Related papers: Nonlinear dynamics of damped DNA systems with long…
In this communication, we examine a nonlinear model with an impurity emulating a bend. We justify the geometric interpretation of the model and connect it with earlier work on models including geometric effects. We focus on both the…
We develop a contact-geometric framework for dissipative nonlinear field theories by extending the least constraint theorem to complex fields and establishing a rigorous link with probability measures. The Complex Ginzburg-Landau Equation…
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…
Allosteric interactions between molecules bound to DNA at distant locations have been known for a long time. The phenomenon has been studied via experiments and numerical simulations, but a comprehensive understanding grounded in a theory…
The discrete complex Ginzburg-Landau equation is a fundamental model for the dynamics of nonlinear lattices incorporating competitive dissipation and energy gain effects. Such mechanisms are of particular importance for the study of…
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…
We investigate the properties of discrete breathers in a Bose-Einstein condensate with two- and three-body interactions in optical lattice. In the tight-binding approximation the Gross-Pitaevskii equation with periodic potential for the…
We consider the dissipative dynamics of a qubit coupled to a nonlinear oscillator (NO) embedded in an Ohmic environment. By treating the nonlinearity up to first order and applying Van Vleck perturbation theory up to second order in the…
We analyze the formation and dynamics of bright unstaggered solitons in the disk-shaped dipolar Bose-Einstein condensate, which features the interplay of contact (collisional) and long-range dipole-dipole (DD) interactions between atoms.…
We study the unexpected high flexibility of short dsDNA which recently has been reported by a number of experiments. Via the Langevin dynamics simulation of our Breathing DNA model, first we observe the formation of bubbles within the…
Nucleic acids have been regarded as stiff polymers with long-range flexibility and generally modeled using elastic rod models of polymer physics. Notwithstanding, investigations carried out over the past few years on single fragments of…
We numerically investigate the dynamics and linear rheology of disordered systems made of patchy particles, focussing on the role of valence, temperature and bonding mechanism. We demonstrate that the dynamics is enslaved to bonding, giving…
Negatively charged DNA can be compacted by positively charged dendrimers and the degree of compaction is a delicate balance between the strength of the electrostatic interaction and the elasticity of DNA. We report various elastic…
We investigate the nonlinear Bloch dynamics and Landau-Zener tunneling of quantum droplets in optical lattices, where the interplay between mean-field repulsion and beyond-mean-field attraction from Lee-Huang-Yang corrections introduces a…
We study the stability of a stationary discrete breather (DB) on a nonlinear trimer in the framework of the discrete nonlinear Schr\"odinger equation (DNLS). In previous theoretical investigations of the dynamics of Bose-Einstein…
We revisit the effect of non-linear Landau (NL) damping on the electrostatic instability of blazar-induced pair beams, using a realistic pair-beam distribution. We employ a simplified 2D model in ${\bf k}$-space to study the evolution of…
The mechanical properties of DNA are typically described by elastic theories with purely local couplings (on-site models). We discuss and analyze coarse-grained (oxDNA) and all-atom simulations, which indicate that in DNA distal sites are…
Two models for energy and charge transport and storage in biomolecules are considered. A model based on the discrete nonlinear Schrodinger equation with long-range dispersive interactions (LRI's) between base pairs of DNA is offered for the…
The paper uses mesoscopic, non-linear lattice dynamics based (Peyrard-Bishop-Dauxois, PBD) modeling to describe thermal properties of DNA below and near the denaturation temperature. Computationally efficient notation is introduced for the…
We study the nonequilibrium dynamics of a many-body bosonic system on a lattice, subject to driving and dissipation. The time-evolution is described by a master equation, which we treat within a generalized Gutzwiller mean field…