Related papers: Lengthscales and Cooperativity in DNA Bubble Forma…
We consider two models of interacting DNA molecules: \textit{First} is (four parametric) bubble coalescence model in interacting DNAs (shortly: BCI-DNA). \textit{Second} is (three parametric) bubble coalescence model in a condensed DNA…
We report model calculations on DNA single strands which describe the equilibrium dynamics and kinetics of hairpin formation and melting. Modeling is at the level of single bases. Strand rigidity is described in terms of simple polymer…
In this study, we present an experimental work on bubble nucleation and growth using a model system comprised of viscoelastic polyvinyl butyral confined in a Hele-Shaw cell geometry that is decompressed at elevated temperatures. The…
The dynamics of the DNA denaturation is studied using the Peyrard-Bishop-Dauxois model. The denaturation rate of double stranded polymers decreases exponentially as function of length below the denaturation temperature. Above Tc, the rate…
We study the unexpected high flexibility of short dsDNA which recently has been reported by a number of experiments. Via the Langevin dynamics simulation of our Breathing DNA model, first we observe the formation of bubbles within the…
There is a long-standing experimental observation that the melting of topologically constrained DNA, such as circular-closed plasmids, is less abrupt than that of linear molecules. This finding points to an intriguing role of topology in…
The detailed investigation of microscopic mechanisms leading to the formation of bubble structures in the nuclei has been performed in the framework of covariant density functional theory. The main emphasis of this study is on the role of…
The spherical dynamics of a bubble in a compressible liquid has been studied extensively since the early work of Gilmore. Numerical codes to study the behavior, including when large non-spherical deformations are involved, have since been…
Bubbles in the interstellar medium are produced by astrophysical sources, which continuously or explosively deposit large amount of energy into the ambient medium. These expanding bubbles can drive shocks in front of them, which dynamics is…
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…
Vapor bubbles are formed in liquids by two mechanisms: evaporation (temperature above the boiling threshold) and cavitation (pressure below the vapor pressure). The liquid resists in these metastable (overheating and tensile, respectively)…
We propose a nonlinear model derived from first principles, to describe bubble dynamics of DNA. Our model equations include a term derived from the dissipative effect of intermolecular vibrational modes. Such modes are excited by the…
The identification and tracking of stellar feedback-driven galaxy bubbles is an important topic in star formation and galactic structure research. However, current observational analysis of bubbles is limited in scope; information on bubble…
The spontaneous formation of tiny bubbles in a liquid is at the root of the nucleation mechanism during the liquid-to-vapor transition of a metastable liquid. The smaller the bubbles the larger their probability to appear, and even for…
We propose a new statistical mechanics model for the melting transition of DNA. Base pairing and stacking are treated as separate degrees of freedom, and the interplay between pairing and stacking is described by a set of local rules which…
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…
DNA inside the cellular environment works under a confined space. An intense research of the transcription and replication of DNA in the confined state is structurally significant to command the self assembly of DNA in a chamber or channel.…
The presence of a thermodynamic phase of a three-stranded DNA, namely, a mixed phase of bubbles of two bound strands and a single one, is established for large dimensions ($d\geq 5$) by using exact real space renormalization group (RG)…
We present a phenomenological model of the dynamics of buoyant bubbles in the atmosphere of a cluster of galaxies. The derived equations describe velocity, size, mass, temperature and density of the buoyant bubbles as functions of time…
The thermodynamical stability of DNA minicircles is investigated by means of path integral techniques. Hydrogen bonds between base pairs on complementary strands can be broken by thermal fluctuations and temporary fluctuational openings…