Branched DNA molecules provide a challenging set of structural problems. Operationally we define branched DNA species as molecules in which double helical segments are interrupted by abrupt discontinuities, and we draw together a number of different kinds of structure in the class, including helical junctions of different orders, and base bulges (Fig. 1).

Rhodopsins are intrinsic membrane retinal-containing proteins composed of 7 hydrophobic a-helical transmembrane columns and hydrophilic sequences of various length connecting the helices and localized at N- and C-ends of the polypeptide. The chromophore (retinal) forms a Schiff base with a lysine residue in the middle part of the last a-helix. Absorption of a photon results in isomerization of retinal which gives rise to a conformational change in the protein moiety.

Nonlinear dynamics of biopolymers is a new and rapidly developing field of biophysical science. It can be considered as a part of the general dynamics which deals with the internal mobility of biopolymers. Theoreticians define it also as the next (anharmonic or nonlinear) approximation after the first harmonic or linear one.