Curriculum Vitæ et Studiorum of. Valentina Tozzini

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1 Curriculum Vitæ et Studiorum of Valentina Tozzini Personal Data Name Current position Work Address Valentina Tozzini Researcher at NEST, Istituto Nanoscienze CNR, Scuola Normale Superiore NEST, piazza San Silvestro, 12, I Pisa Tel: Fax: v.tozzini@sns.it Education July 1988 High School Diploma (Maturità Scientifica) at Liceo Ulisse Dini, Pisa, Italy. Top marks Undergraduate fellowship in Physics at SNS (Scuola Normale Superiore), Pisa - Italy Undergraduate student in Physics University of Pisa March 12th 1993 Degree (MS, Laurea) in Physics at the University of Pisa. Cum laude 1993 Degree in Physics (Diploma) at SNS - Pisa May Oct 1993 Post-graduate fellowship at INFM (National Institute of Condensed Matter Physics - Genova, Italy) and SNS PhD fellowship in Physics at SNS Pisa Oct 16th 1997 PhD Diploma in Phyisics at SNS. Cum Laude School of Medical Physics at the University of Pisa Nov 11th 1999 Medical Physics Specialization Diploma. Cum Laude Career Nov 1997 Nov 1999 Dec 1999 Jan 2000 Feb 2000 Jun 2003 Sep 2003 Mar 2004 Jun 2003 Apr 2008 Apr 2008 Jan 2010 Feb 2010 Post-Doc fellowship at INFM-SNS, Pisa Visiting Researcher at the Institute of Theoretical Physics, University of Nijmegen (NL) Temporary Researcher at NEST (National Enterprise for nanoscience and nanotechnology) INFM, Scuola Normale Superiore, Pisa Visiting Scholar at UCSD (University of California, San Diego, US), Dept of Chemistry and Biochemistry Tenure Track Researcher at NEST INFM CNR (the National Research Council, Italy) Researcher at NEST INFM CNR Researcher at NEST, Istituto Nanoscienze CNR, Pisa Notes Aug 2007 Jan 2008 Jan 2008 Sep 2008 Jun 2010 Nov 2010 Nov 2010 Jun 2011 Maternity leave Part time for breast feeding Maternity leave Part time for breast feeding

2 Research Current research My research currently focuses on multi scale modeling of complex systems (biologic/organic molecules or extended systems), based on the synergistic use of ab-initio methods, atomic Force Field based simulations and on the development of Coarse Grained and mesoscale models. The aim of this research is to reach the large size long time scale in simulations without loosing accuracy. 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 - Elucidating the steps of DNA replication: the first steps of DNA unwrapping in the nucleosomes and the supercoiling and denaturation bubble formation in plasmids were simulated - In general, CG - one bead models for nucleic acids and polipeptides were developed and optimized. These are being included in multi-scale schemes for the study of molecular recognition, interaction and mutation design 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 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) Previous research Study of the structural, electronic and vibrational properties of III-V semiconductor clusters with fullerene topology by means of ab-initio simulations Study of a hybrid QM/MM approach for the simulation of macromolecular systems. Applications to metal and semiconductor clusters embedded in Zeolites Medical Physics Specialization project: Molecular modeling techniques and applications to biological macromolecules and complex systems 1997 Study of phase transitions and defects in quantum crystals within the Density Functional Theory

3 PhD project: Vibrational properties of condensed systems near the solid-liquid transition. Applications to: 3 He and 4 He, metal intercalates in graphite, fast sound in water near freezing 1993 Study of the mechanical properties of high temperature solids with DFT. Applications to alkali halides Degree Thesis project: Dispersion relations of phonons in solids near fusion within the Density Functional Theory Projects and Collaborations 2008 Development of fluorescent proteins for optical nanoscopy oriented to the study of cellular dynamics. National Project (PRIN 2008, ) in collaboration with: Univ Genova, Univ di Milano-Bicocca, Univ Parma and Univ Milano. Local coordinator Connecting Biology with Chemistry through Multiscale Theory and Computer Simulation. NSF-CRC grant in collaboration with Univ of Utah, Center of Biophysical Modeling and Simulation. International collaborator Coarse Grained models for Proteins, collaboration with McCammon Group, UCSD, within NIH grant. International collaborator Coarse Grained models for Nucleic Acids, collaboration with Joanna Trylska s Group, Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University Multi-scale model for the Nucleosome, collaboration with Karine Voltz, Computational Biophysics Group at the University of Heidelberg 2006 Design of inhibitors for the hepatitis C virus protease: A theoretical, computational and experimental approach, National Project (Galileo) in collaboration wiht Politecnico di Torino and Ecole Polytechnique (Paris). Principal Investigator INFM Grants for accessing the parallel computing facility CINECA: Modelling the Structure and Photodynamics of the Green Fluorescent Proteins (2001); Modeling the dark states of the Green Fluorescent Proteins (2002); Photophysics of red and blue fluorescent proteins: tailoring fluorophores at the ends of the visible spectrum (2003); A Coarse Grained Model for Molecular Dynamics Simulations of Biomolecular Aggregates (2005); One-bead coarse grained models for structural transitions in nucleic acids (2006); Coarse Grained modeling of IFP-based FRET systems ( ). Principal Investigator Chromophotes of red homologues of GFPs collaboration with Maurizio Persico s group, Dept of Chemistry, University of Pisa A new approach to drug design: from statistical mechanics to the screening of anti-viral drugs. National project (FISR ), in collaboration with Univ Padova, SISSA Trieste, Univ Palermo, Univ Roma, Univ Modena, CNR Pisa. Local coordinator 2003 Low frequency vibrational modes of GFPs, collaboration with Salvatore Cannistraro s group, Biophysics and NanoScience Centre, Università della Tuscia (Italy) Molecular dynamics of the green fluorescent proteins: An insight into the nature of the dark states. Progetto Avanzato (PA), funded by INFM. Principal Investigator Ab initio simulations of chromophores collaboration with Francesco Buda s group Gorlaeus Laboratories, Leiden University (NL) Ab initio simulations of semiconductor clusters Annalisa Fasolino s group, Institute of Theoretical Physics, Univ of Nijmegen (NL)

4 Teaching Curses and Lessons 2009 Joint professor of Biophysics for undergraduate students in Medical Physics, University of Pisa 2009 Lessons within the course of Molecular Biophysics for PhD students at SNS 2008 Lessons at the CTBP Summer School Coarse Grained Physical Modeling of Biological Systems: Advanced Theory and Methods at UCSD Lessons within the course Computational structural biology for PhD students at SNS 2007 Lessons within the course Introduction to the Structure of Matter for undergraduate students in Biology at SNS 2007 Course A bottom-up approach to the biological matter: Experimental and modeling techniques from the (sub-)molecular to the macroscopic level for PhD students in Applied Physics, University of Pisa 2003 Lessons on Modeling bio-molecules for undergraduate students stage at NEST 1997 Practice lessons of the course Thermodynamics and statistics for undergraduate students at SNS Students Tutorship 2011 Supervisor of MS thesis in Physics (Marco Galimberti, Coarse Grained Model for HIV-1pr selectivity) 2011 Supervisor of MS thesis in Physics (Francesco Tavanti, Bi-stable coarse grained models for proteins: Applications to Bacteriorhodopsin) 2008 Tutor of PhD in Physics (Fabio Trovato Minimalist Models for bio-polymers) 2007 Supervisor of the MS thesis in Physics (Fabio Trovato, Minimalist model for Nucleic Acids: a molecular dynamics study of properties and structural transitions of DNA) 2004 Supervisor of the Graduation thesis in Chemistry (Pietro Amat, Structural and Electronic Properties of the ascp chromophore) Tutor and supervisor of PhD thesis in Physics (Riccardo Nifosí Molecular mechanisms of Green Fluorescent Protein Photophysics) 1998 Occasional activity as tutor for undergraduate students at SNS Dissemination Co-author of scientific divulgation papers for italian on-line journals: V. Pellegrini e V. Tozzini La Nanotecnologia: un passaggio verso un mondo di opportunità nanotecnologie.html; V. Pellegrini e V. Tozzini E l uomo inventò il grafene artificiale in Villaggio Globale Sett Author of papers of divulgation papers about molecular modeling on the journal Fisica in Medicina 2008 Participation to a radiophonic science divulgation program (Piacere Scienza) on the italian station Radio Bruno

5 Assignments 2011 Reviewer of projects of class Tier-1 for assignment of computer time within PRACE (Partnership for Advanced Computing in Europe) Member of the CNR INFM committee for the assignment of computational resources of the CINECA national supercomputing facility Jun 2005 Coordinator of the Topical Session Simulation biomolecular systems at MMD Meeting (Genova) Jul 2003 Director of the conference New Frontiers in NanoBiotechonolgy (SISSA, Trieste) 2000 Regularly member of committees for PhD and Degrees, Post Doc assignment and for students examinations 2000 Regular activity as reviewer for international journals (Phys Rev Lett, J Phys Chem, J Chem Phys, Phys Rev, Biophys J, Biochemistry etc) Occasional activity as reviewer for national and international projects 2000 Habilitation for teaching Mathematics and Physics in High Schools, gained within a public national examination Obtained a permanent position as Mathematics and Physics professor in the High School (Liceo Scientifico Statale C Livi, Prato, Italy), subsequently declined because incompatible with the researcher position Languages spoken comprehension written reading Italian Mother Language English fluent very good Spanish good working knowledge French fair fair German basic basic Basic knowledge and other skills Professional expertise Other technical skills Condensed Matter Physics, Computational Physics, Computer Modeling and Simulations, Biophysics, Biochemistry Programming in Fortran, C, Basic; editing in html Long experience as user of software for molecular modeling and simulation (Accelrys, Amber, DL POLY, CPMD) Experience as system manager of workstations and clusters with Unix or Unix-like operating systems