Related papers: Electronic parameters for the hole transfer in DNA…

The high linear charge density of 20-base-pair oligomers of DNA is shown to lead to a striking non-monotonic dependence of the long-time self-diffusion on the concentration of the DNA in low-salt conditions. This generic non-monotonic…

When the DNA double helix is subjected to external forces it can stretch elastically to elongations reaching 100% of its natural length. These distortions, imposed at the mesoscopic or macroscopic scales, have a dramatic effect on…

The interplay between bending of the molecule axis and appearance of disruptions in circular DNA molecules, with $\sim 100$ base pairs, is addressed. Three minicircles with different radii and almost equal content of AT and GC pairs are…

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…

We use a recently developed coarse-grained model for DNA to study kissing complexes formed by hybridization of complementary hairpin loops. The binding of the loops is topologically constrained because their linking number must remain…

Charge transfer can take place along double helical DNA over distances as long as 30 nanometers. However, given the active role of the thermal environment surrounding charge carriers in DNA, physical mechanisms driving the transfer process…

Although mechanical properties of DNA are well characterized at the kilo base-pair range, a number of recent experiments have suggested that DNA is more flexible at shorter length scales, which correspond to the regime that is crucial for…

Eukaryotic DNA is packaged into chromatin: one-dimensional arrays of nucleosomes separated by stretches of linker DNA are folded into 30-nm chromatin fibers which in turn form higher-order structures. Each nucleosome, the fundamental unit…

We investigate the nature of the electronic ground state and electron-lattice couplings for doped chains of CuO_4 plaquettes or CuO_6 octahedra. The undoped configuration implies here Cu 3d^9 and O 2p^6 formal valence states. The results of…

Charge inversion of a DNA double helix by an oppositely charged flexible polyelectrolyte (PE) is widely used for gene delivery. It is considered here in terms of discrete charges of DNA. We concentrate on the worst scenario case when in the…

We study the Coulomb-to-dipole transition which occurs when the separation $d$ of an electron-hole bilayer system is varied with respect to the characteristic in-layer distances. An analysis of the classical ground state configurations for…

Isotope shifts in dielectronic recombination spectra were studied for Li-like ^{A}Nd^{57+} ions with A=142 and A=150. From the displacement of resonance positions energy shifts \delta E^{142,150}(2s-2p_1/2)= 40.2(3)(6) meV (stat)(sys)) and…

We present a generic model for DNA at the base-pair level. We use a variant of the Gay-Berne potential to represent the stacking energy between neighboring base-pairs. The sugar-phosphate backbones are taken into account by semi-rigid…

One-dimensional arrays of nucleosomes (DNA-bound histone octamers separated by stretches of linker DNA) fold into higher-order chromatin structures which ultimately make up eukaryotic chromosomes. Chromatin structure formation leads to…

Short blunt-ended DNA duplexes comprising 6 to 20 base pairs self-assemble into polydisperse semi-flexible chains due to hydrophobic stacking interactions between terminal base pairs. Above a critical concentration, which depends on…

The rapid progress in the field of molecular electronics has led to an increasing interest on DNA oligomers as possible components of electronic circuits at the nanoscale. For this, however, an understanding of charge transfer and transport…

In this work we present a computational study of the Kinetoplast genome, modelled as a large number of semiflexible unknotted loops, which are allowed to link with each other. As the DNA density increases, the systems shows a percolation…

There are two approaches to describing DNA-ions interactions. The physical approach is an analysis of electrostatic interactions between ions and charges on the DNA molecule. The coordination chemistry approach is a search for modes of…

The strength of the spin-orbit interaction relevant to transport in a low dimensional structure depends critically on the relative geometrical arrangement of current carrying orbitals. Recent tight-binding orbital models for spin transport…

We present a base-pairing model of oligonuleotide duplex formation and show in detail its equivalence to the Nearest-Neighbour dimer methods from fits to free energy of duplex formation data for short DNA-DNA and DNA-RNA hybrids containing…