Theoretical and computational studies on the structure and binding processes between biomolecules in solution and at interfaces

In this PhD thesis the main results of theoretical and computational studies regarding the structure, binding processes and transport phenomena for some biomolecules are reported. All computations have been performed on the Cineca (IT) supercomputing cluster, on a local computer and on the bwHPC (DE) supercomputing cluster. Computational results have been compared with experimental data for the interpretation of the phenomena at molecular level and for prediction purposes. The experimental data performed in our research group and by our collaborators range from Infrared, Anisotropy Fluorescence, Circular Dichroism, Surface Enhanced Resonant Raman Scattering (SERRS), Atomic Force Microscopy and Langmuir-Blodgett isotherm. A wide part of the research involves the interaction of biomolecules with inorganic surfaces. The main computation techniques used are classical Molecular Dynamics (MD) simulations (at Equilibrium and Out of Equilibrium), Enhanced Sampling simulations techniques (like Umbrella sampling and Metadynamics) and Quantum Mechanics calculations with DFT method. Moreover, regarding MD simulations, a main interest of the work has been to explore the possibilities of the coarse grained representation in comparison with an all atoms description of the whole system in exam. For sake of clarity, the references are listed at the end of each chapter, except chapter 3, in which subchapters have their own references.