Institute of Mathematical Problems of Biology RAS, Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Pushchino, Russia

Abstract. A modified Peyrard-Bishop-Dauxios model with non-local nature of the inter-site potential was studied in a collisional thermostat with a Maxwell velocity distribution of short-lived virtual particles at a temperature of 310 K. Introduction of non-locality to the inter-site potential was found to reduce significantly the equilibrium constants for the denaturation bubble formation reaction. This property improves the agreement of calculated data with experiments. The effect is especially pronounced for large bubbles. The end effects in the new version of the model are investigated. The significant contribution of entropy and the important role of the processes of transfer and localization of mechanical energy at the end sections of DNA are shown.

Key words: DNA, Peyrard-Bishop-Dauxois model, collisional thermostat, denaturation bubble, end effects, nucleation.