Related papers: Bubble generation in a twisted and bent DNA-like m…
The equilibrium statistical properties of DNA denaturation bubbles are examined in detail within the framework of the Peyrard-Bishop-Dauxois model. Bubble formation in homogeneous DNA is found to depend crucially on the presence of…
The interaction of multiple bubbles is a complex physical problem. A simplified case of multiple bubbles is studied theoretically with a bubble located at the center of a circular bubble cluster. All bubbles in the cluster are equally…
The closure of long equilibrated denaturation bubbles in DNA is studied using Brownian dynamics simulations. A minimal mesoscopic model is used where the double-helix is made of two interacting bead-spring freely rotating strands, with a…
Stripe-like and bubble-like patterns spontaneously form in numerous physical, chemical, and biological systems when competing long-range and short-range interactions banish uniformity. Stripe-like and the related nematic morphology are also…
Some members of the vegetal kingdom can achieve surprisingly fast movements making use of a clever combination of evaporation, elasticity and cavitation. In this process, enthalpic energy is transformed into elastic energy and suddenly…
The onset of intermediate states (denaturation bubbles) and their role during the melting transition of DNA are studied using the Peyrard-Bishop-Daxuois model by Monte Carlo simulations with no adjustable parameters. Comparison is made with…
The formation of bubble defects of the double stranded DNA is treated according to the Lifshits theory of disordered chains. A molecule of the DNA is modelled on a harmonic lattice with nearest neighbour interaction, elastic constants being…
Heavy and light particles are commonly found in many natural phenomena and industrial processes, such as suspensions of bubbles, dust, and droplets in incompressible turbulent flows. Based on a recent machine learning approach using a…
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 theory for describing the inner structure of the electron bunch in the bubble regime starting from a random distribution of electrons inside the bubble and subsequently minimizing the system's energy. Consequently, we find a…
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 investigate continuous generation of bubbles from a bath of air in viscous liquid in a confined geometry. In our original setup, bubbles are spontaneously generated by virtue of buoyancy and a gate placed in the cell: the gate acts like…
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…
Neglecting the effect of particle production at the moment of bubble nucleation, the spectrum of created particles during the bubble expansion is evaluated in the thin-wall approximation. It is shown that the expanding thin-walled bubble…
Water under tension, as can be found in several systems including tree vessels, is metastable. Cavitation can spontaneously occur, nucleating a bubble. We investigate the dynamics of spon- taneous or triggered cavitation inside water filled…
Winds from massive stars have velocities of 1000 km/s or more, and produce hot, high pressure gas when they shock. We develop a theory for the evolution of bubbles driven by the collective winds from star clusters early in their lifetimes,…
In this work, we present experiments and simulations on the nucleation and successive dynamics of laser-induced bubbles inside liquid droplets in free-fall motion, i.e. a case with a free boundary in all directions. The droplets of a…
We investigate the distribution of bubble lifetimes and bubble lengths in DNA at physiological temperature, by performing extensive molecular dynamics simulations with the Peyrard-Bishop-Dauxois (PBD) model, as well as an extended version…
Fully developed turbulence is a universal and scale-invariant chaotic state characterized by an energy cascade from large to small scales where the cascade is eventually arrested by dissipation. In this article, we show how to harness these…
We study the nonlinear dynamics of a protein-DNA molecular system by treating DNA as a set of two coupled linear chains and protein in the form of a single linear chain sliding along the DNA at the physiological temperature in a viscous…