Related papers: Localization of Denaturation Bubbles in Random DNA…
Dynamics of DNA bubbles are of interest for both statistical physics and biology. We present exact solutions to the Fokker-Planck equation governing bubble dynamics in the presence of a long-range entropic interaction. The complete meeting…
The Kirchhoff elastic theory of thin filaments with spontaneous curvature is employed in the understanding of the onset of the kink transitions observed in short DNA rings. Dynamical analysis shows that when its actual curvature is less…
We study generic aspects of bubble dynamics in DNA under time dependent perturbations, for example temperature change, by mapping the associated Fokker-Planck equation to a quantum time-dependent Schroedinger equation with imaginary time.…
The statistical mechanics of DNA denaturation under fixed linking number is qualitatively different from that of the unconstrained DNA. Quantitatively different melting scenarios are reached from two alternative assumptions, namely, that…
In the presence of disorder, an interacting closed quantum system can undergo many-body localization (MBL) and fail to thermalize. However, over long times even weak couplings to any thermal environment will necessarily thermalize the…
We study the electronic properties of DNA by way of a tight-binding model applied to four particular DNA sequences. The charge transfer properties are presented in terms of localisation lengths, crudely speaking the length over which…
Under applied shear strain, granular and amorphous materials deform via particle rearrangements, which can be small and localized or organized into system-spanning avalanches. While the statistical properties of avalanches under…
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…
Soft colloids allow to explore high density states well beyond random close packing. An important open question is whether softness controls the dynamics under these dense conditions. While experimental works reported conflicting results,…
Active particles under soft confinement such as droplets or vesicles present intriguing phenomena, as collective motion emerges alongside the deformation of the environment. A model is employed to systematically investigate droplet…
The transition between ergodic and many-body localized phases is expected to occur via an avalanche mechanism, in which \emph{ergodic bubbles} that arise due to local fluctuations in system properties thermalize their surroundings leading…
Localised heterogeneities have been recently discovered to act as bubble-nucleation sites in nonlinear field theories. Vacuum decay seeded by black holes is one of the most remarkable applications. This article proposes a simple and exactly…
Knowledge of bubble and drop size distributions in two-phase flows is important for characterizing a wide range of phenomena, including combustor ignition, sonar communication, and cloud formation. The physical mechanisms driving the…
We study localization properties of continuously monitored dynamics and associated measurement-induced phase transitions in disordered quantum many-body systems on the basis of the quantum trajectory approach. By calculating the fidelity…
This review focuses on Direct numerical simulations (DNS) of turbulent flows laden with droplets or bubbles. DNS of these flows are more challenging than those of flows laden with solid particles due to the surface deformation in the…
It has been speculated that bubble formation of several base-pairs due to thermal fluctuations is indicatory for biological active sites. Recent evidence, based on experiments and molecular dynamics (MD) simulations using the…
Co-localization of networks of genes in the nucleus is thought to play an important role in determining gene expression patterns. Based upon experimental data, we built a dynamical model to test whether pure diffusion could account for the…
The competition between toroidal and rod-like conformations as possible ground states for DNA condensation is studied as a function of the stiffness, the length of the DNA and the form of the long-range interactions between neighboring…
We investigate the distribution of bubble lifetimes and bubble lengths in DNA at physiological temperature, by performing extensive molecular dynamics simulations with the Peyrard-Bishop-Dauxois (PBD) model, as well as an extended version…
The dynamics of a loop in DNA molecules at the denaturation transition is studied by scaling arguments and numerical simulations. The autocorrelation function of the state of complementary bases (either closed or open) is calculated. The…