Soliton propagation in homogeneous and inhomogeneous models for DNA torsion dynamics

Abstract

The existence of solitonic excitations is a generic feature of a broad class of homogeneous models for nonlinear DNA internal torsional dynamics, but many properties of solitonic propagation depend on the actual model one is considering. In this paper we perform a detailed and comparative numerical investigation of the profiles and time evolution of solitons for two different models, the Yakushevich one and the more recent "composite" model of [1], and for two different choices of the potential describing the pairing interaction between bases (harmonic and Morse potential). We consider not only homogeneous DNA chains but also inhomogeneous ones (with sequence of bases corresponding to a real organism, the Human Adenovirus 2). We show that twist solitons can propagate in inhomogeneous chains over biologically significant distances. It is also shown that stable soliton propagation is possible for inhomogeneous chains when dissipation and an external force are present. On a more general level, our results indicate that solitonic propagation can take place in highly inhomogeneous nonlinear media. © M. Cadoni, R. De Leo and S. Demelio.