Joseph Brizar Okaly

DNA damage is due to any change that introduces a deviation from the usual double-helical structure. At this state, the study of the motion of DNA molecules requires novel dynamical models. We propose a discrete model to describe the nonlinear dynamics DNA molecule with inharmonic potential. We consider two physical situations, the ideal or homogeneous state, and the inhomogeneous or damage state. The problem of the homogeneous (normal) case with ANHP was considered in the literature, but the dynamics of DNA molecules were not inspected. Here, our objective is to distinguish between the dynamics of DNA in the normal and damaged states. The novelty of the present work stems from a conjuncture that the DNA state can be depicted from the dynamics of the molecules. The unified and extended unified methods are used to find the exact solutions of the systems in both cases, respectively. Numerically, it is found that, in the ideal case, the motion of DNA molecules is periodic and stable. Considering the inhomogeneous case due to damage, the small or moderate values of the backbone rigidity make the motion of the molecule periodic and stable, but for high values, the motion becomes aperiodic and unstable. But for small or moderate values of the backbone rigidity, the motion becomes periodic and stable. These results are of interest in vulgarizing the physical properties of DNA molecules.

Upon the Joyeux-Buyukdagli model of DNA, the helicoidal interactions are introduced, and their effects on the dynamical behaviors of the molecule investigated. A theoretical framework for the analysis is presented in an external force field, taking into account Stokes and hydrodynamics viscous forces. In the semi-discrete approximation, the dynamics of the molecule is found governed by the cubic complex Ginzburg-Landau (CGL) equation. By choosing an appropriate decoupling ansatz, the cubic CGL equation is transformed into a nonlinear differential equation whose analytical solitary wave-like solutions can be explored by means of the direct method, which is more tractable in case where the form of soliton solutions is known. Based on this, a dissipative bright-like soliton solution is obtained. Numerical experiments have been done, and relevant results were brought out, such as the quantitative and qualitative influences of the helical interactions on the parameters of the traveling bubble. The important role-played by these interactions in the DNA biological processes is brought out, showing that depending on the wave number, their effects can increase, decrease, or keep constant the bubble angular frequency, velocity, amplitude, and width, as well as the energy involved by enzymes in the initiation of DNA biological processes. This can prevent some coding or reading errors and resulting genetic damages. Analytical predictions and numerical experiments were in good agreement.

Transport memory effects on nonlinear wave propagation are addressed in a damped Peyrard-Bishop-Dauxois model of DNA dynamics. Under the continuum and overdamped limits, the multiple-scale expansion method is employed to show that an open-state configuration of the DNA molecule is described by a complex nonlinear Schrödinger equation. For the latter, solutions are proposed as bright solitons, which suitably represent the open-state configuration that takes place along the DNA molecule in the form of bubbles. A good agreement between numerical experiments and analytical predictions on the impact of memory effects on the angular frequency, velocity, width, and amplitude of the moving bubble is obtained. It also appears that memory effects can modify qualitatively and quantitatively the nonlinear dynamics of DNA, including the energy brought by enzymes for the initiation of the processes of replication and transcription.

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 nonlinear Schrodinger equation. We carry out a multiple-scale soliton perturbation analysis to find the effects of the variety of nonlinear inhomogeneities on the breatherlike soliton solution. During the crossing of the inhomogeneities, the coherent structure of the soliton is found stable. The global shape of the inhomogeneous molecule is merged with the shape of the homogeneous molecule. However, the velocity, the wavenumber and the angular frequency undergo a time-dependent correction that is proportional to initial width of the soliton and depends on the nature of the inhomogeneities.

We investigate the nonlinear dynamics of a damped Peyrard-Bishop DNA model taking into account long-range interactions with distance dependence |l|^-s on the elastic coupling constant between different DNA base pairs. Considering both Stokes and long-range hydrodynamical damping forces, we use the discrete difference operator technique and show in the short wavelength modes that the lattice equation can be governed by the complex Ginzburg-Landau equation. We found analytically that the technique leads to the correct expression for the breather soliton parameters. We found that the viscosity makes the amplitude of the breather to damp out. We compare the approximate analytic results with numerical simulations for the value s = 3 (dipole-dipole interactions).