Pushchino, Moscow, Russian Federation
The nonlinear conformation distortions - kinks, which are locally unwound regions of the DNA double helix, play an important role in the processes of transcription, replication and denaturation. In the “nonrelativistic” approximation, the DNA kinks can be considered as quasiparticles with a certain mass, velocity, and rest energy. If not one, but N kinks are formed in the DNA molecule, then it is legitimate to raise the question of the statistics of an ensemble of N DNA kinks. The statistical properties of the ensemble are still poorly understood. In this paper, we consider the question of the statistics of an ensemble of kinks activated in the plasmid pTTQ18. The ideal gas approximation is used to calculate the thermodynamic potentials. Analytical formulas for the partition function, free energy, and entropy in the parameters of the plasmid are presented. The temperature dependence graphs of these characteristics are constructed. It is shown that with increasing temperature the free energy of the kink ensemble decreases, and the average energy and entropy increase, and in the same given temperature range, the increase in entropy is quite noticeable, and the average energy increases very slowly. The calculations show that the heat capacity of the kink ensemble does not depend either on temperature or on the type of sequence, and the kink velocity distribution function has the shape of a bell, the height of which reaches a maximum at zero kink velocity.
plasmid pTTQ18, DNA kinks, statistics of the ensemble of kinks, statistical sum, free energy, entropy
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