Animportantfunctioningmechanismofbiologicalmacromoleculesisthetransitionbetweendifferentconformedstatesduetothermalfluctuation.Inthepresentpaper,abiologicalmacromoleculeismodeledastwostrandswithsidechainsfacingeachother,anditsstochasticdynamicsincludingthestatisticsofstationarymotionandthestatisticsofconformationaltransitionisstudiedbyusingthestochasticaveragingmethodforquasiHamiltoniansystems.ThetheoreticalresultsareconfirmedwiththeresultsfromMonteCarlosimulation.
