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The effect of sequence heterogeneity on the dynamics of molecular motors is reviewed and analyzed using a set of recently introduced lattice models. First, we review results for the influence of heterogenous tracks such as a single-strand…
The interplay between structure and dynamics in non-equilibrium steady-state is far from understood. We address this interplay by tracking Brownian Dynamics trajectories of particles in a binary colloid of opposite charges in an external…
The paper presents results of numerical experiments simulating Bloch oscillations of solitons in a deformable molecular chain in a constant electric field. By the example of a homogeneous polynucleotide chain it is shown that the system…
The nonlinear dynamics of a one-dimensional molecular crystal in the form of a chain of planar coronene molecules is analyzed. Using molecular dynamics, it is shown that a chain of coronene molecules supports acoustic solitons,…
We investigate the effect of the breaking of integrability in the integrals of motion of a sine-Gordon-like system. The class of quasi-integrable models, discussed in the literature, inherits some of the integrable properties they are…
In this short communication, we shall explore a nonlinear discrete dynamical system that naturally occurs in population systems to describe a transmission of a trait from parents to their offspring. We consider a Mendelian inheritance for a…
The approach for the description of the DNA conformational transformations on the mesoscopic scales in the frame of the double helix is presented. Due to consideration of the joint motions of DNA structural elements along the conformational…
We propose a nonlinear model derived from first principles, to describe bubble dynamics of DNA. Our model equations include a term derived from the dissipative effect of intermolecular vibrational modes. Such modes are excited by the…
We study quantum dynamics of bosonic atoms that are excited to form a phase kink, or several kinks, by an imprinting potential in a one-dimensional trap. We calculate dissipation due to quantum and thermal fluctuations in soliton…
The physical mass scales that determine the behaviour of general (simply-laced) Homogeneous Sine-Gordon models are investigated by means of a study of their finite-size effects, using the thermodynamic Bethe ansatz. These models describe…
We propose a system of sine-Gordon equations, with the $\mathcal{PT}$ symmetry represented by balanced gain and loss in them. The equations are coupled by sine-field terms and first-order derivatives. The sinusoidal coupling stems from…
The sine-Gordon equation on a metric graph with a structure represented by a $\mathcal{Y}$-junction, is considered. The model is endowed with boundary conditions at the graph-vertex of $\delta'$-interaction type, expressing continuity of…
We investigate the dynamics of solitons in generalized Klein-Gordon equations in the presence of nonlinear damping and spatiotemporal perturbations. We will present different mechanisms for soliton explosions. We show (both analytically and…
The aim of this work is to establish a linear instability result of stationary, kink and kink/anti-kink soliton profile solutions for the sine-Gordon equation on a metric graph with a structure represented by a $\mathcal Y$-junction. The…
We propose a simple phenomenological model for describing the conformational dynamics of biopolymers via the nonlinearity-induced buckling and collapse (i.e. coiling up) instabilities. Taking into account the coupling between the internal…
We address the issue of internal modes of a kink of a discrete sine-Gordon equation. The main point of the present study is to elucidate how the antisymmetric internal mode frequency dependence enters the quasicontinuum spectrum of…
We study a variant of poly-nuclear growth where the level boundaries perform continuous-time, discrete-space random walks, and study how its asymptotic behavior is affected by the presence of a columnar defect on the line. We prove that…
The influence of decoherence and bonding on the linear conductance of single double-stranded DNA molecules is examined by fitting a phenomenological statistical model developed recently (EPJB {\bf 68}, 237 (2009)) to experimental results.…
We study a model for polaron-like charge transport mechanism along DNA molecules with emphasis on the impact of parametrical and structural disorder. Our model Hamiltonian takes into account the coupling of the charge carrier to two…
A model of nonlinear elastic medium with internal structure is considered. The medium is assumed to contain cavities, microcracks or blotches of substances that differ sharply in physical properties from the base material. To describe the…