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The classic Birkhoff- von Neumann theorem states that the set of doubly stochastic matrices is the convex hull of the permutation matrices. In this paper, we study a generalisation of this theorem in the type $II_1$ setting. Namely, we…
Integrable models of resonant interaction of two or more waves in 1+1 dimensions are known to be of applicative interest in several areas. Here we consider a system of three coupled wave equations which includes as special cases the vector…
The method of Darboux transformation, which is applied on cnoidal wave solutions of the sine-Gordon equation, gives solitons moving on a cnoidal wave background. Interesting characteristics of the solution, i.e., the velocity of solitons…
The n-fold Darboux transformation (DT) is a 2\times2 matrix for the Kaup-Newell (KN) system. In this paper,each element of this matrix is expressed by a ratio of $(n+1)\times (n+1)$ determinant and $n\times n$ determinant of eigenfunctions.…
We review some recent developments in the theory of nonlinear von Neumann equations. We distinguish between the von Neumann equation (which can be nonlinear) and the Liouville equation (which should be linear). Explicit examples illustrate…
It was first suggested by Englander et al to model the nonlinear dynamics of DNA relevant to the transcription process in terms of a chain of coupled pendulums. In a related paper [q-bio.BM/0604014] we argued for the advantages of an…
A one-fold Darboux transformation between solutions of the semi-discrete massive Thirring model is derived using the Lax pair and dressing methods. This transformation is used to find the exact expressions for soliton solutions on zero and…
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 consider the statistical mechanics of a system of topologically linked polymers, such as for instance a dense solution of polymer rings. If the possible topological states of the system are distinguished using the Gauss linking number as…
We study the dynamics of two strongly-interacting fermions moving in 2D lattices under the action of a periodic electric field, both with and without a magnetic flux. Due to the interaction, these particles bind together forming a doublon.…
This paper concentrates on relationships of formal systems with biology. The paper is based on previous papers by the author. We have freely used texts of those papers where the formulations are of use, and we have extended the concepts and…
A multiscale approach is used to simulate the translocation of DNA through a nanopore. Within this scheme, the interactions of the molecule with the surrounding fluid (solvent) are explicitly taken into account. By generating polymers of…
Solitons in nonlinear optics holds a special role both in theoretical and experimental studies. Several types of evolution equations are seen to govern different situation of physical relevance. One such is the existence of both resonant…
The denaturation dynamics of a long double-stranded DNA is studied by means of a model of the Poland-Scheraga type. We note that the linking of the two strands is a locally conserved quantity, hence we introduce local updates that respect…
We study the fluctuational dynamics of a tagged base-pair in double stranded DNA. We calculate the drift force which acts on the tagged base-pair using a potential model that describes interactions at base pairs level and use it to…
Consider at a finite temperature $T$ a superfluid moving with a velocity $v$ relative to the thermal bath or its normal component. From Landau's argument there exists a critical $v_c (T)$ beyond which excitations can be spontaneously…
Polynomial dynamical systems describing interacting particles in the plane are studied. A method replacing integration of a polynomial multi--particle dynamical system by finding polynomial solutions of a partial differential equations is…
In the context of the full line Schrodinger equation, we revisit the binary Darboux transformation (double commutation method) which inserts or removes any number of positive eigenvalues embedded into the absolutely continuous spectrum…
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…
The problem of linear instability of a nonlinear traveling wave in a canonical Hamiltonian system with translational symmetry subject to superharmonic perturbations is discussed. It is shown that exchange of stability occurs when energy is…