Iuzzolino, Gabriele (2025) Photoinduced Dynamics of DNA-Protein Model Systems in Condensed Phase. [Tesi di dottorato]

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Abstract

Interaction of light with matter is a very useful tool to unveil the properties of biological system in vivo. Across the electromagnetic spectrum, biomolecules can undergo photoabsorption, stimulated and induced emission, synthesis of covalent bonds and, at higher energies, photoionization and photolysis and rearrangement. Several spectroscopic technique rely on them to study the living matter: steady state and transient optical spectroscopy, fluorescence upconversion, photoelectron and photoelectron-photoion coincidence spectroscopy. Model system have been developed to study the effect of such type of reaction on system in condensed phase and shed light on the analogous behaviour of complex biopolimers. The modeling of such system is vital for the improvement of spesctroscopic techniques; at the same time, it require advanced computational methods, able to consider the flexibility of such systems, the effect of the environment, but also investigate ultrafast time-scales and the coupling between the nuclear motion and electron dynamics. In this thesis work, we focused on two model systems of nucleic acid-protein photo-crosslinking, which are prototype systems of the experimental and computational challenges faced in the field. We accurately simulated their thermal equilibrium in liquid phase and found out that their photophysics heavily depends on the microsolvation; we simulated their ultrafast fluorescence by non-adiabatic dynamics and developed a new computational protocol compare it with low-time resolution experimental data; we efficiently simulated their photoionization and photofragmentation pathways. Finally, a new software interface was developed to perform non-adiabatic molecular dynamics with multilayered extrapolative partition schemes.

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