Related papers: Base pair dynamic assisted charge transport in DNA
The experiment that the high spin selectivity and the length-dependent spin polarization are observed in double-stranded DNA [Science ${\bf 331}$, 894 (2011)], is elucidated by considering the combination of the spin-orbit coupling, the…
We present a phenomenological dynamical model able to describe the stretching features of the curve of DNA length vs applied force. As concerns the chain, the model is based on the discrete wormlike chain model with elastic modifications,…
In a one dimensional lattice thermal fluctuations destroy the long-range order making particles of the lattice move on a scale much larger than the lattice spacing. We discuss the assumption that this motion may be responsible for the…
Understanding how the mechanism of charge transport through molecular tunnel junctions depends on temperature is crucial to control electronic function in molecular electronic devices. With just a few systems investigated as a function of…
We investigate the transport of excitations through a chain of atoms with non-local dissipation introduced through coupling to additional short-lived states. The system is described by an effective spin-1/2 model where the ratio of the…
We propose a dynamical model for non-specific DNA-protein interaction, which is based on the 'bead-spring' model previously developed by other groups, and investigate its properties using Brownian Dynamics simulations. We show that the…
In this work, using the time-dependent density functional theory, we address the electron tunneling triggered by short (single-cycle and several-cycle) optical pulses in narrow metallic gaps under conditions relevant for actual experiments.…
We study charge transport in an ionic solution in a confined nanoscale geometry in the presence of an externally applied electric field and immobile background charges. For a range of parameters, the ion current shows non-monotonic behavior…
Based on the direct method of molecular dynamics, the temperature dependence of energy, partition function, entropy and free energy, describing the first-order phase transition, is calculated for the classical Peyrard-Bishop-Dauxois model…
The charge carrier transport in metal phthallocyanine based disordered thin films has been investigated. Charge carrier mobility in these disordered thin films strongly depends on the electric field and temperature due to hopping…
Recent experiments measuring the electrical conductivity of DNA molecules highlight the need for a theoretical model of ion transport along a charged surface. Here we present a simple theory based on the idea of unbinding of ion pairs. The…
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 use a statistical mechanical model to study nonthermal denaturation of DNA in the presence of protein-mediated loops. We find that looping proteins which randomly link DNA bases located at a distance along the chain could cause a…
Motivated by novel results in the theory of correlated sequences, we analyze the dynamics of random walks with long-term memory (binary chains with long-range correlations). In our model, the probability for a unit bit in a binary string…
We investigate irreversibility and dissipation in single molecules that cooperatively fold/unfold in a two state manner under the action of mechanical force. We apply path thermodynamics to derive analytical expressions for the average…
Statistical DNA models available in the literature are often effective models where the base-pair state only (unbroken or broken) is considered. Because of a decrease by a factor of 30 of the effective bending rigidity of a sequence of…
Gel electrophoresis allows to separate knotted DNA (nicked circular) of equal length according to the knot type. At low electric fields, complex knots being more compact, drift faster than simpler knots. Recent experiments have shown that…
The protonic conductivity in the hydrogen bonded chains is investigated theoretically in the framework of the two-stage transport model. The strong interactions with optical phonon stretching mode are considered. We obtain the transition…
We introduce a probabilistic model for protein sliding motion along DNA during the search of a target sequence. The model accounts for possible effects due to sequence-dependent interaction between the nonspecific DNA and the protein. As an…
The low-field electron diffusion, noise, and the conduction in amorphous chalcogenides are investigated by means of a Monte Carlo implementation of a full three- dimensional variable-range hopping transport model between localized states.…