Related papers: Conformation dependent electronic transport in a D…
In our report we consider two weakly coupled Schr\"odinger equations as a model of the interchain energy transport in the DNA double-helix. We use the reduction of the Yakushevich-type model considering the torsional dynamics of the DNA. In…
DNA supercoiling is central to many fundamental processes of living organisms. Its average level along the chromosome and over time reflects the dynamic equilibrium of opposite activities of topoisomerases, which are required to relax…
DNA has a well-defined structural transition -- the denaturation of its double-stranded form into two single strands -- that strongly affects its thermal transport properties. We show that, according to a widely implemented model for DNA…
Cells deploy robust mechanisms to repair DNA damage, safeguarding genomic stability and cellular health, but the physical principles underlying these processes remain incompletely understood. Experiments show \emph{in vitro} that upon a DNA…
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…
The in vivo free energy of looping double-stranded DNA by the lac repressor has a remarkable behavior whose origins are not fully understood. In addition to the intrinsic periodicity of the DNA double helix, the in vivo free energy has an…
We investigate the dynamics of DNA translocation through a nanopore driven by an external force using Langevin dynamics simulations in two dimensions (2D) to study how the translocation dynamics depend on the details of the DNA sequences.…
In this present work we report the results of our investigation on the electronic specific heat (ESH) of DNA molecule modelled within the tight-binding framework. We take four different DNA sequences ranging from periodic, quasi-periodic to…
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…
To characterize the thermodynamical equilibrium of DNA chains interacting with a solution of non-specific binding proteins, a Flory-Huggins free energy model was implemented. We explored the dependence on DNA and protein concentrations of…
Charge inversion of a DNA double helix by an oppositely charged flexible polyelectrolyte (PE) is considered. We assume that, in the neutral state of the DNA-PE complex, each of the DNA charges is locally compensated by a PE charge. When an…
In this letter, we study the structure-transport property relationships of small ligand intercalated DNA molecules using a multiscale modelling approach where extensive ab-initio calculations are performed on numerous MD-simulated…
We studied the electrical conductivity of DNA molecules with conducting atomic force microscopy as a function of the chemical nature of the substrate surfaces, the nature of the electrical contact, and the number of DNA molecules (from a…
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…
In the present paper we address the general problem of selective electrodynamic interactions between DNA and protein, which is motivated by decades of theoretical study and our very recent experimental findings (M. Lechelon et al,…
Negatively charged DNA can be compacted by positively charged dendrimers and the degree of compaction is a delicate balance between the strength of the electrostatic interaction and the elasticity of DNA. We report various elastic…
We study the electronic transport through short DNA chains with various sequences of base pairs between voltage-biased leads. The strong coupling of the charge carriers to local vibrations of the base pairs leads to the formation of…
We propose a model Hamiltonian for describing charge transport through short homogeneous double stranded DNA molecules. We show that the hybridization of the overlapping pi orbitals in the base-pair stack coupled to the backbone is…
We discuss theoretically how electrons confined to two dimensions in a delta-doped heterostructure can arrange themselves in a droplet-like spatial distribution due to disorder and screening effects when their density is low. We apply this…
Charge transport through a short DNA oligomer (Dickerson dodecamer) in presence of structural fluctuations is investigated using a hybrid computational methodology based on a combination of quantum mechanical electronic structure…