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.
- 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
- 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
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
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
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 video on "Graphene for energy storage"
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)