Related papers: Improving sequencing by tunneling with multiplexin…
Motivation: Next generation methods of DNA sequencing produce relatively high rate of reading errors, which interfere with de novo genome assembly of newly sequenced organisms and particularly affect the quality of SNP detection important…
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,…
In genomics, pattern matching against a sequence of nucleotides plays a pivotal role for DNA sequence alignment and comparing genomes. This helps tackling some diseases, such as cancer in humans. The complexity of searching biological…
DNA storage is a promising archival data storage solution to today's big data problem. A DNA storage system encodes and stores digital data with synthetic DNA sequences and decodes DNA sequences back to digital data via sequencing. For…
RNA sequencing (RNA-seq) enables characterization and quantification of individual transcriptomes as well as detection of patterns of allelic expression and alternative splicing. Current RNA-seq protocols depend on high-throughput…
This thesis investigates the mechanically controlled break junctions, with a particular emphasis on elucidating the behaviour of molecular currents at room temperature. The core of this experimental investigation involves a detailed…
Nanopore sequencing, superior to other sequencing technologies for DNA storage in multiple aspects, has recently attracted considerable attention. Its high error rates, however, demand thorough research on practical and efficient coding…
DNA sequence alignment is important today as it is usually the first step in finding gene mutation, evolutionary similarities, protein structure, drug development and cancer treatment. Covid-19 is one recent example. There are many…
We study the amount of reliable information that can be stored in a DNA-based storage system with noisy sequencing, where each codeword is composed of short DNA molecules. We analyze a concatenated coding scheme, where the outer code is…
The sequence-dependent elasticity of double-helical DNA on a nm length scale can be captured by the rigid base-pair model, whose strains are the relative position and orientation of adjacent base-pairs. Corresponding elastic potentials have…
The long term scaling prospects for solid-state quantum computing architectures relies heavily on the ability to simply and reliably measure and control the coherent electron interaction strength, known as the tunnel coupling, $t_c$. Here,…
Several of the next generation sequencers are limited in their sample preparation process by the need to make an absolute measurement of the number of template molecules in the library to be sequenced. As currently practiced, the practical…
DNA emerges as a promising medium for the exponential growth of digital data due to its density and durability. This study extends recent research by addressing the \emph{coverage depth problem} in practical scenarios, exploring optimal…
We study electron transfer between two separated nuclei using local control theory. By conditioning the algorithm in a symmetric system formed by two protons, one can favored slow transfer processes, where tunneling is the main mechanism,…
We propose an aqueous functionalized molybdenum disulfide nanoribbon suspended over a solid electrode as the first capacitive displacement sensor aimed at determining the DNA sequence. The detectable sequencing events arise from the…
The genetic information that dictates the structure and function of all life forms is encoded in the DNA. In 1953, Watson and Crick first presented the double helical structure of a DNA molecule. Their findings unearthed the desire to…
Many modern biological assays, including RNA sequencing, yield integer-valued counts that reflect the number of molecules detected. These measurements are often not at the desired resolution: while the unit of interest is typically a single…
Process of quantum tunneling of particles in various physical systems can be effectively controlled even by a weak and slow varying in time electromagnetic signal if to adapt specially its shape to a particular system. During an…
We study electronic transport in long DNA chains using the tight-binding approach for a ladder-like model of DNA. We find insulating behavior with localizaton lengths xi ~ 25 in units of average base-pair seperation. Furthermore, we observe…
We present a method for controlled connection of gold electrodes with dsDNA molecules (locally on a chip) by utilizing polymerase to elongate single-stranded DNA primers attached to the electrodes. Thiol-modified oligonucleotides are…