USC.edu

Rosa Di Felice

Professor of Physics and Astronomy and Quantitative and Computational Biology
Rosa Di Felice
Pronouns She / Her / Hers Email difelice@usc.edu Office RRI 413J Office Phone (213) 740-2999

Center, Institute & Lab Affiliations

  • Rohslab, Associated Lab Member

Biography

PROFESSIONAL HISTORY

  • Associate Professor (Research) of Physics and Astronomy, University of Southern California, Los Angeles, CA, USA (9/1/2013-8/31/2015).
  • Senior CNR research staff member at the Center S3, CNR-NANO Institute, Modena, Italy (04/2009-).
  • Member of the research staff of INFM-CNR at the National Center S3 in Modena, Italy (06/2006-04/2009).
  • Tenure Track INFM Researcher, INFM National Center S3, Modena, Italy (01/2003-05/2006).
  • Fixed-term INFM Researcher, Unit of Modena, Italy (12/1999-12/2002).
  • INFM Postdoctoral Research Assistant, Department of Physics, University of Modena and Reggio Emilia, Modena, Italy (12/1997-11/1999).
  • DARPA Postdoctoral Research Assistant, Xerox Palo Alto Research Laboratory, Palo Alto, CA, USA (01/1996-01/1998).

 

EDUCATION HISTORY

  • 1992-1995: PhD in Physics, University of Rome “Tor Vergata”, Rome, Italy. Defense 17/10/1996, University of Bologna, Bologna, Italy.
  • 1986-1992: BSc & MSc in Physics, University of Rome “Tor Vergata”, Summa cum Laude. Defense 10/04/1992, University of Rome “Tor Vergata”, Rome, Italy.

 

VISITING STAYS

  • 1 year 2012: Dept. Biology, Molecular and Computational Biology section, University of Southern California, Los Angeles, CA, USA.
  • 3 months October-December 2012: Dept. Physics, University of Southern California, Los Angeles, CA, USA.
  • 3 weeks May 2010: Dept. Physics, University of Southern California, Los Angeles, CA, USA.
  • 3 weeks September 2008: CNMS at Oak Ridge National Laboratory, TN, USA.
  • 1 week July 2008: Institute of Physical Chemistry at the Hebrew University of Jerusalem (HUJI), Israel.
  • 1 week August 2007: Institute of Physical Chemistry, HUJI, Jerusalem, Israel.
  • 3 weeks December 2004 – January 2005: Department of Physics, University of São Paulo, Brazil.
  • 1 week November 2004: Tel Aviv University and Hebrew University of Jerusalem, Israel.
  • 3 weeks December 2003: Department of Physics, University of São Paulo, Brazil.
  • 2 weeks August-September 2003: Department of Chemistry, Princeton University, NJ, USA.
  • 1 month December 2002: Department of Physics, University of São Paulo, Brazil.
  • 1 month March-April 2002: Department of Chemistry, Princeton University, NJ, USA.
  • 1 month October 2001: Department of Chemistry, Princeton University, NJ, USA.
  • 2 months April-May 2001: Department of Physics, University of São Paulo, Brazil.

 

  • Research 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 (DFT), Molecular Dynamics (MD), Quantum Computation applied to problems in nanosciences.

    Detailed Statement of Research Interests

     

    Theoretical and computational physics of matter, with emphasis on ab-initio studies of biological molecules and molecules interacting with surfaces. 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 b-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. Application to DNA duplexes, triplexes, tetraplexes and duplexes with non-natural bases.

    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, with aromatic and alkylic molecules, in the diluted coverage range and in the range of self-assembled-monolayers: nucleobases/Au(111), amino-acids/Au(111), methanethiol/Au(111), pentacene/Cu(100), mercaptobenzoxazole/Cu(100), DPDI/Cu(111). 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. Free-standing polymers, interfaces with metal surfaces, and junctions with two metal electrodes. Current investigations are devoted to specific polymers MMX (metal-metal-halogen chains that coordinate various lateral organic groups) and MoSI compounds.

    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 the structure, electronic properties and optical excitations 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. 

  • Journal Article

    • Li, R., Di Felice, R., Rohs, R., Lidar, D. (2018). Quantum versus classical machine learning applied to a simplified computational biology problem. NPJ Quantum Inf.. Vol. 4, pp. 14.
    • Di Felice, R., Rosa, M., Corni, S. (2018). Adsorption mechanisms of nucleobases on the hydrated Au(111) surface. Langmuir. Vol. XXX, pp. XXX. 10.1021/acs.langmuir.8b00065
    • Di Felice, R., Bellucci, L., Bussi, G., Corni, S. (2017). Fibrillation-prone conformations of the amyloid-beta-42 peptide at the gold/water interface. Nanoscale. Vol. 9, pp. 2279.
    • Tangprasertchai, N., Di Felice, R., Zhang, X., Slaymaker, I. M., Vazquez Reyes, C., Jiang, W., Rohs, R., Qin, P. Z. (2017). CRISPR-Cas9 mediated DNA unwinding detected using site-directed spin labeling. ACS Chem. Biol.. Vol. 12, pp. 1489.
    • Zhang, X., Xu, C., Di Felice, R., Sponer, J., Islam, B., Stadlbauer, P., Ding, Y., Mao, L., Mao, Z., Qin, P. Z. (2016). Conformations of Human Telomeric G-Quadruplex Studied Using a Nucleotide-Independent Nitroxide Label. Biochemistry. Vol. 55, pp. 360-372.
    • Mohn, S., Stolyarchuk, N., Markurt, T., Kirste, R., Hoffmann, M. P., Collazo, R., Courville, A., Di Felice, R., Sitar, Z., Vennéguès, P., Albrecht, M. Polarity control in Group-III-Nitrides beyond Pragmatism. Physical Review Applied2016:054004
    • Sun, W., Varsano, D., Di Felice, R. Effect of G quadruplex topology on Electronic Transfer Integrals. Nanomaterials. Vol. 6. 2016:184
    • Di Felice, R., Rosa, M., Koch, D., Corni, S., R. Wade, R. Docking of DNA duplexes on a gold surface. Journal of Self-Assembly and Molecular Electronics 3 2015:1-18
    • Livshits, G. I., Stern, A., Rotem, D., Borovok, N., Eidelshtein, G., Migliore, A., Penzo, E., Wind, S. J., Di Felice, R., Skourtis, S. S., Cuevas, J., Gurevich, L., Kotlyar, A. B., Porath, D. (2014). Long-range charge transport in single G-quadruplex DNA molecules. Nature Nanotechnology. Vol. 9, pp. 1040.
    • Rosa, M., Corni, S., Di Felice, R. (2014). van der Waals effects at molecule-metal interfaces. Phys. Rev. B. Vol. 90, pp. 125448.
    • Sun, W., Ferretti, A., Varsano, D., Brancolini, G., Corni, S., Di Felice, R. (2014). Electron Transfer Rates at a Bio-Inorganic Interface. J. Phys. Chem. C. Vol. 118, pp. 18820.
    • Rosa, M., Corni, S., Di Felice, R. (2014). Enthalpy-Entropy Tuning in the Aggregation of Nucleobases at the Au(111) Surface. J. Chem. Theory Comput.. Vol. 10, pp. 1707.
    • Dong, R., Calzolari, A., Di Felice, R., El-Shafei, A., Hussain, M., Buongiorno Nardelli, M. (2014). Optical enhancement in heteroleptic Ru(II) isomeric dyes with extended carbazole antennas. J. Phys. Chm. C. Vol. 118, pp. 8747.
    • Ngo, V., Di Felice, R., Haas, S. (2014). Ion Selectivity and Conduction of a synthetic tetramolecular G-quadruplex. J. Phys. Chem. B. Vol. 118, pp. 864.
    • Bellucci, L., Corni, S., Di Felice, R., Paci, E. (2013). The Structure of Neuronal Calcium Sensor-1 in Solution Revealed by Molecular Dynamics Simulations. PloS ONE. Vol. 8, pp. e74383.
    • Brancolini, G., Migliore, A., Corni, S., Fuentes-Cabrera, M., Luque, F., Di Felice, R. (2013). Dynamical treatment of charge transfer through duplex nucleic acids containing modified adenines. ACS Nano. Vol. 7, pp. 9396.
    • Casalini, S., Bertoni, M., Leonardi, F., Operamolla, A., Bortolotti, C., Borsari, M., Sun, W., Di Felice, R., Corni, S., Albonetti, C., Hassan Omar, O., Farinola, G., Biscarini, F. (2013). Self-Assembly of mono-/bi-dentate oligoarylene thiols onto polycrystalline Au. Langmuir. Vol. 29, pp. 13198.
    • Rosa, M., Corni, S., Di Felice, R. (2013). Interaction of DNA bases with the Au(111) surface. J. Chem. Theo. Comput.. Vol. 9, pp. 4552.
    • Sun, W., Corni, S., Di Felice, R. (2013). Reactivity of the ZnS(1010 ) surface to small organic ligands by density functional theory. J. Phys. Chem. C. Vol. 117, pp. 16034.
    • Hancock, S. P., Ghane, T., Cascio, D., Rohs, R., Di Felice, R., Johnson, R. C. (2013). Control of DNA minor groove width and Fis protein binding by the purine 2-amino group. Nucl. Acids Res.. Vol. 41, pp. 6750-6760.
    • Zhou, T., Yang, L., Lu, Y., Dror, I., Dantas Machado, A., Ghane, T., Di Felice, R., Rohs, R. (2013). DNAshape: high-throughput prediction of DNA shape on a genomic scale. Nucl. Acids Res.. Vol. 41, pp. W56-W62.
    • Di Felice, R., Sun, W. (2012). Nature of the Interaction between Natural and Size-Expanded Guanine with Gold Clusters: A Density Functional Theory Study. J. Phys. Chem. C. Vol. 116, pp. 24954-24961.
    • Rosa, M., Corni, S., Di Felice, R. (2012). A Density Functional Theory Study of Cytosine on Au(111). J. Phys. Chem. C. Vol. 116, pp. 21366-21373.
    • Lee, M. H., Brancolini, G., Gutierrez, R., Di Felice, R., Cuniberti, G. (2012). Probing Charge Transport in Oxidatively Damaged DNA Sequences under the Influence of Structural Fluctuations. J. Phys. Chem. B. Vol. 116, pp. 10977-10985.
    • Ghane, T., Brancolini, G., Varsano, D., Di Felice, R. (2012). Optical Properties of Triplex DNA from Time-Dependent Density Functional Theory. J. Phys. Chem. B. Vol. 116, pp. 10693-10702.
    • Di Felice, R., Corni, S. (2011). Simulation of Peptide-Surface Recognition. J. Phys. Chem. Lett.. Vol. 2, pp. 1510-1519.
    • Shapir, E., Brancolini, G., Molotsky, T., Kotlyar, A. B., Di Felice, R., Porath, D. (2011). Energy Gap Reduction in DNA by Complexation with Metal Ions. Adv. Mater.. Vol. 23, pp. 4290-4294.
    • Welte, L., Calzolari, A., Di Felice, R., Zamora, F., Gomez-Herrero, J. (2010). Highly conductive self-assembled nanoribbons of coordination polymers. Nature Nanotech.. Vol. 5, pp. 110-115.
    • Shapir, E., Sagiv, L., Molotsky, T., Kotlyar, A. B., Di Felice, R., Porath, D. (2010). Electronic Structure of G4-DNA by Scanning Tunneling Spectroscopy. J. Phys. Chem. C. Vol. 114, pp. 22079-22084.
    • Iori, F., Di Felice, R., Molinari, E., Corni, S. (2009). GoIP: An Atomistic Force-Field to Describe the Interaction of Proteins With Au(111) Surfaces in Water. J. Comput. Chem.. Vol. 30, pp. 1465-1476.
    • Migliore, A., Corni, S., Varsano, D., Di Felice, R., Klein, M. L. (2009). First Principles Effective Electronic Couplings for Hole Transfer in Natural and Size-Expanded DNA. J. Phys. Chem. B. Vol. 113, pp. 9402-9415.
    • Shapir, E., Cohen, H., Calzolari, A., Cavazzoni, C., Ryndyk, D. A., Cuniberti, G., Kotlyar, A. B., Di Felice, R., Porath, D. (2008). Electronic structure of single DNA molecules resolved by transverse scanning tunnelling spectroscopy. Nature Mater.. Vol. 7, pp. 68-74.
    • Iori, F., Corni, S., Di Felice, R. (2008). Unraveling the interaction between histidine side chain and the Au(111) surface: A DFT study. J. Phys. Chem. C. Vol. 112, pp. 13540-13545.
    • Brancolini, G., Di Felice, R. (2008). Electronic Properties of Metal-Modified DNA Base Pairs. J. Phys. Chem. B. Vol. 112, pp. 14281-14290.
    • Ferretti, A., Baldacchini, C., Calzolari, A., Di Felice, R., Ruini, A., Molinari, E., Betti, M. (2007). Mixing of electronic states in pentacene adsorption on copper. Phys. Rev. Lett.. Vol. 99, pp. 046802.
    • Varsano, D., Garbesi, A., Di Felice, R. (2007). Ab initio optical absorption spectra of size-expanded xDNA base assemblies. J. Phys. Chem. B. Vol. 111, pp. 14012-14021.
    • Varsano, D., Di Felice, R., Marques, M. A., Rubio, A. (2006). A TDDFT study of the excited states of DNA bases and their assemblies. J. Phys. Chem. B. Vol. 110, pp. 7129-7138.
    • Cavallari, M., Calzolari, A., Garbesi, A., Di Felice, R. (2006). Stability and migration of metal ions in G4-wires by molecular dynamics simulations. J. Phys. Chem. B. Vol. 110, pp. 26337-26348.
    • Migliore, A., Corni, S., Di Felice, R., Molinari, E. (2006). First-principles density-functional theory calculations of electron-transfer rates in azurin dimers. J. Chem. Phys.. Vol. 124, pp. 064501.
    • Ferretti, A., Calzolari, A., Di Felice, R., Manghi, F., Caldas, M. J., Buongiorno Nardelli, M., Molinari, E. (2005). First-principles theory of correlated transport through nanojunctions. Phys. Rev. Lett.. Vol. 94, pp. 116802.
    • Di Felice, R., Bertoni, C., Pignedoli, C., Catellani, A. (2005). Hydrogen-induced surface metallization of ss-SiC(100)-(3 x 2) revisited by density functional theory calculations. Phys. Rev. Lett.. Vol. 94, pp. 116103.
    • Zhang, H., Calzolari, A., Di Felice, R. (2005). On the magnetic alignment of metal ions in a DNA-mimic double helix. J. Phys. Chem. B. Vol. 109, pp. 15345-15348.
    • Porath, D., Cuniberti, G., Di Felice, R. (2004). Charge transport in DNA-based devices. Top. Curr. Chem. Vol. 237, pp. 183-227.
    • Di Felice, R., Selloni, A., Molinari, E. (2003). DFT study of cysteine adsorption on Au(111). J. Phys. Chem. B. Vol. 107, pp. 1151-1156.
    • Calzolari, A., Di Felice, R., Molinari, E., Garbesi, A. (2002). G-quartet biomolecular nanowires. Appl. Phys. Lett.. Vol. 80, pp. 3331-3333.
    • Di Felice, R., Calzolari, A., Molinari, E., Garbesi, A. (2002). Ab initio study of model guanine assemblies: The role of pi-pi coupling and band transport. Phys. Rev. B. Vol. 65, pp. 045104.
    • Di Felice, R., Northrup, J. E. (1998). Energetics of AlN thin films on the Al2O3(0001) surface. Appl. Phys. Lett.. Vol. 73, pp. 936-938.

  • Committees

    • PhD defense, Atanu Acharya, Chemistry, 10/18/2016, 2016-2017

  • Conferences Organized

    • Chair, Charge Transfer in Biosystems, Universitätszentrum Obergurgl, Obergurgl, Austria, 07/2011
    • Chair, DNA-based Nanowires: on the Way from Biomolecules to Nanodevices, University of Modena, Italy, 10/2005

    Editorships and Editorial Boards

    • Associate Editor, Scientific Reports”, 03/2013 – 12/2020
    • Associate Editor, European Physical Journal B”, 06/2008 – 12/2020

    Reviewer for Publications

    • Nature Nanotechnology, Referee, 01/2006 – 12/2020
    • Journal of Physical Chemistry (A,B,C,Lett), Referee, 01/2004 – 12/2020
    • Journal of the American Chemical Society, Referee, 01/2004 – 12/2020
    • Nano Letters, Referee, 01/2004 – 12/2020
    • Physical Review Letters, Referee, 01/2000 – 12/2020