Instructor: Spiros Skourtis
• Basics of structure and function of most important biomolecules (proteins, DNA, RNA)
• Electronic and vibrational states of molecules: The Born-Oppenheimer approximation, molecular electronic states, and potential energy surfaces. Molecular vibrational states, normal coordinates, and electron-phonon coupling. The adiabatic and diabatic representations of the molecular Hamiltonian.
• Quantum mechanics of open systems: The reduced density matrix for a system interacting with a bath. The bath correlation function. Quantum master equations. The Markov approximation and the Redfield equations for calculation of quantum transition rates within the system.
• Methods for the computation of the electronic structure of molecules: Many-electron states. The Hartree-Fock method. The density functional method. Methods based on pertrurbation theory. The configuration interaction method. Electronic structure programs
• Molecular dynamics and Monte Carlo simulations with classical force fields Molecular dynamics programs
• Applications to biomolecular systems. Charge transfer Reactions: Marcus and Levich-Dogonadze theories. Electron transfer pathways in proteins. DNA electron transfer. Proton transfer in enzymatic reactions.
• Energy transfer reactions: Relaxation and redistribution of vibrational energy in biomolecules. Exciton transfer in photosynthesis.
Assesment: Grade is based on the evaluation of the written research proposal and of its defense