Related papers: Thermodynamics of DNA loops with long-range correl…
We use a statistical mechanical model to study nonthermal denaturation of DNA in the presence of protein-mediated loops. We find that looping proteins which randomly link DNA bases located at a distance along the chain could cause a…
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…
It is well known that the contribution of harmonic phonons to the thermal conductivity of 1D systems diverges with the harmonic chain length $L$ (explicitly, increases with $L$ as a power-law with a positive power). Furthermore, within…
We consider a Brownian particle in harmonic confinement of stiffness $k$, in one dimension in the underdamped regime. The whole setup is immersed in a heat bath at temperature $T$. The center of harmonic trap is dragged under any arbitrary…
The flexibility of short DNA chains is investigated via computation of the average correlation function between dimers which defines the persistence length. Path integration techniques have been applied to confine the phase space available…
The quasi-coherent effects in two-dimensional incompressible turbulence are analyzed starting from the test particle trajectories. They can acquire coherent aspects when the stochastic potential has slow time variation and the motion is not…
The interplay between structure and dynamics in non-equilibrium steady-state is far from understood. We address this interplay by tracking Brownian Dynamics trajectories of particles in a binary colloid of opposite charges in an external…
Understanding the relationship between the microscopic structure and topology of a material and its macroscopic properties is a fundamental challenge across a wide range of systems. Here, we investigate the viscoelasticity of DNA nanostar…
When a periodic 1D system described by a tight-binding model is uniformly initialized with equal amplitudes at all sites, yet with completely random phases, it evolves into a thermal distribution with no spatial correlations. However, when…
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…
The effect of disorder on the static and dynamic behaviour of one-dimensional charge density waves at low temperatures is studied by analytical and numerical approaches. In the low temperature region the spatial behaviour of the phase-phase…
The theory of first order density-driven phase transitions with frustration due to the long range Coulomb (LRC) interaction develop on paper I of this series is applied to the following physical systems: i) the low density electron gas ii)…
The importance of nonlinearities in material constitutive relations has long been appreciated in the continuum mechanics of macroscopic rods. Although the moment (torque) response to bending is almost universally linear for small deflection…
In this paper we study the role of topology in DNA gel electrophoresis experiments via molecular dynamics simulations. The gel is modelled as a 3D array of obstacles from which half edges are removed at random with probability p, thereby…
The thermodynamic properties of subsystems in strong interaction with the neighborhood can largely differ from the standard behavior. Here we study the thermodynamic properties of rings and triplets in equilibrated disordered 2D-silica.…
Predicting when rupture occurs or cracks progress is a major challenge in numerous elds of industrial, societal and geophysical importance. It remains largely unsolved: Stress enhancement at cracks and defects, indeed, makes the macroscale…
$\alpha$-RuCl$_3$, a well-known candidate material for Kitaev quantum spin liquid, is prone to stacking disorder due to the weak van der Waals bonding between the honeycomb layers. After a decade of intensive experimental and theoretical…
Using both analytical and numerical means, we demonstrate that linear stability analysis of a hydrodynamic stratified atmosphere or a 1D coronal loop model in non-adiabatic settings features a thermal continuum corresponding to highly…
Thermodynamic uncertainty relations (TURs) are recently established relations between the relative uncertainty of time-integrated currents and entropy production in nonequilibrium systems. For small perturbations away from equilibrium,…
We discuss the structure and asymptotic long-time properties of coupled equations for the moments of a Brownian particle's momentum derived microscopically beyond the lowest approximation in the weak coupling parameter. Generalized…