Related papers: Some Effective Tight-Binding Models for Electrons …
We investigate theoretically the translocation of structured RNA/DNA molecules through narrow pores which allow single but not double strands to pass. The unzipping of basepaired regions within the molecules presents significant kinetic…
It has been suggested by several authors that nonlinear excitations, in particular solitary waves, could play a fundamental functional role in the process of DNA transcription, effecting the opening of the double chain needed for RNA…
A theoretical framework for evaluating the approximate energy and dynamic properties associated with the folding of DNA into nucleosomes and chromatin is presented. For this purpose experimentally determined elastic constants of linear DNA…
We call \textit{monomer} a B-DNA base pair and study, analytically and numerically, electron or hole oscillations in \textit{monomers}, \textit{dimers} and \textit{trimers}. We employ two Tight Binding (TB) approaches: (I) at the base-pair…
We introduce a coarse-grained model of DNA with bases modeled as rigid-body ellipsoids to capture their anisotropic stereochemistry. Interaction potentials are all physicochemical and generated from all-atom simulation/parameterization with…
While the thermodynamics of DNA hybridization is well understood, much less is known about the kinetics of this classic system. Filling this gap in our understanding has new urgency because DNA nanotechnology often depends critically on…
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 transport of deformable particles through porous media underlies a wealth of applications ranging from filtration to oil recovery to the transport and spreading of biological agents. Using direct numerical simulations, we analyze the…
We address the relation between long range correlations and charge transfer efficiency in aperiodic artificial or genomic DNA sequences. Coherent charge transfer through the HOMO states of the guanine nucleotide is studied using the…
We have studied the peculiarities of electron transport in one-dimensional (1D) disordered chain at the presence of correlations between on-site interaction and tunneling integrals. In the considered models the disorder in host-lattice…
While stretching of most polymer chains leads to rather featureless force-extension diagrams, some, notably DNA, exhibit non-trivial behavior with a distinct plateau region. Here we propose a unified theory that connects force-extension…
The encapsulation of polyanions, whether single-stranded RNAs or synthetic polymers, is primarily driven by attractive electrostatic interactions between the positively charged, structurally disordered RNA-binding domains of virus coat…
Electronic transport through DNA wires in the presence of a strong dissipative environment is investigated. We show that new bath-induced electronic states are formed within the bandgap. These states show up in the linear conductance…
We study numerically scattering and transport statistical properties of tight-binding random networks characterized by the number of nodes $N$ and the average connectivity $\alpha$. We use a scattering approach to electronic transport and…
In this study, we investigate the electronic structure, charge transport dynamics, and optical properties of a quantum dot light-emitting diode (QD-LED) featuring a double nanorod (NR) emission layer composed of CdSe-ZnS core-shell…
We study the elastic behaviour of a supercoiled DNA molecule. The simplest model is that of a rod like chain, involving two elastic constants, the bending and the twist rigidities. We show that this model is singular and needs a small…
Although the two-dimensional model of random networks of metallic nanowires or carbon nanotubes is widely used, it significantly overestimates the number of contacts between elements compared to quasi-three-dimensional models. This, within…
We develop a detailed analysis of electron transport in normal diffusive conductors in the presence of proximity induced superconducting correlation. We calculated the linear conductance of the system and the profile of the electric field.…
We investigate the interplay of electron-phonon (EP) coupling and strong electronic correlations in the frame of the two-dimensional (2D) Holstein t-J model (HtJM), focusing on polaronic ordering phenomena for the quarter-filled band case.…
Double-stranded DNA translocates through sufficiently large nanopores either in a linear, single-file fashion or in a folded hairpin conformation when captured somewhere along its length. We show that the folding state of DNA can be…