RESEARCH

Research interests summary

My main research interest concerns the study of the electronic, thermodynamic and structural properties of complex systems combining computational methods and advanced molecular theories.

I have active international collaborations with top-groups in the field of X-ray crystallography, NMR, Small-X-ray Scattering and Molecular Biology where the “in-silico” modeling of the experiment is used to elucidate key-steps of the reaction mechanisms and to propose nontrivial explanations of the experimental findings. 

We have developed PyMM a python package to apply the Perturbed Matrix Method. You can download it here: https://github.com/ChenGiuseppe/PyMM

Main research lines:


We studied the Src kinase conformational transitions between the open (active) and closed (inactive) state via Molecular Dynamics simulations and enhanced sampling techniques. We characterized the associated path for both Lck and c-Src and highlight the key structural-dynamical determinants of these large conformational rearrangements.  In the Figure these pathways are represented  in the protein essential space.

Coupling Molecular Dynamics simulations and electronic structure calculations via advanced molecular theories, it is possible to reconstruct the kinetics and the thermodynamics of chemical reactions in complex environments (i.e. in solution, in protein).


For example, by such an approach, we modeled the kinetics of the hydroxide-promoted hydrolysis of phosphoric diesters in solution.

Nardi, A.N.; Olivieri, A.; Amadei, A.; Salvio, R.; D’Abramo, M. Modelling Complex Bimolecular Reactions in a Condensed Phase: The Case of Phosphodiester Hydrolysis. Molecules 2023, 28, 2152. https://doi.org/10.3390/molecules28052152


For example, we model the complex temperature dependence of the fluorescence properties of Indole in aqueous solution, with results further validating the proposed relaxation scheme. This scheme is able to explain the temperature effects on the fluorescence behavior indicating the water fluctuations as the main cause of (i) the stabilization of the dark state and (ii) the increase in temperature of the kinetics of the irreversible transition towards such a state.

We extend the previously described general model for charge transfer reactions, introducing specific changes to treat the hopping between energy minima of the electronic ground state (i.e., transitions between the corresponding vibrational ground states). We applied the theoretical–computational model to the charge transfer reactions in DNA molecules which still represent a challenge for a rational full understanding of their mechanism. Results show that the presented model can provide a valid, relatively simple, approach to quantitatively study such reactions shedding light on several important aspects of the reaction mechanism.