Related papers: Thermal Denaturation of Fluctuating DNA Driven by …
One-dimensional thermodynamic instabilities are phase transitions not prohibited by Landau's argument, because the energy of the domain wall (DW) which separates the two phases is infinite. Whether they actually occur in a given system of…
As a neutron star spins down, the nuclear matter continuously is converted into quark matter due to the core density increase and then latent heat is released. We have investigated the thermal evolution of neutron stars undergoing such…
The stability of a discrete time crystal against thermal fluctuations has been studied numerically by solving a stochastic Landau-Lifshitz-Gilbert equation of a periodically-driven classical system composed of interacting spins, each of…
Thermal denaturation of DNA is often studied with coarse-grained models in which native sequential base pairing is mimicked by the existence of attractive interactions only between monomers at the same position along strands (Poland and…
We find numerically that the sample to sample fluctuation of the entropy, $\Delta S$, is a tool more sensitive in distinguishing how from high temperature behaviors, than the corresponding fluctuation in the free energy. In 1+1 dimensions…
We propose a model for the fluctuation dynamics of the local denaturation zones (bubbles) in double-stranded DNA. In our formulation, the DNA strand is model as a one dimensional Rouse chain confined at both the ends. The bubble is formed…
We examine the elastic model of short circular DNA. We obtain analytic expressions for configurations, elastic energy, twist and linking number of our solutions. We find the onset of the plectonemic transition. We suggest ways to use our…
Almost a century ago, Johnson and Nyquist presented evidence of fluctuating electrical current and the governing fluctuation dissipation theorem (FDT). Whether, likewise, temperature T can fluctuate is a controversial topic and has led to…
We discuss the phenomenon of spontaneous self-compactification in a model colloidal system, proposed in a recent work on DNA-mediated self-assembly. We focus on the effect of thermal fluctuations on the stability of membrane-like…
Cells regulate gene expression in part by forming DNA-protein condensates in the nucleus. While existing theories describe the equilibrium size and stability of such condensates, their dynamics remain less understood. Here, we use…
Helical molecules change their twist number under the effect of a mechanical load. We study the twist-stretch relation for a set of short DNA molecules modeled by a mesoscopic Hamiltonian. Finite temperature path integral techniques are…
Turbulent flows frequently accompany physical, chemical and biological processes, such as mixing, two-phase flow, combustion and even foraging by bacteria and plankton larvae, all of which are in principle subject to thermal fluctuations…
The quantum thermodynamic property of the fractional damping system is investigated extensively. A fractional power-law decaying entropy function is revealed which presents another evidence for the validity of the third law of…
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…
The effect of heterogeneous sequence composition on the denaturation of double stranded DNA is investigated. The resulting pair-binding energy variation is found to have a negligible effect on the critical properties of the smooth second…
Anisotropic thermal conduction plays an important role in various astrophysical systems. One of the most stringent tests of thermal conduction can be found in supernova remnants. In this paper we study anisotropic thermal conduction and…
The mechanisms of cold- and pressure-denaturation of proteins are matter of debate and are commonly understood as due to water-mediated interactions. Here we study several cases of proteins, with or without a unique native state, with or…
For a model of DNA denaturation, exponents describing the distributions of denaturated loops and unzipped end-segments are determined by exact enumeration and by Monte Carlo simulations in two and three dimensions. The loop distributions…
We study the fluctuation-electromagnetic interaction and dynamics of a small spinning polarizable particle moving with a relativistic velocity in a vacuum background of arbitrary temperature. Using the standard formalism of the fluctuation…
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…