Related papers: Nonlinear waves in double-stranded DNA
We study small-amplitude, nonlinear pulsations of uniformly and differentially rotating neutron stars employing a two-dimensional evolution code for general-relativistic hydrodynamics. Using Fourier transforms at several points inside the…
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…
Nonlinear evolution equations of the fourth order and its partial cases are derived for describing nonlinear pressure waves in a mixture liquid and gas bubbles. Influence of viscosity and heat transfer is taken into account. Exact solutions…
Granular materials are defined as collections of macroscopic dissipative particles. Although these systems are ubiquitous in our lives, the nature and the causes of their non-trivial collective dynamics still remain elusive and have…
Homogeneous nucleation of a vapor bubble from a bulk metastable phase is studied here for the first time using the multibody dissipative particle dynamics model. The van der Waals equation of state is used to define a conservative force…
We investigate the impact of nonlinear damping on the dynamics of a nanomechanical doubly clamped beam. The beam is driven into nonlinear regime and the response is measured by a displacement detector. For data analysis we introduce a…
We propose a formalism for describing two-strand systems of a DNA type by means of soliton von Neumann equations, and illustrate how it works on a simple example exactly solvably by a Darboux transformation. The main idea behind the…
Non-Markovian dynamics is studied for two interacting quibts strongly coupled to a dissipative bosonic environment. For the first time, we have derived the non-Markovian quantum state diffusion (QSD) equation for the coupled two-qubit…
We present a molecular dynamics study of the effects of carbon- and iron-ion induced shock waves in DNA duplexes in liquid water. We use the CHARMM force field implemented within the MBN Explorer simulation package to optimize and…
Long length-scale structural deformations of DNA play a central role in many biological processes including gene expression. The elastic rod model, which uses a continuum approximation, has emerged as a viable tool to model deformations of…
DNA inside the cellular environment works under a confined space. An intense research of the transcription and replication of DNA in the confined state is structurally significant to command the self assembly of DNA in a chamber or channel.…
We study the basepairing dynamics of DNA with repetitive sequences where local strand slippage can create, annihilate, and move bulge loops. Using an explicit theoretical model, we find a rich dynamical behavior as a function of an applied…
We carry out a comprehensive linear stability analysis of active Brownian particle systems around a constant homogeneous state. These scalar models, being important prototypes for the continuous description of active matter, are…
We developed a low-energy model that can be used at any time to describe the dynamics of DNA bubbles at temperatures below the melting point. The Schr\"odinger equation associated with this problem is solved in imaginary time with a quantum…
In the context of forecasting temperature and pressure fields in high-intensity focussed ultrasound, the accuracy of predictive models is critical for the safety and efficacy of treatment. In such fields inertial cavitation is often…
After crossing an initial barrier to break the first base-pair (bp) in double-stranded DNA, the disruption of further bps is characterized by free energies between less than one to a few kT. This causes the opening of intermittent…
In this article we develop an effective theory of pulse propagation in a nonlinear and disordered medium. The theory is formulated in terms of a nonlinear diffusion equation. Despite its apparent simplicity this equation describes novel…
A novel discrete model (D-model) is presented describing nonlinear wave interactions in systems with small and moderate nonlinearity under narrow frequency band excitation. It integrates in a single theoretical frame two mechanisms of…
The distribution of bubble lengths in double-stranded DNA is presented for segments of varying guanine-cytosine (GC) content, obtained with Monte Carlo simulations using the Peyrard-Bishop-Dauxois model at 310 K. An analytical description…
We consider electromagnetic nonlinear normal modes in cylindrical cavity resonators filled with a nonlinear nondispersive medium. The key feature of the analysis is that exact analytical solutions of the nonlinear field equations are…