  In this paper we suggest a theoretical method based on the statistical
mechanics for treating the alpha-helix-random coil transition in alanine
polypeptides. We consider this process as a first-order phase transition and
develop a theory which is free of model parameters and is based solely on
fundamental physical principles. It describes essential thermodynamical
properties of the system such as heat capacity, the phase transition
temperature and others from the analysis of the polypeptide potential energy
surface calculated as a function of two dihedral angles, responsible for the
polypeptide twisting. The suggested theory is general and with some
modification can be applied for the description of phase transitions in other
complex molecular systems (e.g. proteins, DNA, nanotubes, atomic clusters,
fullerenes).
