相关论文: Bubble Relaxation Dynamics in Double-Stranded DNA

Sheared wet foam, which stores elastic energy in bubble deformations, relaxes stress through bubble rearrangements. The intermittency of bubble rearrangements in foam leads to effectively stochastic drops in stress that are followed by…

We propose a dynamical model for the secondary structure of DNA, which is based on the finite stacking enthalpies used in thermodynamics calculations. In this model, the two strands can separate and the bases are allowed to rotate…

We characterize the late-time scaling state of dry, coarsening, two-dimensional froths using a detailed, force-based vertex model. We find that the slow evolution of bubbles leads to systematic deviations from 120degree angles at three-fold…

The distribution of bubble lengths in double-stranded DNA is presented for segments of varying guanine-cytosine (GC) content, obtained with Monte Carlo simulations using the Peyrard-Bishop-Dauxois model at 310 K. An analytical description…

We study a driven zero range process which models a closed system of attractive particles that hop with site-dependent rates and whose steady state shows a condensation transition with increasing density. We characterise the dynamical…

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…

We study the melting of a double stranded DNA in the presence of stretching forces, via 3D Monte-Carlo simulations, exactly solvable models and heuristic arguments. The resulting force-temperature phase diagram is dramatically different for…

We propose a new statistical mechanics model for the melting transition of DNA. Base pairing and stacking are treated as separate degrees of freedom, and the interplay between pairing and stacking is described by a set of local rules which…

The interaction-site-density-fluctuation correlators, the dipole-relaxation functions, and the mean-squared displacements of a system of symmetric dumbbells of fused hard spheres are calculated for two representative elongations of the…

In this paper we investigate bubble nucleation in a disordered Landau-Ginzburg model. First we adopt the standard procedure to average over the disordered free energy. This quantity is represented as a series of the replica partition…

The role of thermal pressure fluctuations in the ejection of tightly packaged DNA from protein capsid shells is discussed in a model calculation. At equilibrium before ejection we assume the DNA is folded many times into a bundle of…

The buoyancy-driven motion of two identical gas bubbles released in line in a liquid at rest is examined with the help of highly resolved simulations, focusing on moderately inertial regimes in which the path of an isolated bubble is…

Anomalous non-exponential relaxation in hydrated biomolecules is commonly attributed to the complexity of the free-energy landscapes, similarly to polymers and glasses. It was found recently that the hydrogen-bond breathing of terminal DNA…

We consider a simple, purely stochastic model characterized by two conserved quantities (mass density $a$ and energy density $h$) which is known to display a condensation transition when $h > 2a^2$: in the localized phase a single site…

We examine the conformations of a model for a short segment of closed DNA. The molecule is represented as a cylindrically symmetric elastic rod with a constraint corresponding to a specification of the linking number. We obtain analytic…

The effect of electrostatic interactions on the stretching of DNA is investigated using a simple worm like chain model. In the limit of small force there are large conformational fluctuations which are treated using a self-consistent…

The East model is the simplest one-dimensional kinetically-constrained model of $N$ spins with a trivial equilibrium that displays anomalously large spatio-temporal fluctuations, with characteristic "space-time bubbles" in trajectory space,…

We study the thermodynamic and dynamic behaviors of twist-induced denaturation bubbles in a long, stretched random sequence of DNA. The small bubbles associated with weak twist are delocalized. Above a threshold torque, the bubbles of…

We introduce a two-state non-conserving driven-diffusive system in one-dimension under a discrete-time updating scheme. We show that the steady-state of the system can be obtained using a matrix product approach. On the other hand, the…

A statistical method is developed to estimate the maximum amplitude of the base pair fluctuations in a three dimensional mesoscopic model for nucleic acids. The base pair thermal vibrations around the helix diameter are viewed as a Brownian…