Related papers: Abstract DNA-type systems
It has been observed that certain classical chains admit topologically protected zero-energy modes that are localized on the boundaries. The static features of such localized modes are captured by linearized equations of motion, but the…
Discrete-state stochastic models are a popular approach to describe the inherent stochasticity of gene expression in single cells. The analysis of such models is hindered by the fact that the underlying discrete state space is extremely…
DNA torsion dynamics is essential in the transcription process; a simple model for it, in reasonable agreement with experimental observations, has been proposed by Yakushevich (Y) and developed by several authors; in this, the DNA subunits…
Kaup-Newell soliton hierarchy is derived from a kind of Lax pairs different from the original ones. Binary nonlinearization procedure corresponding to the Bargmann symmetry constraint is carried out for those Lax pairs. The proposed Lax…
In complex systems, the interplay between nonlinear and stochastic dynamics, e.g., J. Monod's necessity and chance, gives rise to an evolutionary process in Darwinian sense, in terms of discrete jumps among attractors, with punctuated…
The denaturation of the double helix is a template for fundamental biological functions such as replication and transcription involving the formation of local fluctuational openings. The denaturation transition is studied for heterogeneous…
A polarizable environment, prominently the solvent, responds to electronic changes in biomolecules rapidly. The knowledge of conformational relaxation of the biomolecule itself, however, may be scarce or missing. In this work, we describe…
Anomalous non-exponential relaxation in hydrated biomolecules is commonly attributed to the complexity of the free-energy landscapes, similarly to polymers and glasses. It was found recently that the hydrogen-bond breathing of terminal DNA…
A common technique to verify complex logic specifications for dynamical systems is the construction of symbolic abstractions: simpler, finite-state models whose behaviour mimics the one of the systems of interest. Typically, abstractions…
We investigate the nonlinear dynamics of the Peyrard-Bishop DNA model taking into account site dependent inhomogeneities. By means of the multiple-scale expansion in the semi-discrete approximation, the dynamics is governed by the perturbed…
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…
We introduce a simple model for DNA-cationic-lipid complexes in which galleries between planar bilayer lipid lamellae contain DNA 2D smectic lattices that couple orientationally and positionally to lattices in neighboring galleries. We…
An abstract Newton-like equation on a general Lie algebra is introduced such that orbits of the Lie-group action are attracting set. This equation generates the nonlinear dynamical system satisfied by the group parameters having an…
An abstract network approach is proposed for the description of the dynamics in reactive processes. The phase space of the variables (concentrations in reactive systems) is partitioned into a finite number of segments, which constitute the…
A kind of Bargmann symmetry constraints involving Lax pairs and adjoint Lax pairs is proposed for soliton hierarchy. The Lax pairs and adjoint Lax pairs are nonlinearized into a hierarchy of commutative finite dimensional integrable…
This short note considers varieties of the form $G\times S_{\text{reg}}$, where $G$ is a complex semisimple group and $S_{\text{reg}}$ is a regular Slodowy slice in the Lie algebra of $G$. Such varieties arise naturally in hyperk\"ahler…
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…
The algebraic geometric approach to $N$-component systems of nonlinear integrable PDE's is used to obtain and analyze explicit solutions of the coupled KdV and Dym equations. Detailed analysis of soliton fission, kink to anti-kink…
An overview is given of basic models combining discreteness in their linear parts (i.e. the models are built as dynamical lattices) and nonlinearity acting at sites of the lattices or between the sites. The considered systems include the…
The concept of soliton complex in a nonlinear dispersive medium is proposed. It is shown that strongly interacting identical topological solitons in the medium can form bound soliton complexes which move without radiation. This phenomenon…