Research interests
Keywords. Theoretical biophysics, structure and electronic properties of DNA and proteins, conformational flexibility and thermodynamics, charge transfer in biological systems, molecule/surface interactions, biomolecular nanostructures, protein-DNA binding, hybrid materials and bio-nano-systems, Density Functional Theory, Molecular Dynamics, Quantum Computation applied to problems in nanosciences and biology. Specific topics include:
1. Capabilities, limits, and extensions of solid-state computational tools to study biomolecules appealing for electronic applications. The investigated biomolecules are: (i) natural and modified nucleic acids; (ii) copper metalloproteins; (iii) model ?-sheet peptides on solid surfaces in a wet environment.
2. Theory of charge mobility in biomolecules: links between the solid-state-like charge transport through extended orbitals and the charge transfer between localized molecular sites (Marcus-Hush-Jortner Theory).
3. Methodological development to compute electron transfer rates in biomolecular systems within density functional theory. Application to: (i) electron exchange between two electron transfer proteins in an azurin dimer; (ii) hole exchange between two adjacent planes in stacked dimers of DNA and xDNA with different sequences.
4. Use of molecular dynamics simulations to sample the conformational effects on the electronic and optical properties of biological molecules.
5. Role of the solvent in the electronic structure and charge properties of DNAs and proteins. Investigation of a continuum solvent and discrete coordination water molecules.
6. Optical absorption and circular dichroism of chiral molecules including natural and modified DNAs.
7. DFT-based parametrization of classical force fields for modified nucleobases and for protein-surface and DNA-surface interaction.
8. DFT studies of the adsorption of organic molecules and biomolecules on metal surfaces. Different regimes of molecule-metal hybridization from chemisorption to weak interaction.
9. Molecular dynamics simulations of protein-binding DNA oligomers and of protein-DNA bound complexes.
10. Electronic structure of organic and inorganic polymers that can serve as new nanowires for electronic applications.
11. Methodological development to address excited-state transport mechanisms, as well as dispersion interactions for a suitable description of molecule-molecule and molecule-inorganic coupling.
12. Ab-initio theory and empirical modeling of hybrid metal/semiconductor interfaces and nanoparticles (nano-dumbbells).
13. Impact of quantum computation on nanosciences spanning chemistry, materials science, physics and biology.
Many of these activities include direct collaboration with experimental groups for guidance and interpretation.
Biographical sketch
PROFESSIONAL HISTORY
- Senior research staff member at CNR-NANO-S3, Modena, Italy (02/2010-).
- Senior research staff at CNR-INFM-S3, Modena, Italy (04/2009-01/2010).
- Research staff member at CNR-INFM-S3, Modena, Italy (06/2006-04/2009).
- Tenure Track Researcher at CNR-INFM-S3, Modena, Italy (01/2003-05/2006).
- Fixed-term Researcher, INFM Unit of Modena, Italy (12/1999-12/2002).
- INFM postdoc, Modena, Italy (12/1997-11/1999).
- DARPA postdoc, Xerox Palo Alto Research Laboratory, CA, USA (01/1996-01/1998).
EDUCATION HISTORY
1992-1995: PhD in Physics, University of Rome “Tor Vergata”, Rome, Italy. Defense 17/10/1996.
1986-1992: BSc & MSc in Physics, University of Rome “Tor Vergata”, Summa cum Laude. Defense 10/04/1992.
VISITING STAYS
University of Southern California, Los Angeles, USA (3 weeks 05/2010, 3 months 2011, 1 year 2012, extended periods 2013-2018).
Oak Ridge National Laboratory, USA (3 weeks 09/2008).
Hebrew Univ. Of Jerusalem, Israel (1 week 07/2008, 1 week 08/2007).
University of São Paulo, Brazil (3 weeks 12/2004, 3 weeks 12/2003, 4 weeks 12/2002, 2 months 04-05/2011).
Tel Aviv Univ., Israel (1 week 11/2004).
Princeton Univ., USA (2 weeks 08-09/2003, 1 month 03-04/2002, 1 month 10/2001).
SUPERVISION & HOSTING (APPENDIX V).
- 7 PhD students
- 12 postdocs
- 5 undergraduate students
- 9 undergraduate internships
PUBLICATIONS AND TALKS
122 papers in international peer-reviewed journals. H-index (ISI) = 33.
6 book chapters and 12 proceedings/newsletters.
Selected publications
• R. D. Teo, B. J. G. Rousseau, E. R. Smithwick, R. Di Felice, D. N. Beratan, A. Migliore, “Delineating the mechanisms of DNA-mediated signaling between [4Fe4S] proteins”, Chem. 5, 1-16 (2019).
• R. Li, R. Di Felice, R. Rohs, D. Lidar, “Quantum versus classical machine learning applied to a simplified computational biology problem”, NPJ QI 4, 14 (2018).
• N. Tangprasertchai, X. Zhang, R. Di Felice, I. Slaymaker, C. Vazquez Reyes, W. Jiang, R. Rohs, P. Qin, “CRISPR-Cas9 mediated DNA unwinding detected using site-directed spin labeling”, ACS Chem. Biol. 12, 1489 (2017).
• L. Bellucci, G. Bussi, R. Di Felice, S. Corni, “Fibrillation-prone conformations of the amyloid-β-42 peptide at the gold/water interface”, Nanoscale 9, 2279 (2017).
• S. Mohn, N. Stolyarchuk, T. Markurt, R. Kirste, M. P. Hoffmann, R. Collazo, A. Courville, R. Di Felice, Z. Sitar, P. Vennéguès, M. Albrecht, “Polarity control in Group-III-Nitrides beyond Pragmatism”, Phys. Rev. Applied 5, 054004 (2016).
• W. Sun, A. Ferretti, D. Varsano, G. Brancolini, S. Corni, R. Di Felice, “Electron Transfer Rates at a Bio-Inorganic Interface”, J. Phys. Chem. C 118, 18820 (2014).
• M. Rosa, S. Corni, R. Di Felice, “Enthalpy-Entropy Tuning in the Aggregation of Nucleobases at the Au(111) Surface”, J. Chem. Theory Comput. 10, 1707 (2014).
• G. I. Livshits, A. Stern, D. Rotem, N. Borovok, G. Eidelshtein, A. Migliore, E. Penzo, S. J. Wind, R. Di Felice, S. Skourtis, J. C. Cuevas, L. Gurevich, A. B. Kotlyar, D. Porath, “Long-range charge transport in single G-quadruplex DNA molecules”, Nature Nanotech. 9, 1040 (2014).
• T. Zhou, L. Yang, Y. Lu, I. Dror, A. C. Dantas Machado, T. Ghane, R. Di Felice, R. Rohs, “DNAshape: high-throughput prediction of DNA shape on a genomic scale”, Nucl. Acids Res. 41, W56-W62 (2013).
• S. P. Hancock, T. Ghane, D. Cascio, R. Rohs, R. Di Felice, R. C. Johnson, “Control of DNA Minor Groove Width and Fis Protein Binding by the Purine 2-amino Group”, Nucl. Acids Res. 41, 6750-6760 (2013).
• A. Migliore, S. Corni, D. Varsano, M. L. Klein, R. Di Felice, “First-principles effective electronic couplings for hole transfer in natural and size-expanded DNA”, J. Phys. Chem. B 113, 9402 (2009).
• D. Varsano, L. A. Espinosa-Leal, X. Andrade, M. A. L. Marques, R. Di Felice, A. Rubio, “A gauge invariant method for molecular chiroptical properties in TDDFT”, Phys. Chem. Chem. Phys. 11, 4481 (2009).
• E. Shapir, A. Calzolari, C. Cavazzoni, D. Ryndyk, G. Cuniberti, A. B. Kotlyar R. Di Felice, and D. Porath, “Electronic structure of single DNA molecules resolved by scanning tunneling spectroscopy”, Nature Materials 7, 68 (2008).