Related papers: Electronic parameters for the hole transfer in DNA…
The interaction of DNA nucleobases with monolayer GaSe has been studied with in DFT framework using vdW functional. We found that nucleobases are physisorbed on the GaSe monolayer. The order of binding energy per atom is C > T > G > A. The…
The electronic structure of an infinite poly-guanine - poly-cytosine DNA molecule in its dry A-helix structure is studied by means of density-functional calculations. An extensive study of 30 nucleic base pairs is performed to validate the…
In the high-transition-temperature (high-Tc) superconductors the pseudogap phase becomes predominant when the density of doped holes is reduced1. Within this phase it has been unclear which electronic symmetries (if any) are broken, what…
In this paper we consider dipole-mediated correlations between DNA and enzymes in the context of their water environment. Such correlations emerge from electric dipole-dipole interactions between aromatic ring structures in DNA and in…
We characterize the equilibrium thermodynamics of a thick polymer confined in a spherical region of space. This is used to gain insight into the DNA packaging process. The experimental reference system for the present study is the recent…
Base stacking is crucial in nucleic acid stabilization, from DNA duplex hybridization to single-stranded DNA (ssDNA) protein binding. While stacking energies are tiny in ssDNA, they are inextricably mixed with hydrogen bonding in DNA base…
Numerous experiments on charge transfer in DNA yield a contradictory picture of the transfer: on the one hand they suggest that it is a very slow process and the charge is almost completely localized on one Watson-Crick pair, but on the…
The structure of DNA in the nucleosome core particle is studied using an elastic model that incorporates anisotropy in the bending energetics and twist-bend coupling. Using the experimentally determined structure of nucleosomal DNA [T.J.…
Excited states of the of the double-stranded DNA model (A)$_{12}\cdot$(T)_{12} were calculated in the framework of the exciton theory. The off-diagonal elements of the exciton matrix were calculated using the transition densities and ideal…
We model the electron clouds of nucleic acids in DNA as a chain of coupled quantum harmonic oscillators with dipole-dipole interaction between nearest neighbours resulting in a van der Waals type bonding. Crucial parameters in our model are…
We investigate quantum transport characteristics of a ladder model, which effectively mimics the topology of a double-stranded DNA molecule. We consider the interaction of tunneling charges with a selected internal vibrational degree of…
A detailed study of poly-[Ni(Salen)] polymer in its oxidized (Ox) and reduced (Red) states was conducted using X-ray photoelectron (XPS) and ultraviolet photoemission (UV PES) spectroscopy, near-edge X-ray absorption fine structure (NEXAFS)…
The electronic spectra for double-wall zigzag and armchair nanotubes are found. The influence of nanotube curvatures on the electronic spectra is also calculated. Our finding that the outer shell is hole doped by the inner shell is in the…
A method for increasing the accuracy of configuration interaction (CI) calculations of molecules and other electronic systems is proposed. The energy defect of a given calculation is associated with the electron pair origin of…
The thermodynamical stability of DNA minicircles is investigated by means of path integral techniques. Hydrogen bonds between base pairs on complementary strands can be broken by thermal fluctuations and temporary fluctuational openings…
We investigate the electron (hole) transport through short double-stranded DNA wires in which the electrons are strongly coupled to the specific vibrational modes (vibrons) of the DNA. We analyze the problem starting from a tight-binding…
The translocation of double-stranded DNA through a solid-state nanopore may either decrease or increase the ionic current depending on the ionic concentration of the surrounding solution. Below a certain crossover ionic concentration, the…
We present a detailed analysis of several time-dependent DFT (TD-DFT) methods, including conventional hybrid functionals and two types of non-empirically tuned range-separated functionals, for predicting a diverse set of electronic…
The lack of molecular-level understanding for the electronic excitation response of DNA to charged particle radiation, such as high-energy protons, remains a fundamental scientific bottleneck in advancing proton and other ion beam cancer…
We study sequence dependent complexation between oligonucleotides (single strand DNA) and various generation ethylene diamine (EDA) cored poly amido amide (PAMAM) dendrimers through atomistic molecular dynamics simulations accompanied by…