a superconducting-normal tunnel interface is due to tunneling of electrons in pairs. The probability for this process is shown to depend on the layout of the electrodes near the tunnel junction,…
The DNA sequencing is the process of identifying the exact order of nucleotides within a given DNA molecule. The new portable and relatively inexpensive DNA sequencers, such as Oxford Nanopore MinION, have the potential to move DNA…
Recent experiments have demonstrated the feasibility of storing digital information in macromolecules such as DNA and protein. However, the DNA storage channel is prone to errors such as deletions, insertions, and substitutions. During the…
Nanopore sequencing can read substantially longer sequences of nucleic acid molecules, called reads, than other sequencing methods, which has led to advances in genomic analysis such as the gapless human genome assembly. By analyzing the…
In this short note, a correction is made to the recently proposed solution [1] to a 1D biased diffusion model for linear DNA translocation and a new analysis will be given to the data in [1]. It was pointed out [2] by us recently that this…