Related papers: Hyper-sound as a means for generating inter-strand…
How topological defects affect the dynamics of particles hopping between lattice sites of a distorted, two-dimensional crystal is addressed. Perturbation theory and numerical simulations show that weak, short-ranged topological disorder…
Localization property in the disordered few-chain DNA systems with a long-range correlation is numerically investigated. We apply the chain system with the correlated disorder in the interchain and/or intrachain hoppings to the simple model…
By exploring a recent model [Palmeri, J., M. Manghi, and N. Destainville. 2007. Phys. Rev. Lett. 99:088103] where DNA bending elasticity, described by the wormlike chain model, is coupled to base-pair denaturation, we demonstrate that small…
We present an atomic scale theory of lattice distortions using strain related variables and their constraint equations. Our approach connects constrained atomic length scale variations to continuum elasticity and describes elasticity at all…
A complete methodology, based on a two-scale asymptotic approach, that enables the homogenisation of elastic lattices at non-zero frequencies is developed. Elastic lattices are distinguished from scalar lattices in that two or more types of…
The two-dimensional Hubbard model on the square lattice is studied in the presence of lattice distortions in the adiabatic approximation. The self energy is computed within perturbation theory up to second order, which provides a way for…
It appears that thermally activated DNA bubbles of different sizes play central roles in important genetic processes. Here we show that the probability for the formation of such bubbles is regulated by the number of soft AT pairs in…
The nonlinear excitations induced in DNA by external force are considered on the basis of Peyrard-Bishop-Dauxois model. It is shown that such impact can lead to creation of bubbles which can propogate through the molecule. The interaction…
We study the nonlinear dynamics of a deformed Deoxyribonucleic acid (DNA) molecular chain which is governed by a perturbed sine-Gordon equation coupled with a linear wave equation representing the lattice deformation. The DNA chain…
Motivated by the recent progress in realizing and controlling extended Bose-Hubbard systems using excitonic or atomic devices, the present Letter theoretically investigates the case of a two-band Bose-Hubbard chain with nearest-neighbor…
In scattering experiments, the dynamical structure factor (DSF) characterizes inter-particle correlations and their time evolution. We analytically evaluated the DSF of disordered solids with disorder in the spring constant, by averaging…
We investigate the effects of disorder in a hybridized two-dimensional two-band s-wave superconductor model. The situation in which electronic orbitals form these bands with angular momentum such that the hybridization $V_{i,j}$ among them…
Double-strand breaks (DSBs) in DNA are naturally occurring destructive events in all organisms that may lead to genome instability. Cells employ various repair methods known as non-homologous end joining (NHEJ), microhomology mediated end…
The formation of local denaturation zones (bubbles) in double-stranded DNA is an important example for conformational changes of biological macromolecules. We study the dynamics of bubble formation in terms of a Fokker-Planck equation for…
In this paper we consider a physical system in which two DNA molecules braid about each other. The distance between the two molecular ends, on either side of the braid, is held at a distance much larger than supercoiling radius of the…
We study the effect of random forces on a double stranded DNA in unzipping the two strands, analogous to the problem of an adsorbed polymer under a random force. The ground state develops bubbles of various lengths as the random force…
Biological information is not only stored in the digital chemical sequence of double helical DNA, but is also encoded in the mechanical properties of the DNA strands, which can influence biochemical processes involving its readout. For…
We present results of theoretical description of ultrasonic phenomena in molecular liquids. In particular, we are interested in the development of microscopical, i.e., statistical-mechanical framework capable to explain the long living…
It is shown that, an entire class of off-diagonally disordered linear lattices composed of two basic building blocks and described within a tight binding model can be tailored to generate absolutely continuous energy bands. It can be…
We investigate the localization property of an electron in the disordered two-chain system (ladder model) with long-range correlation as a simple model for electronic property in DNA sequence. The chains are constructed by repetition of the…