Estimate of the Free Energy Using Calculations of Dynamics in the Semiclassical Holstein Model
Lakhno V.D., Fialko N.S.
Institute of Mathematical Problems of Biology, Pushchino, Moscow Region, Russia
Abstract. We considered two ways of finding the free energy, using thermodynamic equilibrium characteristics, which are calculated by direct computational experiments. The results of calculations are described for homogeneous nucleotide dimers AA, GG and TT. Both of these methods yield similar results for biologically relevant temperatures.
Key words: DNA, dimer, Langevin equation, the total energy, entropy.