Related papers: Moving breathers in a bent DNA-related model
Using molecular dynamics simulations, we have determined that the nature of dynamical heterogeneity in jammed liquids is very sensitive to short-ranged attractions. Weakly attractive systems differ little from dense hard-sphere and…
The interaction of discrete breathers with the primary lattice defects in transition metals such as vacancy, dislocation, and surface is analyzed on the example of bcc iron employing atomistic simulations. Scattering of discrete breathers…
We investigate active particles that exhibit long-range interactions only restricted by a field of view, which is characterized by an angle $\beta$. We show that constraining attractive interactions to a field of view leads to the emergence…
Existence of large-amplitude time-periodic breathers localized near a single site is proved for the discrete Klein--Gordon equation, in the case when the derivative of the on-site potential has a compact support. Breathers are obtained at…
The structure of DNA Binding Proteins enables a strong interaction with their specific target site on DNA. However, recent single molecule experiment reported that proteins can diffuse on DNA. This suggests that the interactions between…
While the thermodynamics of DNA hybridization is well understood, much less is known about the kinetics of this classic system. Filling this gap in our understanding has new urgency because DNA nanotechnology often depends critically on…
We investigate DNA breathing dynamics by suggesting and examining several different Brownian functionals associated with bubble lifetime and reactivity. Bubble dynamics is described as an overdamped random walk in the number of broken base…
We study collision processes of moving breathers with the same frequency, traveling with opposite directions within a Klein-Gordon chain of oscillators. Two types of collisions have been analyzed: symmetric and non-symmetric, head-on…
We derive the long-time dynamics of a tracer immersed in a one-dimensional active bath. In contrast to previous studies, we find that the damping and noise correlations possess long-time tails with exponents that depend on the tracer…
The translocation of structured RNA or DNA molecules through narrow pores necessitates the opening of all base pairs. Here, we study the interplay between the dynamics of translocation and base-pairing theoretically, using kinetic Monte…
We investigate the conditions under which a moving condensate may exist in a driven mass transport system. Our paradigm is a minimal mass transport model in which $n-1$ particles move simultaneously from a site containing $n>1$ particles to…
We explore the dynamics of strongly localized periodic solutions (discrete solitons, or discrete breathers) in a finite one-dimensional chain of asymmetric vibro-impact oscillators. The model involves a parabolic on-site potential with…
The behavior of mobile linkers connecting two semi-flexible charged polymers, such as polyvalent counterions connecting DNA or F-actin chains, is studied theoretically. The chain bending rigidity induces an effective repulsion between…
We analyze a model for a walker moving on a ratchet potential. This model is motivated by the properties of transport of motor proteins, like kinesin and myosin. The walker consists of two feet represented as two particles coupled…
Exact solutions for symmetric discrete breathers (DBs) are obtained in forced-damped linear chain with on-site vibro-impact constraints. The damping is related to inelastic impacts; the forcing may be chosen from broad class of periodic…
We study the parameter sensitivity of hetero-polymeric DNA within the purview of DNA breathing dynamics. The degree of correlation between the mean bubble size and the model parameters are estimated for this purpose for three different DNA…
Discrete time quantum walks are unitary maps defined on the Hilbert space of coupled two-level systems. We study the dynamics of excitations in a nonlinear discrete time quantum walk, whose fine-tuned linear counterpart has a flat band…
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 study theoretically the nonlinear interactions of vector breathers propagating on an unstable wavefield background. As a model, we use the two-component extension of the one-dimensional focusing nonlinear Schrodinger equation -- the…
We study numerically synchronization phenomena of mobile discrete breathers in dissipative nonlinear lattices periodically forced. When varying the driving intensity, the breather velocity generically locks at rational multiples of the…