Related papers: DNA Barcodes using a Cylindrical Nanopore
A general theoretical framework is put forth to organize and understand various observed phenomena and mathematical relationships in the field of molecular biology. By modeling each cell in eukaryotic organisms as a processor having a…
Although carbon nanotubes are potential candidates for DNA encapsulation and subsequent delivery of biological payloads to living cells, the thermodynamical spontaneity of DNA encapsulation under physiological conditions is still a matter…
We present Brownian dynamics simulations of the facilitated diffusion of a protein, modelled as a sphere with a binding site on its surface, along DNA, modelled as a semi-flexible polymer. We consider both the effect of DNA organisation in…
A tandem cell is proposed for DNA sequencing in which an exonuclease enzyme cleaves bases (mononucleotides) from a strand of DNA for identification inside a nanopore. It has two nanopores and three compartments with the structure [cis1,…
This work exploits the zeptoliter sensing volume of electrolyte-filled nanopores to determine, simultaneously and in real time, the approximate shape, volume, charge, rotational diffusion coefficient, and dipole moment of individual…
Nanopore sequencing technology remains highly error-prone, making efficient error correction essential in DNA-based data storage. Prior work addressed high error rates using convolutional codes with their decoder coupled with the…
The bioinformatical methods to detect lateral gene transfer events are mainly based on functional coding DNA characteristics. In this paper, we propose the use of DNA traits not depending on protein coding requirements. We introduce several…
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…
Previous theoretical studies have shown that measuring the transverse current across DNA strands while they translocate through a nanopore or channel may provide a statistically distinguishable signature of the DNA bases, and may thus allow…
The recently proposed compressed backbone theory suggested that the intrinsic curvature in DNA can result from a geometric mismatch between the specific backbone length and optimal base stacking orientations. It predicted that the curvature…
We investigate the process of biopolymer translocation through a narrow pore using a multiscale approach which explicitly accounts for the hydrodynamic interactions of the molecule with the surrounding solvent. The simulations confirm that…
We present a theoretical description of the dynamics of a semi-flexible polymer being pulled through a nanopore by an external force acting at the pore. Our theory is based on the tensile blob picture of Pincus in which the front of the…
Recent experimental and theoretical approaches have attempted to quantify the physical organization (compaction and geometry) of the bacterial chromosome with its complement of proteins (the nucleoid). The genomic DNA exists in a complex…
The information contained in the genome is insufficient for the control of organism development. Thus, the whereabouts of actual operational directives and workings of the genome remain obscure. In this work, it is suggested that the genome…
Since the birth of computer and networks, fuelled by pervasive computing and ubiquitous connectivity, the amount of data stored and transmitted has exponentially grown through the years. Due to this demand, new solutions for storing data…
DNA-based biodiversity surveys involve collecting physical samples from survey sites and assaying the contents in the laboratory to detect species via their diagnostic DNA sequences. DNA-based surveys are increasingly being adopted for…
Vital biological processes such as genome repair require fast and efficient binding of selected proteins to specific target sites on DNA. Here we propose an active target search mechanism based on "chromophoresis", the dynamics of…
Computing the epipolar geometry between cameras with very different viewpoints is often problematic as matching points are hard to find. In these cases, it has been proposed to use information from dynamic objects in the scene for…
We provide an overview of current approaches to DNA-based storage system design and accompanying synthesis, sequencing and editing methods. We also introduce and analyze a suite of new constrained coding schemes for both archival and random…
Modeling charge transport in DNA is essential to understand and control the electrical properties and develop DNA-based nanoelectronics. DNA is a fluctuating molecule that exists in a solvent environment, which makes the electron…