Related papers: Two-state dynamics for replicating two-strand syst…
An abstract DNA-type system is defined by a set of nonlinear kinetic equations with polynomial nonlinearities that admit soliton solutions associated with helical geometry. The set of equations allows for two different Lax representations:…
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…
In this paper we propose a systematic method to solve the inverse dynamical problem for a quantum system governed by the von Neumann equation: to find a class of Hamiltonians reproducing a prescribed time evolution of a pure or mixed state…
A new form of a binary Darboux transformation is used to generate analytical solutions of a nonlinear Liouville-von Neumann equation. General theory is illustrated by explicit examples.
The KP-II equation was derived by Kadomtsev and Petviashvili to explain stability of line solitary waves of shallow water. Using the Darboux transformations, we study linear stability of 2-line solitons whose line solitons interact…
DNA renaturation is the recombination of two complementary single strands to form a double helix. It is experimentally known that renaturation proceeds through the formation of a double stranded nucleus of several base pairs (the rate…
Complementary DNA strands in solution reliably hybridize to form stable duplexes. We study the kinetics of the hybridization process and the mechanisms by which two initially isolated strands come together to form a stable double helix. We…
The dynamical properties of double-stranded DNA are studied in the framework of the Peyrard-Bishop-Dauxois model using Langevin dynamics. Our simulations are analyzed in terms of two probability functions describing coherently localized…
We study Darboux transformations for the two boson (TB) hierarchy both in the scalar as well as in the matrix descriptions of the linear equation. While Darboux transformations have been extensively studied for integrable models based on…
We propose a dynamical model for the secondary structure of DNA, which is based on the finite stacking enthalpies used in thermodynamics calculations. In this model, the two strands can separate and the bases are allowed to rotate…
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…
The Darboux process, also known by many other names, played a very important role in some extremely enjoyable joint work that Hans and I did 25 years ago. I revisit a version of this problem in a case when scalars are replaced by matrices,…
The dynamics of the DNA denaturation is studied using the Peyrard-Bishop-Dauxois model. The denaturation rate of double stranded polymers decreases exponentially as function of length below the denaturation temperature. Above Tc, the rate…
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 $\rho$,…
A recent development in the derivation of soliton solutions for initial-boundary value problems through Darboux transformations, motivated to reconsider solutions to the nonlinear Schr\"odinger (NLS) equation on two half-lines connected via…
Using bidifferential calculus, we derive a vectorial binary Darboux transformation for an integrable matrix version of the first negative flow of the Kaup-Newell hierarchy. A reduction from the latter system to an integrable matrix version…
We develop the Darboux procedure for the case of the two-level system. In particular, it is demonstrated that one can construct the Darboux intertwining operator that does not violate the specific structure of the equations of the two-level…
The conserved densities of hydrodynamic type system in Riemann invariants satisfy a system of linear second order partial differential equations. For linear systems of this type Darboux introduced Laplace transformations, generalising the…
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…
A Darboux-type method of solving the nonlinear von Neumann equation $i\dot \rho=[H,f(\rho)]$, with functions $f(\rho)$ commuting with $\rho$, is developed. The technique is based on a representation of the nonlinear equation by a…