相关论文: DNA bubble dynamics as a quantum Coulomb problem

Near the melting transition the bending elastic constant, $\kappa$, an emergent property of double-stranded DNA (dsDNA), is shown not to follow the rod-like scaling for small length $N$. The reduction in $\kappa$ with temperature is…

Motivated by a number of realizations of long-range interacting systems, including ultra-cold atomic and molecular gases, we study a neutral plasma with power-law interactions longer-ranged than Coulombic. We find that beyond a crossover…

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…

In the demanding biosensing environment, improving selection efficiency strategies has become an issue of great significance. DNA minicircles containing between 200 and 400 base-pairs, also named microDNA, are representative of the…

Using a field theory equivalent to a lattice version of the Poland-Scheraga (PS) model, the phase diagram for a long DNA molecule is derived in closed form. A one-loop renormalization group calculation for the generalized PS model with…

A double-stranded DNA unravels thermally through intermediate denatured bubble segments. Intrinsically, fluctuations ensue at the bubble boundaries from non-equilibrium (NE) energy exchanges with the environment. However, such details gets…

A theory of Brownian motion is presented for an assembly of vortices. The attempt is motivated by a realization of Dyson' Coulomb gas in the context of quantum condensates. By starting with the time-dependent Landau-Ginzburg (LG) theory,…

The dynamics of the 2D Coulomb glass model is investigated by kinetic Monte Carlo simulation. An exponential divergence of the relaxation time signals a zero-temperature freezing transition. At low temperatures the dynamics of the system is…

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 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…

A degenerate fourth-order parabolic equation modeling condensation phenomena related to Bose-Einstein particles is analyzed. The model is a Fokker-Planck-type approximation of the Boltzmann-Nordheim equation, only keeping the leading order…

We compare results of previous simulations of a simple model of DNA denaturation to the predictions of the Poland-Scheraga model. Concentrating on the critical region of the latter model we calculate both thermodynamic quantities and the…

The behavior of a heavy tagged intruder immersed in a bath of particles evolving under ballistic annihilation dynamics is investigated. The Fokker-Planck equation for this system is derived and the peculiarities of the corresponding…

We numerically study the binary disordered Poland-Scheraga model of DNA denaturation, in the regime where the pure model displays a first order transition (loop exponent $c=2.15>2$). We use a Fixman-Freire scheme for the entropy of loops…

We have measured the temperature driven denaturing, or melting transition in poly d(A)-poly d(T) DNA oligomers of various lengths in different buffer conditions. Our findings are in clear disagreement with two state, reaction kinetics…

We discuss possible mechanisms that may impact the order of the transition between denaturated and bound DNA states and lead to changes in the scaling laws that govern conformational properties of DNA strands. To this end, we re-consider…

The stochastic differential equations for a model of dissipative particle dynamics with both total energy and total momentum conservation in the particle-particle interactions are presented. The corresponding Fokker-Planck equation for the…

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…

We extend the static theory of disorder-induced exponential decay of the averaged Green function of a quantum charged particle in a classical one-component plasma to the dynamic regime by incorporating the temporal evolution of the ionic…

The Poland-Scheraga (PS) model for the helix-coil transition of DNA considers the statistical mechanics of the thermally induced binding of two complementary strands of DNA. In this paper, we show how to modify the PS model when a torque is…