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Nome: Andrea Amadei Data e luogo di nascita: 14 Gennaio 1966, Roma. Posizione attuale: Ricercatore (confermato) di Chimica Fisica (CHIM02) presso il Dipartimento di Chimica dell'Università di Roma "Tor Vergata". Studi: Dottorato di Ricerca (Ph.D.) in Chimica Fisica teorica (Università di Groningen, 1998), Laurea in Scienze Biologiche, indirizzo di Biologia Molecolare (Università di Roma "La Sapienza", 1990). Borse e contratti: Visiting Professor presso il Barcelona Supercomputer Center (BSC) (Prof. M. Orozco 2008) Post Dottorato presso l'Università di Roma "La Sapienza" Dipartimento di Chimica (Prof. A. Di Nola 1998-2000) Research Fellow e dottorando presso l'Università di Groningen (NL)-Dipartimento di Chimica Fisica Biologica (Prof. H.J.C. Berendsen 1992-1998) Attività didattica: a partire dal 2001 il Dr. Amadei ha svolto attività didattica insegnando Biofisica Molecolare (Università di Roma "Tor Vergata") e Meccanica e Dinamica Molecolare (Università di Roma "La Sapienza"). Attualmente il Dr. Amadei insegna Chimica Teorica per gli studenti di chimica dell'Università di Roma "Tor Vergata". Attività di ricerca: Il Dr. Amadei è autore di oltre 110 publicazioni (in massima parte articoli su importanti riviste scientifiche internazionali) che spesso hanno avuto un forte impatto scientifico. L'attività scientifica del Dr Amadei è dedicata allo studio teorico-computazionale dei sistemi molecolari complessi (dai liquidi alle macromolecole biologiche) finalizzato alla razionalizzazione e caratterizzazione dei processi classici e quantistici, coinvolgendo lo sviluppo di modelli teorici e metodi computazionali originali. Di seguito sono brevemente riassunti i principali risultati ottenuti dal Dr. Amadei, riportando specificamente i suoi contributi allo sviluppo di modelli e metodi per la chimica teorica e computazionale. 1) Dinamica Essenziale Il metodo della Dinamica Essenziale (ED) si basa su l'uso dell'analisi multivariata delle fluttuazioni posizionali atomiche ottenute dalle simulazioni di Dinamica Molecolare e fornisce un mezzo molto efficace per identificare i gradi di liberta' "essenziali" nelle macromolecole biologiche, ovvero quelle coordinate generalizzate interne responsabili delle transizioni conformazionali principali. Tale metodo ha fornito importanti informazioni sulle transizioni conformazionali biologicamente significative e recentemente ha reso possibile una modellizzazione quantitativa della termodinamica e cinetica di denaturazione-rinaturazione dei peptidi. 2) La teoria dell'entropia quasi-Gaussiana La teoria dell'entropia quasi-Gaussiana (QGE) e' essenzialmente una estensione della teoria delle fluttuazioni di Meccanica Statistica, in grado di fornire dei modelli rigorosi per la termodinamica dello stato condensato. Tale approccio teorico, basato sulla modellizzazione delle distribuzioni di probabilità per le fluttuazioni di proprietà meccaniche significative (per esempio l'energia), si e' dimostrato molto accurato ed efficiente per lo studio di una grande varietà di sistemi (in stato fluido-liquido e solido), fornendo uno strumento davvero potente, in combinazione con la Dinamica Molecolare, per ottenere le proprietà molari parziali in soluzione come per descrivere la termodinamica di proteine e peptidi. 3) Dinamica Molecolare in presenza di vincoli di roto-traslazione Nelle simulazioni di Dinamica Molecolare di macromolecole come per effettuare calcoli su molecole più semplici immerse in ambienti complessi, può essere importante simulare la molecola centrale (di solito il soluto) in presenza di vincoli (ideali) per le roto-traslazioni (ovvero le equazioni del moto sono definite sulla superficie di vincolo). Il Dr. Amadei ha sviluppato una tale procedura mostrando che se l'algoritmo e' correttamente implementato la traiettoria di Dinamica Molecolare ottenuta in presenza dei vincoli e' pienamente consistente dal punta di vista meccanico statistico. 4) Il Metodo della Matrice Perturbata} Il Metodo della Matrice Perturbata (PMM), basato su i principi primi della Meccanica Quantistica, e' una metodologia mista classico-quantistica finalizzata alla valutazione delle proprietà elettroniche di un centro quantistico immerso in un ambiente molecolare complesso. Ciò e' reso possibile attraverso la descrizione esplicita dell'accoppiamento tra i moti atomici e molecolari classici, ottenuti dalla Dinamica Molecolare, con le proprietà elettroniche di interesse per mezzo della matrice Hamiltoniana perturbata del sistema quantistico considerato. Attraverso la diagonalizzazione della matrice Hamiltoniana si possono ottenere tutte le proprietà quantistiche del sistema interagente in funzione del tempo (ovvero in funzione delle configurazioni fornite dalla traiettoria di Dinamica Molecolare). Tale metodologia teorica, usata con successo per riprodurre le eccitazioni elettroniche e vibrazionali di molecole in soluzione e cromofori in proteine, e' stata estesa per lo studio delle reazioni chimiche in sistemi complessi come le reazioni nei liquidi e in proteina

Name: Andrea Amadei Date and place of birth: 14th of January 1966, Rome Italy. Present position: senior Research Scientist (CHIM02-Physical Chemistry) at the Dep. 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 (A. Di Nola 1998-2000) Research Fellow and Ph.D student at the University of Groningen (NL)-Dept. of Biophysical Chemistry (H.J.C. Berendsen 1992-1998). 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 110 publications (mostly articles published in top international scientific journals) which often had an important scientific impact. 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 recently an efficient modelization 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 diagonalization 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.

a:91:{i:0;a:14:{s:9:"citazione";s:239:"Daidone, I., Amadei, A., Aschi, M., & Zanetti-Polzi, L. (2018). On the nature of solvatochromic effect: The riboflavin absorption spectrum as a case study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY, 192, 451-457.";s:4:"data";s:4:"2018";s:2:"id";s:20:"PUBBLICAZIONE_331474";s:6:"handle";s:11:"2108/198639";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";s:87:"Absorption spectrum; Molecular dynamics; Quantum chemistry; Riboflavin; Solvatochromism";s:9:"metadata3";s:32:"Settore CHIM/02 - Chimica Fisica";s:9:"metadata4";s:935:"We present here the calculation of the absorption spectrum of riboflavin in acetonitrile and dimethyl sulfoxide using a hybrid quantum/classical approach, namely the perturbed matrix method, based on quantum mechanical calculations and molecular dynamics simulations. The calculated spectra are compared to the absorption spectrum of riboflavin previously calculated in water and to the experimental spectra obtained in all three solvents. The experimentally observed variations in the absorption spectra upon change of the solvent environment are well reproduced by the calculated spectra. In addition, the nature of the excited states of riboflavin interacting with different solvents is investigated, showing that environment effects determine a recombination of the gas-phase electronic states and that such a recombination is strongly affected by the polarity of the solvent inducing significant changes in the absorption spectra.";s:9:"metadata5";s:90:"On the nature of solvatochromic effect: The riboflavin absorption spectrum as a case study";s:9:"metadata6";s:49:"Daidone, I; Amadei, A; Aschi, M; Zanetti-Polzi, L";s:9:"metadata7";s:25:"10.1016/j.saa.2017.11.031";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:1;a:14:{s:9:"citazione";s:197:"Daidone, I., Amadei, A., Del Galdo, S., & D’Abramo, M. (2018). Density discriminates between thermophilic and mesophilic proteins. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 36(12), 3265-3273.";s:4:"data";s:4:"2018";s:2:"id";s:20:"PUBBLICAZIONE_335045";s:6:"handle";s:11:"2108/201624";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";N;s:9:"metadata3";s:32:"Settore CHIM/02 - Chimica Fisica";s:9:"metadata4";s:799:"Despite an intense interest and a remarkable number of studies on the subject, the relationships between thermostability and (primary, secondary and tertiary) structure of proteins are still not fully understood. Here, comparing the protein density - defined by the ratio between the residue number and protein excluded volume - for a set of thermophilic/mesophilic pairs, we provide evidence that this property is connected to the optimal growth temperature. In particular, our results indicate that thermophilic proteins have - in general - a lower density with respect to the mesophilic counterparts, being such a correlation more pronounced for optimal growth temperature differences greater than 40°C. The effect of the protein thermostability changes on the molecular shape is also presented.";s:9:"metadata5";s:66:"Density discriminates between thermophilic and mesophilic proteins";s:9:"metadata6";s:50:"Daidone, I; Amadei, A; Del Galdo, S; D’Abramo, M";s:9:"metadata7";s:29:"10.1080/07391102.2017.1385537";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:2;a:14:{s:9:"citazione";s:248:"Carrillo-Parramon, O., Del Galdo, S., Aschi, M., Mancini, G., Amadei, A., & Barone, V. (2017). Flexible and Comprehensive Implementation of MD-PMM Approach in a General and Robust Code. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 13(11), 5506-5514.";s:4:"data";s:4:"2017";s:2:"id";s:20:"PUBBLICAZIONE_335043";s:6:"handle";s:11:"2108/201622";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";N;s:9:"metadata3";s:32:"Settore CHIM/02 - Chimica Fisica";s:9:"metadata4";s:975:"The Perturbed Matrix Method (PMM) approach to be used in combination with Molecular Dynamics (MD) trajectories (MD-PMM) has been recoded from scratch, improved in several aspects, and implemented in the Gaussian suite of programs for allowing a user-friendly and yet flexible tool to estimate quantum chemistry observables in complex systems in condensed phases. Particular attention has been devoted to a description of rigid and flexible quantum centers together with powerful essential dynamics and clustering approaches. The default implementation is fully black-box and does not require any external action concerning both MD and PMM sections. At the same time, fine-tuning of different parameters and use of external data are allowed in all the steps of the procedure. Two specific systems (Tyrosine and Uridine) have been reinvestigated with the new version of the code in order to validate the implementation, check the performances, and illustrate some new features.";s:9:"metadata5";s:89:"Flexible and Comprehensive Implementation of MD-PMM Approach in a General and Robust Code";s:9:"metadata6";s:78:"Carrillo-Parramon, O; Del Galdo, S; Aschi, M; Mancini, G; Amadei, A; Barone, V";s:9:"metadata7";s:24:"10.1021/acs.jctc.7b00341";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:3;a:14:{s:9:"citazione";s:259:"Zanetti-Polzi, L., Aschi, M., Amadei, A., & Daidone, I. (2017). Alternative Electron- Transfer Channels Ensure Ultrafast Deactivation of Light-Induced Ex- cited States in Riboflavin Binding Protein. THE JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 8(14), 3321-3327.";s:4:"data";s:4:"2017";s:2:"id";s:20:"PUBBLICAZIONE_335039";s:6:"handle";s:11:"2108/201618";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";N;s:9:"metadata3";s:32:"Settore CHIM/02 - Chimica Fisica";s:9:"metadata4";s:1061:"Flavoproteins, containing flavin chromophores, are enzymes capable of transferring electrons at very high speeds. The ultrafast photoinduced electron-transfer (ET) kinetics of riboflavin binding protein to the excited riboflavin was studied by femtosecond spectroscopy and found to occur within a few hundred femtoseconds [Zhong and Zewail, Proc. Natl. Acad. Sci. U.S.A.2001, 98, 11867–11872]. This ultrafast kinetics was attributed to the presence of two aromatic rings that could transfer the electron to riboflavin: the side chains of tryptophan 156 and tyrosine 75. However, the underlying ET mechanism remained unclear. Here, using a hybrid quantum mechanical–molecular dynamics approach, we perform ET dynamics simulations taking into account the motion of the protein and the solvent upon ET. This approach reveals that ET occurs via a major reaction channel involving tyrosine 75 (83%) and a minor one involving tryptophan 156 (17%). We also show that the protein environment is designed to ensure the fast quenching of the riboflavin excited state.";s:9:"metadata5";s:133:"Alternative Electron- Transfer Channels Ensure Ultrafast Deactivation of Light-Induced Ex- cited States in Riboflavin Binding Protein";s:9:"metadata6";s:49:"Zanetti-Polzi, L; Aschi, M; Amadei, A; Daidone, I";s:9:"metadata7";s:27:"10.1021/acs.jpclett.7b01575";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:4;a:14:{s:9:"citazione";s:148:"Zanetti-Polzi, L., Aschi, M., Daidone, I., & Amadei, A. (2017). Theoretical modeling of the absorption spectrum of aqueous riboflavin, 669, 119-124.";s:4:"data";s:4:"2017";s:2:"id";s:20:"PUBBLICAZIONE_335037";s:6:"handle";s:11:"2108/201616";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";N;s:9:"metadata3";s:32:"Settore CHIM/02 - Chimica Fisica";s:9:"metadata4";s:704:"In this study we report the modeling of the absorption spectrum of riboflavin in water using a hybrid quantum/classical mechanical approach, the MD-PMM methodology. By means of MD-PMM calculations, with which the effect of riboflavin internal motions and of solvent interactions on the spectroscopic properties can be explicitly taken into account, we obtain an absorption spectrum in very good agreement with the experimental spectrum. In particular, the calculated peak maxima show a consistent improvement with respect to previous computational approaches. Moreover, the calculations show that the interaction with the environment may cause a relevant recombination of the gas-phase electronic states.";s:9:"metadata5";s:69:"Theoretical modeling of the absorption spectrum of aqueous riboflavin";s:9:"metadata6";s:49:"Zanetti-Polzi, L; Aschi, M; Daidone, I; Amadei, A";s:9:"metadata7";s:28:"10.1016/j.cplett.2016.12.022";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:5;a:14:{s:9:"citazione";s:231:"Zanetti-Polzi, L., Davis, C.m., Gruebele, M., Dyer, R.b., Amadei, A., & Daidone, I. (2017). Parallel folding pathways of Fip35 WW domain explained by infrared spectra and their computer simulation. FEBS LETTERS, 591(20), 3265-3275.";s:4:"data";s:4:"2017";s:2:"id";s:20:"PUBBLICAZIONE_335041";s:6:"handle";s:11:"2108/201620";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";s:65:"fast-folding peptides; molecular dynamics simulations; β-hairpin";s:9:"metadata3";s:32:"Settore CHIM/02 - Chimica Fisica";s:9:"metadata4";s:802:"We present a calculation of the amide I' infrared (IR) spectra of the folded, unfolded, and intermediate states of the WW domain Fip35, a model system for β-sheet folding. Using an all-atom molecular dynamics simulation in which multiple folding and unfolding events take place we identify six conformational states and then apply perturbed matrix method quantum-mechanical calculations to determine their amide I' IR spectra. Our analysis focuses on two states previously identified as Fip35 folding intermediates and suggests that a three-stranded core similar to the folded state core is the main source of the spectroscopic differences between the two intermediates. In particular, we propose a hypothesis for why folding via one of these intermediates was not experimentally observed by IR T-jump";s:9:"metadata5";s:104:"Parallel folding pathways of Fip35 WW domain explained by infrared spectra and their computer simulation";s:9:"metadata6";s:73:"Zanetti-Polzi, L; Davis, Cm; Gruebele, M; Dyer, Rb; Amadei, A; Daidone, I";s:9:"metadata7";s:23:"10.1002/1873-3468.12836";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:6;a:14:{s:9:"citazione";s:155:"Besker, N., Amadei, A., & D'Abramo, M. (2014). Molecular mechanisms of activation in CDK2. 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THE JOURNAL OF CHEMICAL PHYSICS, 140(164104).";s:4:"data";s:4:"2014";s:2:"id";s:20:"PUBBLICAZIONE_195605";s:6:"handle";s:10:"2108/93249";s:9:"metadata1";s:19:"Articolo su rivista";s:9:"metadata2";N;s:9:"metadata3";s:32:"Settore CHIM/02 - Chimica Fisica";s:9:"metadata4";N;s:9:"metadata5";s:183:"Theoretical modeling of UV-Vis absorption and emission spectra in liquid state systems including vibrational and conformational effects: Explicit treatment of the vibronic transitions";s:9:"metadata6";s:32:"D'Abramo, M; Aschi, M; Amadei, A";s:9:"metadata7";s:17:"10.1063/1.4871626";s:9:"metadata8";N;s:9:"metadata9";N;s:10:"metadata10";N;}i:8;a:14:{s:9:"citazione";s:245:"Daidone, I., Amadei, A., Zaccanti, F., Borsari, M., & Bortolotti, C.A. (2014). How the Reorganization Free Energy Affects the Reduction Potential of Structurally Homologous Cytochromes. 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