Related papers: Lengthscales and Cooperativity in DNA Bubble Forma…
The formation of condensates is now considered as a major organization principle of eukaryotic cells. Several studies have recently shown that the properties of these condensates are affected by enzymatic reactions. We propose here a simple…
We study the dynamics of denaturation bubbles in double-stranded DNA on the basis of the Poland-Scheraga model. We demonstrate that the associated Fokker-Planck equation is equivalent to a Coulomb problem. Below the melting temperature the…
Although mechanical properties of DNA are well characterized at the kilo base-pair range, a number of recent experiments have suggested that DNA is more flexible at shorter length scales, which correspond to the regime that is crucial for…
We quantize subcritical bubbles which are formed in the weakly first order phase transition. We find that the typical size of the thermal fluctuation reduces in the quantum-statistical physics. We estimate the typical size and the amplitude…
The melting behavior of long, heterogeneous DNA chains is examined within the framework of the nonlinear lattice dynamics based Peyrard-Bishop-Dauxois (PBD) model. Data for the pBR322 plasmid and the complete T7 phage have been used to…
We analyze the statistical properties of bubble models for the large-scale distribution of galaxies. To this aim, we realize static simulations, in which galaxies are mostly randomly arranged in the regions surrounding bubbles. As a first…
We study how bubbles grow after the initial nucleation event in generic first-order cosmological phase transitions characterised by the values of latent heat, interface tension and correlation length, and driven by a scalar order parameter…
We examine the crystallization dynamics of nanoparticles reversibly tethered by DNA hybridization. We show that the crystallization happens readily only in a narrow temperature "slot," and always proceeds via a two-step process, mediated by…
The Peyrard-Bishop-Dauxois (PBD) model of DNA denaturation, although successful in the description of melting profiles, fails to predict melting entropies, unzipping forces and dynamical properties, e.g. hairpin dynamics. The paper presents…
We investigate the kinetics of bubble coarsening in a single component Lennard-Jones fluid using large-scale molecular dynamics simulations. A homogeneous high-temperature system is quenched below the critical temperature to induce the…
Living cells provide a fluctuating, out-of-equilibrium environment in which genes must coordinate cellular function. DNA looping, which is a common means of regulating transcription, is very much a stochastic process; the loops arise from…
The familiar process of bubbles generated via breaking waves in the ocean is foundational to many natural and industrial applications. In this process, large pockets of entrained gas are successively fragmented by the ambient turbulence…
Heat conduction has been found a plausible solution to explain discrepancies between expected and measured temperatures in hot bubbles of planetary nebulae (PNe). While the heat conduction process depends on the chemical composition, to…
We study the parameter sensitivity of hetero-polymeric DNA within the purview of DNA breathing dynamics. The degree of correlation between the mean bubble size and the model parameters are estimated for this purpose for three different DNA…
Literature data on the properties of DNA open states are reviewed and analyzed. These states are formed as a result of strong DNA fluctuations and have a great impact on a number of biochemical processes; among them is charge transfer in…
We calculate bubble-nucleation rates for (2+1)-dimensional scalar theories at high temperature. Our approach is based on the notion of a real coarse-grained potential. The region of applicability of our method is determined through internal…
The role of thermal pressure fluctuation excited within tightly packaged DNA prior to ejection from protein capsid shells is discussed in a model calculation. At equilibrium before ejection we assume the DNA is folded many times into a…
The structure and evolution of wind-blown bubbles (WBBs) around massive stars has primarily been investigated using an energy-conserving model of wind-blown bubbles. While this model is useful in explaining the general properties of the…
Phase separation, the spontaneous segregation of density, is a ubiquitous phenomenon observed across diverse physical and biological systems. Within a crowd of motile elements, active phase separation emerges from the interplay of activity…
DNA toroids are compact torus-shaped bundles formed by one or multiple DNA molecules being condensed from the solution due to various condensing agents. It has been shown that the DNA toroidal bundles are twisted. However, the global…