Francesco Zonta, Ph.D.


  Francesco Zonta, Ph.D.

Research Associate Professor,
Laboratory: Lab of Computational Biology (Co-PI)
Research interest: Computational Biology, Molecular Modelling, Statistical Mechanics

My scientific background is that of a Theoretical and Mathematical Physicist. Prior to my graduation (Italian Laurea, in 2003), my studies were mainly focused on Statistical Mechanics, Thermodynamics, Classical Mechanics and Topology.

In 2004, I was admitted to the Ph.D. school in Physics in Padua University, under the supervision of Prof. Attilio L. Stella and Prof. Enzo Orlandini. I focused on the connection between statistical and topological properties of polymers, aiming at determining to what extent the presence and the size of knots in a polymer could alter its statistical properties. The study was conducted using coarse grained models and Monte Carlo simulations. During the Ph.D. period (2004-2006) I also participated in several summer schools and workshops on polymer physics and molecular biology, hence my research interests gradually shifted towards the simulation of biological macromolecules.

As a post-doctoral fellow (2007-2010), I joined the laboratory of Prof. Fabio Mammano at the Venetian Institute of Molecular Medicine (VIMM, Padua), where I started to work on a computational model, based on Quantum Mechanics and Molecular Dynamics simulations, of a gap-junction hemichannel. This ongoing collaboration aims to create a theoretical model of the permeation process of ions and molecules through membrane channels, in order to provide an interpretative framework for the experimental data.

In the following years (2011-2012), I was awarded a Young Researcher grant from Padua University, followed by a Senior Post Doc position, and continued the work on gap-junction channels.

In 2015 I moved to the Shanghai Institute for Advanced Immunochemical Studies (SIAIS) of Shanghaitech University as Research Associate Professor. From 2015 to 2018 I have been a researcher in the Phenotypic Screening lab of Prof. Guang Yang, and the director of the Informatics and Computation Platform. In 2018 I joined as Co-PI the newly established Laboratory of Computational Biology, led by Prof. Michael Levitt.

My research interest is focused on multi scale simulation and on the characterization at atomistic level of the interaction between antibodies and molecules that are potential target for drug discovery.


National Science Foundation of China grant N 31770776: Multiscale Molecular Dynamics approach for the study of the permeation properties of gap junction channels and hemichannels.


1. Min Qiang, Xue Dong, Zhao Zha, Xiao-Kun Zuo, Xing-Lei Song, Lixia Zhao, Chao Yuan, Chen Huang, Pingdong Tao, Qin Hu, Wei-Guang Li, Wanhui Hu, Jie Li, Yan Nie, Damiano Buratto, Francesco Zonta, Peixiang Ma, Zheng Yu, Lili Liu, Yi Zhang, Bei Yang, Jia Xie, Tian-Le Xu, Zhihu Qu, Guang Yang, Richard A. Lerner. Selection of an ASIC1a-blocking combinatorial antibody that protects cells from ischemic death. Proceedings of the National Academy of Sciences, 115, 32 (2018).

2. Francesco Zonta*, Damiano Buratto, Giulia Crispino, Andrea Carrer, Francesca Bruno, Guang Yang, Fabio Mammano, Sergio Pantano, Cues to opening mechanisms from in silico electric field excitation of Cx26 hemichannel and in vitro mutagenesis studies in HeLa trasnfectans. Frontiers in Molecular Neuroscience, 11, 170 (2018).

3. Liang Xu*, Andrea Carrer*, Francesco Zonta*, Zhihu Qu, Peixiang Ma, Sheng Li, Federico Ceriani, Damiano Buratto, Giulia Crispino, Veronica Zorzi, Gaia Ziraldo, Francesca Bruno, Chiara Nardin, Chiara Peres, Flavia Mazzarda, Anna Maria Salvatore, Marcello Raspa, Ferdinando Scavizzi, Youjun Chu, Sichun Xie, Xuemei Yang, Jun Liao, Xiao Liu, Wei Wang, Shanshan Wang, Guang Yang, Richard Lerner, Fabio Mammano, Design and Characterization of a Human Monoclonal Antibody that Modulates Mutant Connexin 26 Hemichannels Implicated in Deafness and Skin Disorders, Front. Mol. Neurosci., 22 September 2017 (2017).

4. Enzo Orlandini, Marco Baiesi, Francesco Zonta, How Local Flexibility Affects Knot Positioning in Ring Polymers, Macromolecules, 49 (12), pp 4656-4662 (2016).

5. Francesco Zonta*, Damiano Buratto, Chiara Cassini, Mario Bortolozzi, Fabio Mammano, Molecular dynamics simulations highlight structural and functional alterations in deafness-related M34T mutation of connexin 26, Front. Physiol. - Membrane Physiology and Membrane Biophysics. (85), 1-9. Invited article for research topic: Hemichannels; from the molecule to the function (2014).

6. Francesco Zonta*, Guido Polles, Giuseppe Zanotti, Fabio Mammano, Permeation pathway of homomeric connexin 26 and connexin 30 channels investigated by molecular dynamics, Journal of Biomolecular Structure and Dynamics 29 (5), 985-998 (2012).

7. Marco Baiesi, Enzo Orlandini, Attilio L Stella, Francesco Zonta*, Topological signatures of globular polymers, Physical Review Letters 106 (25), 258301 (2011).

8. Boris Marcone, Enzo Orlandini, Attilio L Stella, Francesco Zonta*, Size of knots in ring polymers, Physical Review E 75 (4), 041105 (2007).

9. Boris Marcone, Enzo Orlandini, Attilio L Stella, Francesco Zonta*, What is the length of a knot in a polymer? Journal of Physics A: Mathematical and General 38, L15 (2005).