Research interests
Multi-scale modeling Biomolecular Systems
Minimalist Coarse Grained (CG) models for proteins and nucleic acids are developed and integrated in multi-scale approaches (QM, MM and CG) for the simulation of bimolecular systems on the large size and time scales.
Recent results:
- The CG models were applied to the study of the large scale dynamics of proteins involved in the HIV-1 replication cycle (protease and integrase), revealing their action mechanism (capture of the substrate for protease, binding with HAT proteins for integrase) and possible strategies for their inhibition.
- The dynamics of denaturation and supercoiling in an entire small plasmid was studied with the CG model, revealing the behavior of the denaturation bubbles
- Coarse Grained and multi-scale approaches were used to address the slow dynamics hybrid DNA-proteins systems: Ribosomes and Nucleosomes. The fundamental motions correlated to the translocation (in the Ribosome) and the first steps of DNA unwrapping (in the Nucleosome) were studied.
- A CG model for Green Fluorescent Proteins embedded in a meso-scale cytoplasm model is currently under development, with the aim of studying their diffusional and aggregation behavior
- On the methodological level, strategies to improve the transferability and predictive power of CG models are under development, involving the use of genetic algorithms to optimize the model parameters.
Multi-scale models of graphene based structures
Graphene-based structures at different levels of hydrogen saturation are studied by means of DFT based and atomistic Force Field based simulations
Recent results:
- Nanoribbons of grapheme sculpted in a graphane matrix were studied, revealing the role of Peierls instability in determining their structural and electronic properties
- Hydrogen affinity for curved graphene sheets was studied and the control of corrugation as a mechanism for adsorbing and desorbing hydrogen was explored by means of Car-Parrinello simulations.
Previous research interests
- Study of the relationship between optical, structural and vibrational properties within the family of (Green) Fluorescent Proteins
- Study of semiconductor cluster with fullerenes topology by means of Density Functional Theory and Car Parrinello simulations
Biographical sketch
Education
1993: Laurea (Master 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: Scientist at NEST-INFM, SNS, Pisa
2003 - 2004: Visiting Scholar at the University of California - San Diego
2003 - 2009: Scientist at NEST-CNR-INFM, SNS, Pisa
2010 - present: Scientist at NEST-CNR-Istituto Nanoscienze, SNS, Pisa
Teaching
2009-present: Joint professor of Biophysics for the Degree in Medical Physics, University of Pisa
2007-2012: Lessons within the courses of Molecular Biophysics, Introduction to the condensed matter physics for biologists and Computational structural biology for PhD students at SNS
2008: Lessons at the CTBP Summer School Coarse Grained Physical Modeling of Biological Systems;
2006-2007: Course for the PhD in Applied Physics at the University of Pisa
Didactic material
Didactic video on "Graphene for energy storage"
Selected publications
Reversible hydrogen storage by controlled buckling of graphene layers V Tozzini, V Pellegrini, J Phys Chem C (2011) Press release
Minimalist models for proteins: a comparative analysis V Tozzini, Q Rev Biophys (2010)
Electronic structure and Peierls instability in Graphene nanoribbons sculpted in Graphane V Tozzini, V Pellegrini, Phys Rev B (2010)
Multi-Scale Modeling of Proteins V Tozzini, Acc Chem Res (2010)
Supercoiling and Local Denaturation of Plasmids with a Minimalist DNA Model F Trovato, V Tozzini. J Phys Chem B (2008)
Flap opening dynamics in HIV-1 protease explored with a coarse-grained model V Tozzini, J Trylska, C-E Chang, J A McCammon, J Stuct Biol (2007)
Exploring Global Motions and Correlations in the Ribosome J Trylska, V Tozzini, J A McCammon, Biophys J (2005)
Coarse Grained Models for Proteins V Tozzini, Curr Opinion Struct Biol (2005)
Relationship between structure and optical properties in Green Fluorescent Proteins: A quantum mechanical study of the chromophore environment T Laino, R Nifosí, V Tozzini, Chem Phys (2004)