Related papers: Two-state dynamics for replicating two-strand syst…
We study numerically the mechanical stability and elasticity properties of duplex DNA molecules within the frame of a network model incorporating microscopic degrees of freedom related with the arrangement of the base pairs. We pay special…
The von Neumann equation with delta self-interaction kernel serves as a statistical model for nonlinear waves, and it exhibits a bifurcation between stable and unstable regimes. In oceanography it is known as the Alber equation, and its…
The paper develops a second-order time-domain moment matching framework for the structure-preserving model reduction of second-order dynamical systems of high dimension, avoiding the first-order double-sized equivalent system. The moments…
The two-dimensional generalization of the Polyelectolite model of DNA is proposed. It is reduced to the boundary problem for nonlinear completely integrable equation $\sh$-Gordon. In the linearisible version the exact solution is…
This paper aims at a comprehensive understanding on the novel elastic property of double-stranded DNA (dsDNA) discovered very recently through single-molecule manipulation techniques. A general elastic model for double-stranded biopolymers…
The general approach to chain equations derivation for the function generated by a Miura transformation analog is developing to account evolution (second Lax equation) and illustrated for Sturm-Liouville differential and difference…
An integrable system of two-component nonlinear Ablowitz-Ladik (AL) equations is used to construct complex rogue-wave (RW) solutions in an explicit form. First, the modulational instability of continuous waves is studied in the system.…
A prototypical example of a rogue wave structure in a two-dimensional model is presented in the context of the Davey-Stewartson~II (DS~II) equation arising in water waves. The analytical methodology involves a Taylor expansion of an…
The mechanical properties of molecules are today captured by single molecule manipulation experiments, so that polymer features are tested at a nanometric scale. Yet devising mathematical models to get further insight beyond the commonly…
We prove that second-order hyperbolic Monge-Ampere equations for one function of two variables are connected to the wave equation by a Backlund transformation if and only if they are integrable by the method of Darboux at second order. One…
We propose a lattice model, in both one- and multidimensional versions, which may give rise to matching conditions necessary for the generation of solitons through the second-harmonic generation. The model describes an array of linearly…
In many stochastic models, the observables of interest are naturally encoded in double transforms (e.g., Laplace transforms) that couple spatial and temporal variables. Notably, the double transform often provides the only analytically…
A method is proposed to transform any analytic solution of the Bloch equation into an analytic solution of the Landau-Lifshitz-Gilbert equation. This allows for the analytical description of the dynamics of a two level system with damping.…
We consider systems of particles coupled with fluids. The particles are described by the evolution of their density, and the fluid is described by the Navier-Stokes equations. The particles add stress to the fluid and the fluid carries and…
Replication and transcription are two important processes in living systems. To execute such processes, various proteins work far away from equilibrium in a staggered way. Motivated by this, aspects of hysteresis during unzipping of DNA…
A simplified model is introduced and analysed to show, that for the Landau-Lifshitz equation stable, steady state solutions of domain type exist in ferromagnetic systems, strongly driven by external transverse fields. These dynamic domain…
We discuss two methods of an exact stochastic representation of the non-Markovian quantum dynamics of open systems. The first method employs a pair of stochastic product vectors in the total system's state space, while the second method…
We investigate the computing power of a restricted class of DNA strand displacement structures: those that are made of double strands with nicks (interruptions) in the top strand. To preserve this structural invariant, we impose…
A mechanism of double strand breaking (DSB) in DNA due to the action of two electrons is considered. These are the electrons produced in the vicinity of DNA molecules due to ionization of water molecules with a consecutive emission of two…
Rarefactive waves and dispersive shock waves are generated from the step-like initial data in many nonlinear evolution equations including the classical example of the Korteweg-de Vries (KdV) equation. When a solitary wave is injected on…