Related papers: Bubble Relaxation Dynamics in Double-Stranded DNA
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…
We study dynamical (quasi)-condensation in the Fermi-Hubbard model starting from a completely uncorrelated initial state of adjacent doubly occupied sites. We show that upon expansion of the system in one dimension, dynamical…
As a key molecule of Life, Deoxyribonucleic acid (DNA) is the focus of numbers of investigations with the help of biological, chemical and physical techniques. From a physical point of view, both experimental and theoretical works have…
By using large-scale molecular dynamics simulations, the dynamics of two-dimensional (2D) supercooled liquids turns out to be dependent on the system size, while the size dependence is not pronounced in three dimensional (3D) systems. It is…
We consider the ABC dynamics, with equal density of the three species, on the discrete ring with $N$ sites. In this case, the process is reversible with respect to a Gibbs measure with a mean field interaction that undergoes a second order…
In this paper, we investigate the open tight-binding model with $N$ sites coupled to two reservoirs on its edges with the nonequilibrium Green function method to understand effects of open boundaries. As a result, we obtain an analytical…
We study the relaxation dynamics of systems of straight, parallel crystal dislocations, starting from initially random and uncorrelated positions of the individual dislocations. A scaling model of the relaxation process is constructed by…
A nonlocal diffuse interface model is used to study bubble assemblies in ternary systems. As model parameters vary, a large number of morphological phases appear as stable stationary states. One open question related to the polarity…
The "Brownian bees" model describes a system of $N$ independent branching Brownian particles. At each branching event the particle farthest from the origin is removed, so that the number of particles remains constant at all times.…
We explore the intrinsic dynamics of spherical shells immersed in a fluid in the vicinity of their buckled state, through experiments and 3D axisymmetric simulations. The results are supported by a theoretical model that accurately…
Molecular dynamics simulations were employed to investigate the phase separation process of a two-dimensional active Brownian dumbbell model. We evaluated the time dependence of the typical size of the dense component using the scaling…
We theoretically investigated the temperature fluctuations of DNA close to denaturation and observed a strong enhancement of these fluctuations at the critical temperature. Although in a much lower frequency range, such a sharp increase was…
To characterize the thermodynamical equilibrium of DNA chains interacting with a solution of non-specific binding proteins, a Flory-Huggins free energy model was implemented. We explored the dependence on DNA and protein concentrations of…
The square-gradient density-functional model with triple-parabolic free energy, that was used previously to study the homogeneous bubble nucleation [J. Chem. Phys. 129, 104508 (2008)], is used to study the stability of the critical bubble…
We investigate the dynamics of a homogenous Bose-Einstein condensate (BEC) following a sudden quench of the scattering length. Our focus is the time evolution of short-range correlations via the dynamical contact. We compute the dynamics…
Cavitation and bubble dynamics are central concepts in engineering, the natural sciences, and the mathematics of fluid mechanics. Due to the nonlinear nature of their dynamics, the governing equations are not fully solvable. Here, the…
Circular double stranded DNA has different topological states which are defined by their linking numbers. Equilibrium distribution of linking numbers can be obtained by closing a linear DNA into a circle by ligase. Using Monte Carlo…
A coarsened model for a binary system with limited miscibility of components is proposed; the system is described in terms of structural states in small parts of the material. The material is assumed to have two alternative types of…
We explore the melting of a lattice DNA in the presence of atmospheric disorder, which mimics the crowded environment inside the cell nucleus, using Monte Carlo simulations. The disorder is modeled by randomly retaining lattice sites with…
We present a theory for the number fluctuations of a quasi-two-dimensional (quasi-2D) dipolar Bose-Einstein condensate measured with finite resolution cells. We show that when the dipoles are tilted to have a component parallel to the plane…