Related papers: Abstract DNA-type systems
We propose a formalism for describing two-strand systems of a DNA type by means of soliton von Neumann equations, and illustrate how it works on a simple example exactly solvably by a Darboux transformation. The main idea behind the…
Dynamics of topological solitons describing open states in the DNA double helix are studied in the frameworks of the model which takes into account asymmetry of the helix. It is shown that three types of topological solitons can occur in…
We propose a model for DNA dynamics by introducing the helical structure through twist deformation in analogy with the structure of helimagnet and cholesteric liquid crystal system. The dynamics in this case is found to be governed by the…
In order to solve a system of nonlinear rate equations one can try to use some soliton methods. The procedure involves three steps: (1) Find a `Lax representation' where all the kinetic variables are combined into a single matrix $\rho$,…
Lax pairs with operator valued coefficients, which are explicitly connected by means of an additional condition, are considered. This condition is proved to be covariant with respect to the Darboux transformation of a general form.…
A couple of models are explained. Helicoidal PB model is studied in more details. It is shown that semi-discrete approximation yields to breather-type soliton moving along the chain. The model can explain local opening as a resonance mode.…
Generalized Euler-Arnold-von Neumann density matrix equations can be solved by a binary Darboux transformation given here in a new form: $\rho[1]=e^{P\ln(\mu/\nu)}\rho e^{-P\ln(\mu/\nu)}$ where $P=P^2$ is explicitly constructed in terms of…
We present a unified operator-theoretic framework for constructing deterministic KdV soliton gases and step-type KdV solutions. Starting from Dyson's determinantal formula, we obtain a broad class of reflectionless solutions and describe…
We study the nonlinear dynamics of a protein-DNA molecular system by treating DNA as a set of two coupled linear chains and protein in the form of a single linear chain sliding along the DNA at the physiological temperature in a viscous…
We study nonlinear dynamics of a periodic inhomogeneous DNA double helical chain under dynamic plane-base rotator model by considering angular rotation of bases in a plane normal to the helical axis. The dynamics is governed by a perturbed…
This work is devoted to the establishment of a Poisson structure for a format of equations known as Generalized Lotka-Volterra systems. These equations, which include the classical Lotka-Volterra systems as a particular case, have been…
In the frameworks of algebraic topology {\alpha}-helix and different DNA-conformations are determined as the local latticed packing, confined by peculiar minimal surfaces which are similar to helicoids. These structures are defined by…
In this paper an effective integrable non-linear model describing the electron spin dynamics in a deformable helical molecule with weak spin-orbit coupling is presented. Non-linearity arises from the electron-lattice interaction and it…
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 introduce the notion of a real form of a Hamiltonian dynamical system in analogy with the notion of real forms for simple Lie algebras. This is done by restricting the complexified initial dynamical system to the fixed point set of a…
We present a stochastic, time-discrete boolean model which mimics the mesoscopic dynamics of the desorption reactions $A+A\to A+S$ and $A+A\to S+S$ in a 1D lattice. In the continuous-time limit, we derive a hierarchy of dynamical equations…
We present the results of our numerical analysis of a "composite" model of DNA which generalizes a well-known elementary torsional model of Yakushevich by allowing bases to move independently from the backbone. The model shares with the…
The Yakushevich (Y) model provides a very simple pictures of DNA torsion dynamics, yet yields remarkably correct predictions on certain physical characteristics of the dynamics. In the standard Y model, the interaction between bases of a…
We study the nonlinear dynamics of a completely inhomogeneous DNA chain which is governed by a perturbed sine-Gordon equation. A multiple scale perturbation analysis provides perturbed kink-antikink solitons to represent open state…
Macroscopic dynamics of soliton gases can be analytically described by the thermodynamic limit of the Whitham equations, yielding an integro-differential kinetic equation for the density of states. Under a delta-functional ansatz, the…