Related papers: Osmotic pressure: resisting or promoting DNA eject…
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…
DNA storage is now being considered as a new archival storage method for its durability and high information density, but still facing some challenges like high costs and low throughput. By reducing sequencing sample size for decoding…
Based on our formulation of the DNA electrophoresis near a pore [P. Rowghanian and A. Y. Grosberg, Phys. Rev. E 87, 042723 (2013)], we address the electrophoretic DNA capture into a nanopore as a steady-state process of particle absorption…
We present a critique and extension of the mean-field approach to the mechanical pulling transition in bound polymer systems. Our model is motivated by the theoretically and experimentally important examples of adsorbed polymers and…
Most living systems rely on double-stranded DNA (dsDNA) to store their genetic information and perpetuate themselves. This biological information has been considered the main target of evolution. However, here we show that symmetries and…
We show that a mesoscale model, with a minimal number of parameters, can well describe the thermomechanical and mechanochemical behavior of homogeneous DNA at thermal equilibrium under tension and torque. We predict critical temperatures…
We studied the unzipping kinetics of single molecules of double-stranded DNA by pulling one of their two strands through a narrow protein pore. PCR analysis yielded the first direct proof of DNA unzipping in such a system. The time to unzip…
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…
We study numerically the mechanical stability and elasticity properties of duplex DNA molecules within the frame of a network model incorporating microscopic degrees of freedom related with the arrangement of the base pairs. We pay special…
DNA amplification is the process of replication of a specified DNA sequence \emph{in vitro} through time-dependent manipulation of its external environment. A theoretical framework for determination of the optimal dynamic operating…
Ever since Hershey and Chase used phages to establish DNA as the carrier of genetic information in 1952, the precise mechanisms of phage DNA translocation have been a mystery. While bulk measurements have set a time scale for in vivo DNA…
We propose a new method for electrophoretic separation of DNA in which adsorbed polymers are driven over a disordered two-dimensional substrate which contains attractive sites for the polymers. Using simulations of a model for long polymer…
Motivated by recent experiments we have studied the optical conductivity of DNA in its natural environment containing water molecules and counter ions. Our density functional theory calculations (using SIESTA) for four base pair B-DNA with…
Solid-state nanopore DNA sequencers present mechanical and chemical stability, reusability, and large-scale integrability. However, their development is hindered by the absence of a protein-free mechanism for controlling DNA translocation,…
DNA has emerged as a promising alternative for long-term data storage due to its high capacity, durability, and low-energy potential. However, storing data in DNA presents several challenges. First, it requires complex and costly…
Collective coordinate and direct numerical integration methods are applied to the analysis of a one-dimensional DNA model. A modification of the coupling constant in an extended region is found to be less selective towards the breather it…
The complex mechanisms governing charge migration in DNA oligomers reflect the rich structural and electronic properties of the molecule of life. Controlling the mechanical stability of DNA nanowires in charge transport experiments is a…
DNA is an attractive medium for digital data storage. When data is stored on DNA, errors occur, which makes error-correcting coding techniques critical for reliable DNA data storage. To reduce the errors, a common technique is to include…
This work addresses the question of the interplay of DNA demixing and supercoiling in bacterial cells. Demixing of DNA from other globular macromolecules results from the overall repulsion between all components of the system and leads to…
Single molecule studies, at constant force, of the separation of double-stranded DNA into two separated single strands may provide information relevant to the dynamics of DNA replication. At constant applied force, theory predicts that the…