Related papers: Dynamical phase transition of a periodically drive…
We analyze the dynamics of structural transitions between normal right-handed B form and unusual left-handed Z form for a linear DNA molecule. The dynamics under the external torque in physiological buffer is modeled by a Langevin equation,…
DNA unzipping by nanopore translocation has implications in diverse contexts, from polymer physics to single-molecule manipulation to DNA-enzyme interactions in biological systems. Here we use molecular dynamics simulations and a…
Using Monte Carlo simulations, we study the dynamic transitions in the unzipping of an adsorbed homogeneous polymer on a surface (or wall). We consider three different types of surfaces. One end of the polymer is always kept anchored, and…
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…
We propose the use of recurrent neural networks for classifying phases of matter based on the dynamics of experimentally accessible observables. We demonstrate this approach by training recurrent networks on the magnetization traces of two…
Recent experiments on unzipping of RNA helix-loop structures by force have shown that about 40-base molecules can undergo kinetic transitions between two well-defined `open' and `closed' states, on a timescale = 1 sec [Liphardt et al.,…
We study a system of non-identical bistable particles that is driven by a dynamical constraint and coupled through a non-local mean-field. Assuming piecewise affine constitutive laws we prove the existence of traveling wave solutions and…
The denaturation of the double helix is a template for fundamental biological functions such as replication and transcription involving the formation of local fluctuational openings. The denaturation transition is studied for heterogeneous…
The dynamic phase transition has been studied in the two dimensional kinetic Ising model in presence of a time varying (sinusoidal) magnetic field by Monte Carlo simulation. The nature (continuous or discontinuous) of the transition is…
We study the features on the unzipping process of a modified version of the Peyrard-Bishop- Dauxois model. We show that the inclusion of a barrier in the on-site potential allows for the existence of stable domain wall solutions between…
We study a zero-range process with two species of interacting particles. We show that the steady state assumes a simple factorised form, provided the dynamics satisfy certain conditions, which we derive. The steady state exhibits a new…
The impact of damping effect and external forces to the DNA breathing is investigated within the Peyrard-Bishop model. In in the continuum limit, the dynamics of the breathing of DNA is described by the forced-damped nonlinear Schrodinger…
We present a systematic study of the dynamical phase diagram of a periodically driven BCS system as a function of drive strength and frequency. Three different driving mechanism are considered and compared: oscillating density of states,…
We study the time evolution of spin squeezing in the one-dimensional spin-1/2 XY model subject to a sudden quantum quench of a transverse magnetic field. The initial state is selected from the ground state phase diagram of the model,…
The complexity of the primary structure of human DNA is explored using methods from nonequilibrium statistical mechanics, dynamical systems theory and information theory. The use of chi-square tests shows that DNA cannot be described as a…
Recent experiments [J. van Mameren et al. PNAS 106, 18231 (2009)] provide a detailed spatial picture of overstretched DNA, showing that under certain conditions the two strands of the double helix separate at about 65 pN. It was proposed…
Driven many-body quantum systems where some parameter in the Hamiltonian is varied quasiperiodically in time may exhibit nonequilibrium steady states that are qualitatively different from their periodically driven counterparts. Here we…
Driven dissipative systems at ambient conditions typically exhibit continuous responses shaped by fluctuations and relaxation, with discrete macroscopic states arising only under specific dynamical constraints. Here, we report the emergence…
We study the dynamics of a viscoelastic medium driven through quenched disorder by expanding about mean field theory in $6-\epsilon$ dimensions. The model exhibits a critical point separating a region where the dynamics is hysteretic with a…
The time evolution of the magnetization of a magnetic molecular crystal is obtained in an external time-dependent magnetic field, with sweep rates in the kT/s range. We present the 'exact numerical' solution of the time dependent…