Education
1993: Laurea (Degree) in Physics, Università di Pisa, Italy
1993: Diploma di Licenza in Fisica, Scuola Normale Superiore, Pisa
1997: PhD in Physics, Scuola Normale Superiore
1999: Medical Physics Specialization, Università di Pisa

Career
1997 - 1999: Post-Doc felloship (INFM-SNS, Pisa)
1999 - 2000: Visiting researcher at the University of Nijmegen (NL)
2000 - 2003: research staff at NEST-INFM, Scuola Normale Superiore, Pisa
2003 - 2004: Visiting Scholar at the University of California - San Diego
2003 - 2009: scientist at NEST-CNR-INFM, Scuola Normale Superiore
2010 - present: scientist at NEST-CNR-Istituto di Nanoscienze, Scuola Normale Superiore

Research

• Modeling the Photophysics of the Intrinsically Fluorescent Proteins
  
  Molecular Modeling techniques ranging from first principle methods to Classical Molecular Dynamics, Coarse Grained models and bio-informatic methodologies are applied to the study of the photo-physics of the Intrinsically Fluorescent Proteins (IFP). Recent Results:

• Quantitative relationships between structure, vibrational and optical properties within the Green FP (GFP) mutants were discovered that can quantitatively relate measured properties (optical/vibrational) with structure
• These were used together with experimental vibrational and optical data to clarify some of the molecular mechanisms of the complex FPs photodynamics (Photoconversion, Photobleaching)
• Coarse Grained models are used to study the diffusion and aggregation dynamics of the FPs and to help the interpretation of experimental data of FRET experiments

• Modeling Macro-biomolecules
  
  Coarse Grained (CG) models are developed for the simulation of large biomolecular aggregates on the microseconds-millisecond time scale. Recent results:

• The slow dynamics of the active site opening and substrate capturein HIV-1 protease was studied, including also the effect of mutations and of crowders agents. Possible sites for allosteric inhibition of the process were revealed
• The interactions of HIV-1 integrase with HAT proteins were studied with a multi-scale approach with the aim of finding possible strategies to inhibit the viral DNA integration
• The dynamics of denaturation and supercoiling in an entire small plasmid was studied, revealing the behavior of the denaturation bubbles
• Coarse Grained and multi-scale approaches were used to study some the phases of DNA replication: the first steps of DNA unwrapping in the nucleosomes and the supercoiling and denaturation bubble formation in plasmids
• Development of CG models: improving the transferability and generality, and including CG models them in more general multi-scale schemes for molecular recognition and protein-protein interactions

• Modeling Graphene-based hydrogenated structures
  
  Graphene-based hydrogenated structures at different levels of hydrogen saturation are studied with DFT based methods to explore their electronic properties (for applications in sub-nanoelectronics) and structural/dynamical properties (for applications in hydrogen storage)

Projects and collaborations

• PRIN (2008-2010) Development of fluorescent proteins for optical nanoscopy oriented to the study of cellular dynamics - local coordinator
• NFS-CRC grant Connecting Biology with Chemistry through Multiscale Theory and Computer Simulation (2006-2011) Supervised by Gregory A Voth, Center for Biophysical Modeling and Simulation University of Utah Salt Lake City international collaborator
• Galileo Project Design of inhibitors for the hepatitis C virus protease: A theoretical, computational and experimental approach (2006) in collaboration with Alfonso Jaramillo - Ecole Polytechnique, Alessandro Pelizzola - Politecnico di Torino. Local coordinator
• NIH grant (2004 - ) supervised by J Andrew McCammon, University of California - San Diego International collaborator
• Collaboration (2003 - ) Joanna Trylska, Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University
• Collaboration (2006) Maurizio Persico, Dip di Chimica, Università di Pisa
• FISR (2002-2004) A new approach to drug design: from statistical mechanics to the screening of antiviral drugs - local coordinator
• Collaboration (2003) Anna Rita Bizzarri and Salvatore Cannistraro Biophysics and NanoScience Centre, Università della Tuscia
• Progetto Avanzato (PA - INFM, 2002-2003) Molecular dynamics of the green fluorescent proteins: An insight into the nature of the dark states - Supervisor
• Collaboration (1999-2006) Francesco Buda, Leiden University (NL)
• Collaboration (1999-2001) Annalisa Fasolino, University of Nijmegen (NL)
• Projects for accessing CINECA parallel computing facilities - supervisor
• Coarse Grained modeling of IFP-based FRET systems (2008-2009)
• One-bead coarse grained models for structural transitions in nucleic acids (2006)
• A Coarse Grained Model for Molecular Dynamics Simulations of Biomolecular Aggregates (2005)
• Photophysics of red and blue fluorescent proteins: tailoring fluorophores at the ends of the visible spectrum (2003)
• Modeling the dark states of the Green Fluorescent Proteins (2002)
• Modelling the Structure and Photodynamics of the Green Fluorescent Proteins (2001)

Previous research interest

• Post-doc research project
  Ab initio study of semiconductor III-V nano-clusters with fullerene topology

• PhD research project
• Vibrational properties of quantum solids near zero point melting:Wigner Crystal, 3He and 4He
• Defects in quantum crystals
• Vibrational properties of Alcali metals intercalates in graphite
• Fast sound in water-ice near melting
• Extensions of Density Functional Theory

• Degree and post-graduate fellowship research project
• Density Functional Theory
• Applications to the study of vibrational and mechanical properties of Alcali Halides crystals near melting

Didactics

• Courses
• September - December 2009: Course Biophysics for the Degree in Medical Physics, University of Pisa
• January 2009: Lessons on "Structure and function of nucleic acids" and "Multi-scale modeling of bio-systems" within the course of Molecular Biophysics for PhD students at SNS at SNS
• August 2008: Lessons at the CTBP Summer School Coarse Grained Physical Modeling of Biological Systems: Advanced Theory and Methods: "One-Bead Models: the balance between accuracy and predictive power"
• April 2008: Lessons on "Coarse Grained Models" for the course Computational structural biology at SNS at SNS
• June 2007: Lessons for the course Introduction to the condensed matter physics for biologists at SNS
• May - June 2007: Lessons on "Coarse Grained Models" for the course Computational structural biology at SNS
• May 2007: Course for the PhD in Applied Physics at the University of Pisa "A bottom up approach to the biological matter: Esperimental and modeling techniques from the (sub-)molecular to the macroscopic level"
• 2003: Lessons on "Modeling Bio-molecules" (Stage at NEST)
• 1997: Assistant teacher at the course Termodinamics and Statistics at SNS

• Tutorship
• 2007: Advisor for a Degree in Physics. Title of the Thesis: A minimalist model for Nucleic Acids: a Molecular Dynamics Study
• 2004: Advisor for a Degree in Chemistry. Title of the Thesis: Structural and electronic properties of the AsCP Chromophore
• 2003: Advisor for a PhD in Physics. Title of the Thesis: Molecular mechanisms of Green Fluorescent Protein Photophysics

VT is occasionally tutor for the 3rd and 4th year colloquia of SNS students

Partecipation in committees

- 2007-2008: member of the Committee "Supercalcolo" for the assignment of computer resources on the CINECA national supercomputing facility within the agreement between CINECA and INFM-CNR

- June 2005: Coordinator of the Topical Session Simulation biomolecular systems at MMD Meeting (Genova)

- July 2003: Director of the conference New Frontiers in NanoBiotechnology (ICTP Trieste)

- Participation to committee for examinations, PhD or Degree Theses (about two or three per year)

- Regular activity as reviewer for international journals

Publications

Over 60 papers, including articles on international journals, contribution to books, proceedings, (see publications link)

Partecipation to scientific meetings

Contribution to over 40 scientific meeting (Conferences, Congresses, Workshops, Seminars, etc), most of which as invited speaker

Languages

- Italian: mother language

- English: fluent

- Spanish: scholastic

- French: scholastic

- German: rudimental