Related papers: Critical dynamics of DNA denaturation
Bending of DNA from a straight rod to a circular form in presence of any of the mono-, di-, tri- or tetravalent counterions has been simulated in strong Coulomb coupling environment employing a previously developed energy minimization…
We investigate thermalization in a tight-binding chain with an on-site defect subject to local dephasing noise implemented as random phase kicks. For a single linear defect of strength $\epsilon$, we obtain an exact analytical description…
Recent photoemission data in the high temperature cuprate superconductor Bi2212 have been interpreted in terms of a sharp spectral peak with a temperature independent lifetime, whose weight strongly decreases upon heating. By a detailed…
The fluctuation properties of nuclear giant resonance spectra are studied in the presence of continuum decay. The subspace of quasi-bound states is specified by one-particle one-hole and two-particle two-hole excitations and the continuum…
The closure dynamics of a pre-equilibrated DNA denaturation bubble is studied using both Brownian dynamics simulations and an analytical approach. The numerical model consists of two semi-flexible interacting single strands (ssDNA) and a…
We study overlap of two different eigenfunctions as compared with self-overlap in the framework of an infinite-dimensional version of the disordered tight-binding model. Despite a very sparse structure of the eigenstates in the vicinity of…
It was previously found that at high temperature the lowest part of the QCD Dirac spectrum consists of localized modes obeying Poisson statistics. Higher up in the spectrum, modes become delocalized and their statistics can be described by…
Chain-like macromolecules in solution, whether biological or synthetic, transform from a spatially extended conformation to a compact one upon change of temperature or solvent qualities. This sharp transition plays a key role in various…
DNA regulation and repair processes require direct interactions between proteins and DNA at specific sites. Local fluctuations of the sugar-phosphate backbones and bases of DNA (a form of DNA "breathing") play a central role in such…
We use a coarse-grained model of DNA-functionalized particles to understand the role of DNA chain length on their self-assembly. We find that the increasing chain length for a given particle size decreases the propensity to form ordered…
We evaluate, by means of molecular dynamics simulations employing a realistic DNA coarse-grained model, the phase behaviour and the structural and dynamic properties of tetravalent DNA nanostars, i.e. nanoconstructs completely made of DNA.…
The effect of defects on the melting profile of short heterogeneous DNA chains are calculated using the Peyrard-Bishop Hamiltonian. The on-site potential on a defect site is represented by a potential which has only the short-range…
We investigate the Anderson transition found in the spectrum of the Dirac operator of Quantum Chromodynamics (QCD) at high temperature, studying the properties of the critical quark eigenfunctions. Applying multifractal finite-size scaling…
We report studies of the equilibrium and the dynamics of a general set of lattice models which capture the essence of the force-induced or mechanical DNA unzipping transition. Besides yielding the whole equilibrium phase diagram in the…
We investigate to what extent the temperature dependence of the nuclear symmetry energy can affect the neutronization of the stellar core prior to neutrino trapping during gravitational collapse. To this end, we implement a one-zone…
Large-scale atomistic calculations, using empirical potentials for modeling semiconductors, have been performed on a stressed system with linear surface defects like steps. Although the elastic limits of systems with surface defects remain…
The Poland-Scheraga model for DNA denaturation, besides playing a central role in applications, has been widely studied in the physical and mathematical literature over the past decades. More recently a natural generalization has been…
The melting curves of short heterogeneous DNA chains in solution are calculated on the basis of statistical thermodynamics and compared to experiments. The computation of the partition function is based on the Peyrard-Bishop hamiltonian,…
We introduce a sequence-dependent parametrization for a coarse-grained DNA model [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Chem. Phys. 134, 085101 (2011)] originally designed to reproduce the properties of DNA molecules with…
We present a study on the role of defects on the stability of short DNA molecules. We consider short DNA molecules (16 base pairs) and investigate the thermal as well as mechanical denaturation of these molecules in the presence of defects…