Related papers: Single Stranded DNA Translocation Through A Nanopo…
In order to interpret recent experimental studies of the dependence of conductance of ds-DNA as the DNA is pulled from the 3'end1-3'end2 ends, which find a sharp conductance jump for a very short (4.5 %) stretching length, we carried out…
We investigate the orientational order of transverse polarization vectors of long, stiff polymer molecules and their coupling to bond orientational and positional order in high density mesophases. Homogeneous ordering of transverse…
Knotted proteins, when forced through the pores, can get stuck if the knots in their backbone tighten under force. Alternatively, the knot can slide off the chain, making translocation possible. We construct a simple energy landscape model…
We investigate the coherent transport properties of a DNA chain on a substrate which is subjected to a uniform electric field perpendicular to the surface. On the basis of the effective tight-binding model which simulates charge transport…
We investigated the translation of a protein through model nanopores using coarse-grained (CG) non-equilibrium molecular dynamics (NEMD) simulations and compared the mobilities with those obtained from previous coarse-grained equilibrium…
In recent years polymer translocation, i.e., transport of polymeric molecules through nanometer-sized pores and channels embedded in membranes, has witnessed strong advances. It is now possible to observe single-molecule polymer dynamics…
Protein phosphorylation provides a dynamic readout of cellular signaling yet remains difficult to detect at low abundance and stoichiometry. Single-molecule surface-enhanced Raman spectroscopy (SM-SERS) using particle-in-pore plasmonic…
Base stacking is crucial in nucleic acid stabilization, from DNA duplex hybridization to single-stranded DNA (ssDNA) protein binding. While stacking energies are tiny in ssDNA, they are inextricably mixed with hydrogen bonding in DNA base…
The combination of self-assembly and electronic properties as well as its true nanoscale dimensions make DNA a promising candidate for a building block of single molecule electronics. We argue that the intrinsic double helix conformation of…
Liquid transport through nanopore is central into many applications, from water purification to biosensing or energy harvesting. Ultimately thin nanopores are of major interest in these applications to increase driving potential and reduce…
A simple model of a circularly closed dsDNA in a poor solvent is considered as an example of a semi-flexible polymer with self-attraction. To find the ground states, the conformational energy is computed as a sum of the bending and…
We present a simple model which describes elastic response of single-stranded DNA (ssDNA) to stretching, including the regime of very high force (up to 1000 pN). ssDNA is modelled as a discreet persistent chain, whose ground state is a…
We investigate the ionic current modulation in DNA nanopore translocation setups by numerically solving the electrokinetic mean-field equations for an idealized model. Specifically, we study the dependence of the ionic current on the…
Nanopore sequencing accuracy is inherently limited by the quality of data from individual molecular translocation events, requiring advances beyond traditional sequencing-by-synthesis methods. We introduce an oxidized pyramidal sub-nm pore…
We study the energy structure and the transfer of an extra electron or hole along periodic polymers made of $N$ monomers, with a repetition unit made of $P$ monomers, using a Tight-Binding wire model, where a site is a monomer (e.g., in…
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…
DNA strand displacement is a key reaction in DNA homologous recombination and DNA mismatch repair and is also heavily utilized in DNA-based computation and locomotion. Despite its ubiquity in science and engineering, sequence-dependent…
Solid-state nanopores are emerging platforms for single-molecule protein sequencing due to their tolerance to hash physiology environment and compatibility with different electrical and optical detection methods. However, they suffer from…
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…
We perform two-dimensional Langevin dynamics simulations of electric-field driven polymer translocation through an attractive nanopore. We investigate the effect of the location of the attractive region using different pore patterns. This…