相关论文: Bubble dynamics in DNA

By exploring a recent model [Palmeri, J., M. Manghi, and N. Destainville. 2007. Phys. Rev. Lett. 99:088103] where DNA bending elasticity, described by the wormlike chain model, is coupled to base-pair denaturation, we demonstrate that small…

We study the effect of random forces on a double stranded DNA in unzipping the two strands, analogous to the problem of an adsorbed polymer under a random force. The ground state develops bubbles of various lengths as the random force…

The two strands of a DNA molecule with a repetitive sequence can pair into many different basepairing patterns. For perfectly periodic sequences, early bulk experiments of Poerschke indicate the existence of a sliding process, permitting…

The flexibility and the extension along the direction of the force are shown to be related to the bubble number fluctuation and the average number of bubbles respectively, when the strands of the DNA are subjected to a force along the same…

We report on the statistics of bubble size, topology, and shape and on their role in the coarsening dynamics for foams consisting of bubbles compressed between two parallel plates. The design of the sample cell permits control of the liquid…

We study the dynamical formation of disoriented chiral condensates in very high energy nucleus-nucleus collisions using Bjorken hydrodynamics and relativistic nucleation theory. It is the dynamics of the first order confinement phase…

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 the creation of scalar particles inside a region delimited by a bubble which is expanding with non-zero acceleration. The bubble is modelled as a thin shell and plays the role of a moving boundary, thus influencing the…

We consider the overdamped dynamics of a paradigmatic long-range system of particles residing on the sites of a one-dimensional lattice, in the presence of thermal noise. The internal degree of freedom of each particle is a periodic…

Several controversial issues concerning the packing of linear DNA in bacteriophages and globules are discussed. Exact relations for the osmotic pressure, capsid pressure and loading force are derived in terms of the hole size inside phages…

We study the dynamics of cosmological phase transitions in the case of small velocities of bubble walls, $v_w<0.1$. We discuss the conditions in which this scenario arises in a physical model, and we compute the development of the phase…

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…

Based on the direct method of molecular dynamics, the temperature dependence of energy, partition function, entropy and free energy, describing the first-order phase transition, is calculated for the classical Peyrard-Bishop-Dauxois model…

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…

As a key molecule of Life, Deoxyribonucleic acid (DNA) is the focus of numbers of investigations with the help of biological, chemical and physical techniques. From a physical point of view, both experimental and theoretical works have…

Single-molecule experiments provide new insights into biological processes hitherto not accessible by measurements performed on bulk systems. We report on a study of the kinetics of a triple-branch DNA molecule with four conformational…

The thermodynamical properties of heterogeneous DNA sequences are computed by path integral techniques applied to a nonlinear model Hamiltonian. The base pairs relative displacements are interpreted as time dependent paths whose amplitudes…

We obtain, using transfer matrix methods, the distribution function $P(R)$ of the end-to-end distance, the loop formation probability and force-extension relations in a model for short double-stranded DNA molecules. Accounting for the…

We investigate the kinetics of the DNA melting transition using modified versions of the Peyrard-Dauxois-Bishop and Poland-Scheraga models that include long and short range interactions. Using Brownian dynamics and Monte Carlo simulations,…

We consider the influence of a terahertz field on the breathing dynamics of double-stranded DNA. We model the spontaneous formation of spatially localized openings of a damped and driven DNA chain, and find that linear instabilities lead to…