Related papers: Current enhancement in solid-state nanopores depen…
The electrodynamic response of DNA in the millimeter wave range is investigated. By performing measurements under a wide range of humidity conditions and comparing the response of single strand DNA and double strand DNA, we show that the…
We report an accurate method to determine DNA barcodes from the dwell time measurement of protein tags (barcodes) along the DNA backbone using Brownian dynamics simulation of a model DNA and use a recursive theoretical scheme which improves…
Chain-like macromolecules in solution, whether biological or synthetic, transform from a spatially extended conformation to a compact one upon change of temperature or solvent qualities. This sharp transition plays a key role in various…
Ion transport in highly-confined space is important to various applications, such as biosensing and seawater desalination with nanopores. All-atom molecular dynamics simulations are conducted to investigate the transport of Na$^+$ and…
We discuss multiscale simulations of long biopolymer translocation through wide nanopores that can accommodate multiple polymer strands. The simulations provide clear evidence of folding quantization, namely, the translocation proceeds…
Longitudinal resolution and lateral sensitivity are decisive characteristics that determine the suitability of a nanopore sensor for sequencing a strand of DNA as well as other important polymers. Previous modeling of DNA induced ionic…
The potential of a double nanopore system to determine DNA barcodes has been demonstrated experimentally. By carrying out Brownian dynamics simulation on a coarse-grained model DNA with protein tag (barcodes) at known locations along the…
Ion transport in biological and synthetic nanochannels is characterized by phenomena such as ion current fluctuations and rectification. Recently, it has been demonstrated that nanofabricated synthetic pores can mimic transport properties…
Single T4-DNA molecules were confined in rectangular-shaped channels with a depth of 300 nm and a width in the range 150-300 nm casted in a poly(dimethylsiloxane) nanofluidic chip. The extensions of the DNA molecules were measured with…
Quartz nanopipettes are an important emerging class of electric single-molecule sensors for DNA, proteins, their complexes as well as other biomolecular targets. However, in comparison to other resistive pulse sensors, nanopipettes…
Inspired by its central role in many biological processes, the transport of biopolymers across nanoscale pores is at the heart of a single-molecule sensing technology aimed at nucleic acid and protein sequencing, as well as biomarker…
The dynamics of the DNA denaturation is studied using the Peyrard-Bishop-Dauxois model. The denaturation rate of double stranded polymers decreases exponentially as function of length below the denaturation temperature. Above Tc, the rate…
Molecular carriers represent an increasingly common strategy in the field of nanopore sensing to use secondary molecules to selectively report on the presence of target analytes in solution, allowing for sensitive assays of otherwise…
The translocation of a short DNA fragment through a nanopore is addressed when the perforated membrane contains an embedded electrode. Accurate numerical solutions of the coupled Poisson, Nernst-Planck, and Stokes equations for a realistic,…
Charge transfer in a DNA duplex chain is studied by constructing a system with virtual electrodes connected at the ends of each DNA strand. The systeym is described by the tight-binding model and its transport is analyzed by the transfer…
Polymer translocation experiments typically involve anionic polyelectrolytes such as DNA molecules driven through negatively charged nanopores. Quantitative modelling of polymer capture to the nanopore followed by translocation therefore…
Understanding the three-dimensional (3D) structure and stability of DNA is fundamental for its biological function and the design of novel drugs. In this study, we introduce an improved coarse-grained (CG) model, incorporating a more…
DNA is strong polyelectrolyte macromolecule making metal ions (counterions) condense to a cloud around the double helix. The counterions may be localized outside the macromolecule and inside the minor and major grooves of the double helix.…
Ionic Coulomb blockade in nanopores is a phenomenon that shares some similarities but also differences with its electronic counterpart. Here, we investigate extensively this phenomenon using all-atom molecular dynamics of ionic transport…
In this work we report the study of conformation dependent electronic transport properties of DNA double-helix within tight-binding framework including its helical symmetry. We have studied the changes in localization properties of DNA as…