Related papers: Thermodynamics of DNA loops with long-range correl…
We study the folding of RNA secondary structures with quenched sequence randomness by means of the constrained annealing method. A thermodynamic phase transition is induced by including the conformational weight of loop structures. In…
Crack formation is conventionally described as a nucleation phenomenon despite the fact that the temperatures necessary to overcome the nucleation barrier are far too high. In this paper we consider the possibility that cracks are created…
We analyze a one-dimensional XXZ spin chain in a disordered magnetic field. As the main probes of the system's behavior we use the sensitivity of eigenstates to adiabatic transformations, as expressed through the fidelity susceptibility, in…
Using numerical simulations, we study the dynamical evolution of particles interacting via competing long-range repulsion and short-range attraction in two dimensions. The particles are compressed using a time-dependent quasi-one…
We present a self-contained theory for the mechanical response of DNA in single molecule experiments. Our model is based on a 1D continuum description of the DNA molecule and accounts both for its elasticity and for DNA-DNA electrostatic…
DNA self-assembly is a well-understood nanotechnology to obtain extremely ordered structures from the nanometer to up to the hundred of microns scale. By contrast, DNA hydrogels rely on the disordered assembly of DNA building blocks to…
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…
Ultracold polar molecules, in highly anisotropic traps and interacting via a repulsive dipolar potential, may form one-dimensional chains at high densities. According to classical theory, at low temperatures there exists a critical value of…
Chromonic liquid crystals (CLCs) are lyotropic materials which are attracting growing interest for their adaptability to living systems. A considerable body of works has been devoted to exploring their properties and applications. In this…
We study order-disorder transitions in three-dimensional \textsl{multi-colored} loop models using Monte Carlo simulations. We show that the nature of the transition is intimately related to the nature of the loops. The symmetric loops…
The approach of nonequilibrium evolution thermodynamics earlier offered is developed. It helps to describe the processes of defect formation within the adiabatic approximation. The basic equations system depends on the initial defects…
Cold ions in anisotropic harmonic potentials can form ion chains of various sizes. Here, the density of ions is not uniform, thus the eigenmodes are not phononic-like waves. We study chains of N>>1 ions and evaluate analytically the long…
We examine the thermally-induced fracture of an unstrained polymer chain of discrete segments coupled by an anharmonic potential by means of Molecular Dynamics simulation with a Langevin thermostat. Cases of both under- and over-damped…
Recent experimental data indicate that the elastic wormlike rod model of DNA that works well on long length scales may break down on shorter scales relevant to biology. According to Noy and Golestanian (Phys. Rev. Lett. 109, 228101, 2012)…
We have studied the influence of a particular kind of phason-defect on the Landauer resistance of a Fibonacci chain. Depending on parameters, we sometimes find the resistance to decrease upon introduction of defect or temperature, a…
The equilibrium dynamics of a thin film type II superconductor with spherical geometry are investigated numerically in a simulation based on the lowest Landau level approximation to the time-dependent Ginzburg-Landau equation. Both the…
We aim to study thermodynamics of multiple two-body systems with long-range correlation using non-extensive statistics. Long-range correlation will cause multiple systems in anomalous diffusion. We consider the influence of long-range…
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…
We study the force-induced unfolding of random disordered RNA or single-stranded DNA polymers. The system undergoes a second order phase transition from a collapsed globular phase at low forces to an extensive necklace phase with a…
Storage and retrieval of the genetic information in cells is a dynamic process that requires the DNA to undergo dramatic structural rearrangements. DNA looping is a prominent example of such a structural rearrangement that is essential for…