Related papers: Dynamics of K$^+$ counterions around DNA double he…
The control over DNA elongation in nanofluidic devices holds great potential for large-scale genomic analysis. So far, the manipulation of DNA in nanochannels has been mostly carried out with electrophoresis and seldom with hydrodynamics,…
In the field of DNA nanotechnology, it is common wisdom that charge transport occurs through the {\pi} stacked bases of double-stranded DNA. However, recent experimental findings by Zhuravel et. al. [Nat. Nanotech. 15, 836 (2020)] suggest…
We report Molecular Dynamics (MD) simulations of a generic hydrophobic nanopore connecting two reservoirs which are initially at different Na+ concentrations, as in a biological cell. The nanopore is impermeable to water under equilibrium…
We present results of molecular dynamics simulations of strong, flexible polyelectrolyte chains in solution with added salt. The effect of added salt on the polyelectrolyte chain structure is fully treated for the first time as a function…
We scrutinize the effect of polyvalent ions on polymer-DNA interactions. We extend a recently developed test charge theory to the case of a stiff polymer interacting with a DNA molecule in an electrolyte mixture. The theory accounts for…
Ion transport through charged nanopores is commonly interpreted in terms of electrical double layer structure, leading to the expectation of cation-selective conduction in negatively charged pores. This picture can break down for…
Double ionization (DI) is a fundamental process that despite its apparent simplicity provides rich opportunities for probing and controlling the electronic motion. Even for the simplest multielectron atom, helium, new DI mechanisms are…
Electrical neural signalling typically takes place at the time-scale of milliseconds, and is typically modeled using the cable equation. This is a good approximation for processes when ionic concentrations vary little during the time course…
It is hypothesized that nonlinear solid friction between the gel matrix and DNA molecules inhibits the motion of DNA through the nanopores of the gel during electrophoresis. In this article, it is demonstrated that external noise can…
Dynamics of topological solitons describing open states in the DNA double helix are studied in the frameworks of the model which takes into account asymmetry of the helix. It is shown that three types of topological solitons can occur in…
A theory of the unzipping of double-stranded (ds) DNA is presented, and is compared to recent micromanipulation experiments. It is shown that the interactions which stabilize the double helix and the elastic rigidity of single strands (ss)…
The effect of sequence heterogeneity on polynucleotide translocation across a pore and on simple models of molecular motors such as helicases, DNA polymerase/exonuclease and RNA polymerase is studied in detail. Pore translocation of RNA or…
We use X-ray scattering and molecular simulations to investigate the structural properties of complexes of multivalent cationic lipids and DNA molecules. At low mole fraction of neutral lipids (NLs), $\Phi_{\rm NL}$, the complexes show…
We report current blockade (CB) characteristics of molecular motifs residing on a model dsDNA using electrokinetic Brownian dynamics (EKBD) and study the role of the valence of the counterions as the dsDNA translocates through a solitary…
Observations of flare-heated electrons in the corona typically suggest confinement of electrons. The confinement mechanism, however, remains unclear. The transport of coronal hot electrons into ambient plasma was recently investigated by…
Strong influence of water molecules on the transport and magnetic properties of DNA, observed in this study, opens up real opportunities for application of DNA in molecular electronics. Interaction of the nucleobases with water molecules…
We have managed to correlate the stability constants of complex formation, which can be registered in equilibrium state, to the dynamic characteristic of the complex lifetime. Thus, the principal concept of molecular biophysics regarding…
Crossover motifs are integral components for designing DNA based nanostructures and nanomechanical devices due to their enhanced rigidity compared to the normal B-DNA. Although the structural rigidity of the double helix B-DNA has been…
Potassium (K-) channels catalyze K+ ion permeation across cellular membranes while simultaneously discriminating their permeation over Na+ ions by more than a factor of a thousand. Structural studies show bare K+ ions occupying the…
We use an elastic rod model with contact to study the extension versus rotation diagrams of single supercoiled DNA molecules. We reproduce quantitatively the supercoiling response of overtwisted DNA and, using experimental data, we get an…