Related papers: Dynamics of DNA Melting
This paper aims at a comprehensive understanding on the novel elastic property of double-stranded DNA (dsDNA) discovered very recently through single-molecule manipulation techniques. A general elastic model for double-stranded biopolymers…
Dissipation generally leads to the decoherence of a quantum state. In contrast, numerous recent proposals have illustrated that dissipation can also be tailored to stabilize many-body entangled quantum states. While the focus of these works…
The one-dimensional contact process with weak to intermediate quenched disorder in its transmission rates is investigated via quasi-stationary Monte Carlo simulation. We address the contested questions of both the nature of dynamical…
We predict a novel temperature-driven phase transition of DNA below the melting transition. The additional, intermediate phase exists for repetitive sequences, when the two strands have different lengths. In this phase, the excess bases of…
The viscosity of dilute and semidilute unentangled DNA solutions, in steady simple shear flow, has been measured across a range of temperatures and concentrations. For polystyrene solutions, measurements of viscosity have been carried out…
Dynamics of DNA bubbles are of interest for both statistical physics and biology. We present exact solutions to the Fokker-Planck equation governing bubble dynamics in the presence of a long-range entropic interaction. The complete meeting…
The linking number (topological entanglement) and the writhe (geometrical entanglement) of a model of circular double stranded DNA undergoing a thermal denaturation transition are investigated by Monte Carlo simulations. By allowing the…
We investigate melting transition of DNA sequences embedded in a Langevin fluctuation-dissipation thermal bath. Torsional effects are considered by a twist angle $\varphi$ between neighboring base pairs stacked along the molecule backbone.…
We propose a generic model of driven DNA under the influence of an oscillatory force of amplitude $F$ and frequency $\nu$ and show the existence of a dynamical transition for a chain of finite length. We find that the area of the hysteresis…
We revisit the out-of-equilibrium physics arising during the unitary evolution of a one-dimensional XXZ spin chain initially prepared in a domain wall state $\vert\psi_0\rangle=\vert\dots \uparrow\uparrow\downarrow\downarrow\dots\rangle$.…
Dynamics of a single stranded DNA, which can form a hairpin have been studied in the constant force ensemble. Using Langevin dynamics simulations, we obtained the force-temperature diagram, which differs from the theoretical prediction…
While slowly turning the ends of a single molecule of DNA at constant applied force, a discontinuity was recently observed at the supercoiling transition, when a small plectoneme is suddenly formed. This can be understood as an abrupt…
We study an unbiased, discrete time random walk on the nonnegative integers, with the origin absorbing. The process has a history-dependent step length: the walker takes steps of length v while in a region which has been visited before, and…
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…
DNA is an astonishing material that can be used as a molecular building block to construct periodic arrays and devices with nanoscale accuracy and precision. Here, we present simple bead-spring model of DNA nanostars having three, four and…
DNA looping participates in transcriptional regulation, for instance, by allowing distal binding sites to act synergistically. Here we study this process and compare different regulatory mechanisms based on repression with and without…
Within a simple elastic theory, we study the elongation versus force characteristics of a supercoiled DNA molecule at thermal equilibrium in the regime of small supercoiling. The partition function is mapped to the path integral…
In living systems, DNA undergoes continuous and rhythmic mechanical remodeling through condensation, looping, and disentangling to regulate gene expression, segregate chromosomes, and guide morphogenesis. Here, we demonstrate a purely…
The absorption of ultraviolet light creates excitations in DNA, which subsequently start moving in the helix. Their fate is important for an understanding of photo damage, and is determined by the interplay of electronic couplings between…
We show that a mesoscale model, with a minimal number of parameters, can well describe the thermomechanical and mechanochemical behavior of homogeneous DNA at thermal equilibrium under tension and torque. We predict critical temperatures…