Bubble generation in a twisted and bent DNA-like model

Energy localization and shape transformations in semiflexible polymer rings

Shape transformations in driven and damped molecular chains are considered. Closed chains of weakly coupled molecular subunits under the action of spatially homogeneous time-periodic external field are studied. The coupling between the internal excitations and the bending degrees of freedom of the chain modifies the local bending rigidity of the chain. In the absence of driving the array takes a circular shape. When the energy pumped into the system exceeds some critical value the chain undergoes a nonequilibrium phase transition: The circular shape of the aggregate becomes unstable and the chain takes the shape of an ellipse or, in general, of a polygon. The excitation energy distribution becomes spatially nonuniform: It localizes in such places where the chain is more flat. The weak interaction of the chain with a flat surface restricts the dynamics to a flat manifold.

Long-range interactions between adjacent and distant bases in a DNA and their impact on the ribonucleic acid polymerase-DNA dynamics

When an inhomogeneous RNA-polymerase (RNAP) binds to an inhomogeneous DNA at the physiological temperature, we propose a spin-like model of DNA nonlinear dynamics with long-range interactions (LRI) between adjacent and distant base pairs to study RNAP-DNA dynamics. Using Holstein-Primakoff's representation and Glauber's coherent state representation, we show that the model equation is a completely integrable nonlinear Schrödinger equation whose dispersive coefficient depends on LRI's parameter. Inhomogeneities have introduced perturbation terms in the equation of motion of RNAP-DNA dynamics. Considering the homogeneous part of that equation, a detailed study of the solution shows that the number of base pairs which form the bubble, the height, and the width of that bubble depend on the long-range parameter. The results of the perturbation analysis show that the inhomogeneities due to the DNA and RNAP structures do not alter the velocity and amplitude of the soliton, but introduce some fluctuations in the localized region of the soliton. The events that happen in the present study may represent binding of an RNAP to a promoter site in the DNA during the transcription process.

Formation, control, and dynamics of N localized structures in the Peyrard-Bishop model

We explore in detail the creation of stable localized structures in the form of localized energy distributions that arise from general initial conditions in the Peyrard-Bishop (PB) model. By means of a method based on the inverse scattering transform we study the solutions of PB model equations obtained in the form of planar waves whose amplitudes are described by the nonlinear Schrödinger equation (NLS). For localized initial conditions different from the pure N-soliton shape, we have obtained analytical results that predict and control the number, amplitude, and velocity of the NLS solitary waves. To verify the validity of these results we have carried out numerical simulations of the PB model with the use of realistic values of parameters and the initial conditions in the form of planar waves whose modulated amplitudes are given by the examples studied in the NLS. In the simulations we have found that N localized structures arise in agreement with the prediction of the analytical results obtained in the NLS.

Dynamics of a curved Fermi-Pasta-Ulam chain: effects of geometry, long-range interaction, and nonlinear dispersion

We study the dynamics of the bent Fermi-Pasta-Ulam (FPU) chain, incorporating the complicated effects of geometry, long-range interactions, as well as nonlinear dispersion. Within the rotating wave approximation, we obtain several exact discrete breather (DB) solutions, such as the odd-parity and even-parity discrete breathers, compactlike discrete breathers and moving discrete breathers for various geometries of the chain. In presence of long-range nonlinear dispersive interactions, we show that DBs exist in the discrete curved lattice for next-nearest-neighbor interactions as well. For all neighbors interactions, we treat the problem in the long-wavelength (continuum) and weakly nonlinear limit of the system and obtain exact static breather solutions and large-amplitude, traveling kink-soliton solutions. The curved FPU chain also admits finite amplitude discrete nonlinear sinusoidal wave solutions with short commensurate as well as incommensurate wavelengths. The usefulness of these solutions for energy localization and transport in various physical systems are discussed.

The relevance of nonlinear stacking interactions in simple models of double-stranded DNA

Single molecule DNA experiments provide interesting data that allow a better understanding of the mechanical interactions between the strands and the nucleotides of this molecule. In some sense, these experiments complement the classical ones about DNA thermal denaturation. It is well known that the original Peyrard-Bishop (PB) model by means of a harmonic stacking potential and a nonlinear substrate potential has been able to predict the existence of a critical temperature of full denaturation of the molecule. In the present paper, driven by the findings of single molecule experiments, we substitute the original harmonic intra-strand stacking potential with a Duffing type potential. By elementary and analytical arguments, we show that with this choice it is possible to obtain a sharp transition in the classical domain wall solution of the PB model and the compactification of the classical solitary wave solutions of other models for the dynamics of DNA. We discuss why these solutions may improve our knowledge of the DNA dynamics in several directions.