FEATURES OF THE POTENTIAL FIELD STRUCTURE OF THE PPF1 PLASMID AND THEIR INFLUENCE ON THE CHARACTER OF MOTION OF NONLINEAR CONFORMATIONAL PERTURBATIONS – KINKS

Abstract

In this work, mathematical modeling methods are used to study the features of the dynamics of the nonlinear conformational perturbations, kinks, in the pPF1 plasmid. The motion of kinks is considered as the motion of quasiparticles in the potential field of the plasmid. The behavior of such quasiparticles is largely determined by the type and nature of this field. To simulate the movement of the kink along the pPF1 plasmid, the McLaughlin-Scott equation was used. Using the quasi-homogeneous approximation and the block method, the energy profile of the potential field of the pPF1 plasmid was calculated and 2D kink trajectories were constructed in the region located between the genes of the Egfp and mCherry fluorescent proteins, taking into account the effects of dissipation and exposure to a constant torsion field. It was shown that there are threshold values of the torsion field, below and above which the behavior of the kink changes significantly: there is a transition from the cyclic motion of the kink inside the region located between the genes of the fluorescent proteins Egfp and mCherry to the translational motion and exit from this region. Threshold values have been estimated. It was shown that they depend on the nature of the energy profile near the region located between the genes of the fluorescent proteins Egfp and mCherry.