Computational simulation of excitation transfer in DNA oligomers

In this thesis, HP6 double strand (a DNA oligomer made of adenine and thymine) excited state behaviour is studied, employing an implementation of Frenkel exciton model in a semiempirical (AM1) framework. After an initial full-MM (Tinker) and subsequent QM/MM (NewtonX) Thermalizations, spectra (both adiabatic and diabatic) are produced. In the following, excited state nonadiabatic dynamics is performed (NewtonX), allowing a collective of trajectories to decay to ground state. The results are analyzed and fluorescence decay pathways are proposed, based on excitation localization on chromophores and transfer of excitation among them.