Contact

Andrea Amadei
Research Scientist
Address:
University of Rome Tor Vergata
Rome
Email:
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Phone:
+39 0672594905

Miscellaneous Information

Miscellaneous Information:

Present position: senior Research Scientist (CHIM02-Physical Chemistry) at the Dept. of Chemistry of the University of Rome "Tor Vergata". 

Education: Ph.D in theoretical Physical Chemistry (1998 University of Groningen, NL), Degree in Molecular Biology (1992 University of Rome "La Sapienza"). 

Fellowships: Visiting Professor at the Barcelona Supercomputer Center (BSC) (Prof. M. Orozco 2008)
Post Doctoral position at the University of Rome "La Sapienza"-Dept. of Chemistry (Prof. A. Di Nola 1998-2000)
Research Fellow at the University of Groningen (NL)-Dept. of Biophysical Chemistry (Prof. H.J.C. Berendsen 1992-1997). 

Teaching: Since 2001 Dr. Amadei has been involved in didactical activity teaching Molecular Biophysics (University of Rome "Tor Vergata) and Molecular Mechanics and Dynamics (University of Rome "La Sapienza"). Presently Dr. Amadei teaches Theoretical Chemistry for the Chemistry students of the University of Rome "Tor Vergata". 

Research activity: Dr. Amadei authored more than 120 publications (mostly articles published in top international scientific journals) which often had an important scientific impact, as clearly shown by Dr. Amadei's h-index. Dr. Amadei research activity has been devoted to the theoretical-computational study of complex atomic-molecular systems (ranging from liquids and solutions to biological macromolecules) aiming to rationalize and characterize both classical and quantum mechanical processes and involving the development of original theoretical models and computational methods. Below, a brief outline of Dr. Amadei main scientific achievements is given, specifically reporting his contributions to the development of models and methods to be used in theoretical and computational chemistry. 

1) Essential Dynamics

The Essential Dynamics (ED) method is based on the use of multivariate analysis for atomic positional fluctuations as obtained by Molecular Dynamics (MD) simulations, and provides a very powerful tool to identify the "essential" degrees of freedom in biomacromolecules, i.e. those generalized internal degrees of freedom responsible of the main conformational transitions. Such an approach is now widely used as a standard method in many molecular simulation programs including its extension for enhancing MD to sample large conformational changes. The combined use of MD simulations and ED method provided valuable information on functional protein conformational transitions and efficient modelisations of peptide folding-unfolding thermodynamics and kinetics.

2) The quasi-Gaussian entropy theory

The quasi-Gaussian entropy (QGE) theory is essentially an extension of the statistical mechanical fluctuation theory, providing rigorous models for condensed phase thermodynamics. Such a theoretical approach, based on modeling the fluctuation distributions of relevant mechanical properties (e.g. the energy), proved to be very accurate and efficient for a wide range of systems (from fluid-liquid to solid) and it provided a very powerful tool to obtain, in combination with MD simulations, partial molar properties in solutions as well as to describe the thermodynamics of protein folding and solvated peptides. 

3) Molecular Dynamics with roto-translational constraints

In MD simulations of large and complex macromolecules as well as for calculations on simpler molecules embedded in a complex environment, it can be of interest to simulate the central molecule with roto-translational constraints (i.e. the equations of motions are defined within the corresponding constraints surface). Dr. Amadei developed such a procedure, showing that if the algorithm is properly made the corresponding constrained MD simulation is statistical mechanically fully consistent.

4) Perturbed Matrix Method

The Perturbed Matrix Method (PMM), based on Quantum Mechanics first principles, is a mixed quantum-classical method aimed to obtain electronic properties of a "quantum center" embedded in a complex molecular environment. This is accomplished by evaluating the coupling between the classical atomic and molecular motions, as obtained by MD simulations, with the electronic properties of interest by means of constructing the perturbed Hamiltonian matrix of the quantum system. Hence, by diagonalisation of such a matrix any perturbed quantum property is obtained as a function of time (i.e. as a function of the trajectory configuration). Such a theoretical method, which has been used to succesfully reproduce electronic and vibrational excitations of solvated molecules and chromophores in proteins, was extended for studying chemical reactions in complex systems, such as chemical reactions in liquids and biochemical reactions in proteins. 

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