Related papers: Structural stability versus conformational samplin…
We report a novel simulation strategy that enables us to identify key parameters controlling the experimentally measurable characteristics of structural protein tags on dsDNA construct translocating through a double nanopore setup. First,…
The influence of decoherence and bonding on the linear conductance of single double-stranded DNA molecules is examined by fitting a phenomenological statistical model developed recently (EPJB {\bf 68}, 237 (2009)) to experimental results.…
Most of the anticancer drugs bind to double-stranded DNA (dsDNA) by intercalative-binding mode. Although experimental studies have become available recently, a molecular-level understanding of the interactions between the drug and dsDNA…
The equilibrium structure of a Dinucleosome is studied using an elastic model that takes into account the force and torque balance conditions. Using the proper boundary conditions, it is found that the conformational energy of the problem…
Most living systems rely on double-stranded DNA (dsDNA) to store their genetic information and perpetuate themselves. This biological information has been considered the main target of evolution. However, here we show that symmetries and…
We study a model for polaron-like charge transport mechanism along DNA molecules with emphasis on the impact of parametrical and structural disorder. Our model Hamiltonian takes into account the coupling of the charge carrier to two…
Double-strand DNA breaks (DSBs) are a form of DNA damage that can cause abnormal chromosomal rearrangements. Recent technologies based on high-throughput experiments have obvious high costs and technical challenges.Therefore, we design a…
Sodium orthosilicates Na2MSiO4 (M denotes transition metals) have attracted much attention due to the possibility of exchanging two electrons per formula unit. In this work, we report a group of sodium iron orthosilicates Na2FeSiO4, the…
The oxidative damage of DNA is a compelling issue in molecular biophysics as it plays a vital role in the epigenetic control of gene expression and is believed to be associated with mutagenesis, carcinogenesis, and ageing. To understand the…
Molecular recognition between two double stranded (ds) DNA with homologous sequences may not seem compatible with the B-DNA structure because the sequence information is hidden when it is used for joining the two strands. Nevertheless, it…
The functioning of double-stranded (ds) nucleic acids (NAs) in cellular processes is strongly mediated by their elastic response. These processes involve proteins that interact with dsDNA or dsRNA and distort their structures. The…
We present a theoretical analysis of the environment effects on charge transport in double-stranded synthetic poly(G)-poly(C) DNA molecules attached to two ideal leads. Coupling of the DNA to the environment results in two effects: (i)…
Coarse-grained models have emerged as valuable tools to simulate long DNA molecules while maintaining computational efficiency. These models aim at preserving interactions among coarse-grained variables in a manner that mirrors the…
We report on our theoretical investigations of the electronic states in a DNA molecule. We have used a two-leg charge ladder model where electron-electron interactions and the electron spin have been taken into account. The energy spectra…
The electronic structure and structural evolution of hydrogenated graphene are investigated by Raman spectroscopy with multiple excitations. The excitation energy dependent saturation effect on the ratio of integrated intensities of D and G…
G-quadruplexes (G4s) are helical four-stranded structures forming from guanine-rich nucleic acid sequences, which are thought to play a role in cancer development and malignant transformation. Most current studies focus on G4 monomers, yet…
The flexibility and stiffness of small DNA play a fundamental role ranging from several biophysical processes to nano-technological applications. Here, we estimate the mechanical properties of short double-stranded DNA (dsDNA) having length…
The simplest model of DNA mechanics describes the double helix as a continuous rod with twist and bend elasticity. Recent work has discussed the relevance of a little-studied coupling $G$ between twisting and bending, known to arise from…
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 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…