Topics for Thesis (First Degree in Chemistry and Advanced Degrees in Chemistry and in Pharmaceutical Chemistry and Technology)

1. Calculation of binding free energies of protein-ligand complexes targeted at designing novel compounds with augmented pharmacological power.

2. Molecular dynamics simulations of protein-DNA systems to predict their structural and functional properties.

3. Calculation of complexation constants of chemosensors for anions by using advanced simulation methods (alchemical transformations) and quantum-mechanical calculations.

4. Calculation of free energy surfaces by means of nonequilibrium computer simulations.

5. Development of methods to compute thermodynamical properties of systems in condensed phase. Possible implementation in molecular dynamics simulation programs.

6. Computational strategies for sampling the phase space by using  molecular dynamics and Monte Carlo simulations.