Propagation of twist solitons in fully inhomogeneous DNA chains

In the framework of a recently introduced model of DNA torsional dynamics, we argued — on the basis of perturbative considerations — that an inhomogeneous DNA chain could support long-lived soliton-type excitations due to the peculiar geometric structure of DNA and the effect of this on nonlinear torsional dynamics. Here we consider an inhomogeneous version of this model of DNA torsional dynamics, and investigate numerically the propagation of solitons in a DNA chain with a real base sequence (corresponding to the Human Adenovirus 2); this implies inhomogeneities of up to 50% in the base masses and inter-pair interactions. We find that twist solitons propagate for considerable distances (2–10 times their diameters) before stopping due to phonon emission. Our results show that twist solitons may exist in realistic DNA chain models, and on a more general level that solitonic propagation can take place in highly inhomogeneous media. The most relevant feature for general nonlinear dynamics is that we identify the physical mechanisms allowing this behavior and thus the class of models candidate to support long-lived soliton-type excitations in the presence of significant inhomogeneities.