PERSONAL STATEMENT

I developed an interest in quantitative biology from a background in condensed matter physics. One of my major research goals is to identify the protein sequence features responsible for distinct biological function in different protein families. Unveiling these sequence-function relationships is, in my view, one of the major milestones to advance the field of computational biology. The copious amount of information about sequences, structures, and atomistic molecular dynamics trajectories that became available in the last few years holds promise to render this Holy Grail a reachable scientific goal.

However, while these data brings us into a new and exhilarating era of the life sciences, there is a need to organize the newly acquired knowledge into a solid and coherent framework. As in many other fields of investigations concerned with complexity, the rules governing the interactions among the constituents of biological systems are becoming accessible to empirical analysis thanks to approaches based on logical induction and statistical inference. Due to the high-dimensional nature of these problems, statistical physics appears as a natural methodological choice thanks to its ability to relate microscopic interactions to the emergent, collective behavior of many-body systems.

My research is especially focused on the physico-chemical underpinnings of ion transport across lipid membranes. This molecular process is one of the cornerstones of cell physiology: the distinctive feature of living matter is the ability to maintain different chemical conditions in different compartments and to change these conditions in a highly controlled fashion. Accordingly, ion channels and transporters are ubiquitously present in all organisms from the three domains of life and show recognizable sequence conservation over periods of time of the order of billions of years. Highlighting evolutionary conserved features in light of an atomic-level description of their molecular mechanism is my major strategy to formulate hypothesis and build predictive models to investigate the function of these proteins.

 

EDUCATION

Dec 2007

PhD (summa cum laude) Statistical and Biological Physics Sector, International School for Advanced Studies (SISSA/ISAS), Trieste, Italy Thesis title: “Biological Function of HIV-1 Enzymes Explored by Computational Methods.” Supervisors: Paolo Carloni and Cristian Micheletti

Jan 2003

M. Sc. – Physics – University of Pisa, Pisa, Italy Thesis title: “Two Dimensional Wigner Crystal of Paired Electrons in a Perpendicular Magnetic Field: Dynamics in the Dipolar Approximation.” Supervisor: Mario P. Tosi

Nov 2001

B.Sc. – Physics – University of Pisa, Pisa, Italy

 

CURRENT POSITION

July 2015 –    

Research Associate Professor. Institute for Computational Molecular Science, College of Science and Technology, Temple University. Philadelphia USA

 

 PREVIOUS POSITIONS

Aug 2011 – June 2015

Research Assistant Professor. Institute for Computational Molecular Science and Department of Biology, Temple University. Philadelphia USA

Sep 2009 – Jul 2011

Postdoctoral Researcher, Institute for Computational Molecular Science and Department of Chemistry, Temple University, Philadelphia USA

Jan 2008 – Aug 2009

Postdoctoral Researcher, Department of Chemistry, University of Pennsylvania, Philadelphia USA 

 

FELLOWSHIPS AND AWARDS

Nov 2002 – Dec 2002

Research fellowship INFM-NEST, Scuola Normale Superiore, Pisa, Italy; subject: “Two-dimensional Electron Crystals in Perpendicular Magnetic Field"

Apr 2002 – Nov 2002

Undergraduate student research grant INFM-NEST, Scuola Normale Superiore, Pisa, Italy; subject: “Electron Gas in Magnetic Field"

Jun 2005

Travel award, International School of Solid State Physics, Erice, Italy

 

TITLES AND AFFILIATIONS

Mar 2017–

Abilitazione Scientifica Nazionale II Fascia in “Fisica Teorica della Materia” (Italian national scientific qualification as Associate Professor in “Theoretical Physics of Condensed Matter Systems”)

Apr 2014 –

Adjunct graduate faculty Graduate School at Rutgers University-Camden

 

TEACHING ACTIVITIES   

Jan 2018 – June 2018

Fundamentals of Condensed Matter Physics (Chemistry graduate)

Jan 2012 –

Structural Bioinformatics (Biology graduate)

Sep 2010 – Dec 2010

Statistical Physics (Chemistry graduate)

Aug 2018 –

Member steering committee Professional Science Master’s in Bioinformatics

May 2018 –

Member steering committee PhD program in Bioinformatics

 

SUPERVISION OF STUDENTS AND POSTDOCS

Postdocs:

  • Marina Kasimova (2016 – 2017)
  • Antonio Suma (2018 – )
  • Lucia Coronel (2020 – )

Graduate students:

  • Chu’nan Liu, Bioinformatics 2019 – (co-advised with Ron Levy)
  • Francisco McGee, Bioinformatics 2018 – (co-advised with Ron Levy)

Graduate students mentored as external co-advisor (collaborator):

  • Ruiyu Wang, Chemistry 2017v (advisor: Eric Borguet)
  • Salsabil Abou-Hatab, Chemistry 2018 – (advisor: Spiridoula Matsika)

Master’s students:

  • Lei Qian, Bioinformatics 2019
  • Yankankg Zhang, Bioinformatics 2018
  • Brianna Thomas, Bioinformatics 2017

Undergraduate students:

  • Quentin Novinger, Computer Science & Mathematics + Biochemistry (2018 – )
  • Yiming Xu, Physics (2019)
  • Eugene Palovcak, Biochemistry (2013 – 2014)
  • Jennifer Berman, Mathematics (2013)

Graduate students mentored as thesis committee member:

  • Annika Barber, Jefferson University, Neurobiology (2012)
  • Naoto Tanaka, Temple University, Biology (2013)
  • Elaine Yang, Jefferson University, MD-PhD program (2014)
  • Charles Schwartz, Temple University, Physics (2014)
  • Sruthi Murlidaran, Rutgers University, Physics (2014)
  • Asghar Razavi, Temple University, Chemistry (2016)
  • Yunhui Ge, Temple University, Chemistry (2018)
  • Pratikkumar Dhuvad, Temple University, Physics (2018)
  • Lixin Zheng, Temple University, Physics (2018)

 

EDITORIAL AND PANELIST ACTIVITIES 

Peer reviewer activity:

  • eLife, Nature Communications, Proceedings of the National Academy of Science USA; Biophysical Journal; Journal of General Physiology; PLOS Computational Biology; Science Signaling; Proteins: Structure, Function, and Bioinformatics; Scientific Reports; Journal of Physical Chemistry Letters; Journal of Chemical Theory and Computation; Journal of Chemical Physics; Chemical Physics; Journal of Computational Chemistry; Journal of Molecular Graphics and Modelling; Protein Science; Nanoscience. 

Guest editor:

  • Special issue titled "Computer Modeling of Transport across Membrane Proteins", 2014, BioMed Research International, Hindawi Publishing Corporation

Member of Editorial Board:

  • Scientific Reports – Biological Physics section;
  • Emerging Trends in Kinetics and Thermodynamics;
  • Journal of Molecular Physics

External reviewer:

  • Doctoral Fellowship Programme of the Austrian Academy of Sciences, Czech Science Foundation;
  • Qatar National Research Fund,
  • Israel Science Foundation,
  • National Science Foundation USA – Division of Biology;
  • National Institute of Academic Anaesthesia, UK;
  • National Science Centre (Narodowe Centrum Nauki – NCN) Poland;
  • National Research Foundation of Korea;
  • CINECA (Italian Consortium for Supercomputing and Scientific Visualization).

Panel member:

  • National Science Foundation USA – Division of Advanced Cyberinfrastructure;
  • National Institute of Health, Study Section: Biophysics of Neural Systems.
  • National Academy of Science, USA – Board on Life Sciences.
  • Genome Alberta – Panel on Bioinformatics and Computational Biology.
  • European Research Council – Human Brain Project.

Conference organization:

  • CECAM workshop “Ion Transport from Physics to Physiology: the Missing Rungs in the Ladder”, April 3, 2017 to April 5, 2017; with Brad Rothberg, Lucie Delemotte, Ute Hellmich and Rebecca Howard
  • ICMS – CB2 workshop “Statistical Mechanics of Protein Sequences: From Fitness to Free Energy Landscapes and Back”, Philadelphia May 4th, 2018. With Ron Levy and Allan Haldane 

 

 INVITED TALKS

  • APS Conference for Undergraduate Women in Physics, January 2020, Philadelphia, USA
  • Ions, Membranes and Channels: Multiscale Simulations from Quantum to Coarse-Grain, CECAM, March 2020, Paris, France
  • University of Minnesota, January 2019, Minneapolis, MN
  • CECAM meeting Multiscale modelling in electrophysiology: from atoms to organs, March 2018, Lugano Switzerland
  • iCBSM_2017 (Second International Conference in Bioinformatics, Simulations and Modelling), November 2017, Talca, Chile.
  • 1stProtein Structure, Function and Drug Discovery School, August 2017, Bogota, Colombia
  • Precision Medicine & Ion Channel Retreat, August 2017, Vancouver, Canada
  • Fox Chase Cancer Center, April 2017, Philadelphia, USA
  • Blue Waters Symposium, June 2016, Sunriver Resort, USA
  • 9thInternational Conference on Mechanism of Anaesthesia, June 2015 Bonn, Germany
  • Rutgers New Jersey Medical School, April 2015, Newark, USA
  • University of Pennsylvania, March 2015, Philadelphia, USA
  • KTH Royal Institute of Technology, February 2015, Stockholm, Sweden.
  • International School for Advanced Studies, December 2014, Trieste, Italy
  • 248thACS National Meeting of the American Chemical Society, Session: Theory of Liquids August 2014, San Francisco, USA
  • CNRS and University of Lorraine, October 2013, Nancy, France
  • CECAM-HQ-EPFLInnovative Approaches to Computational Drug Discovery, October 2013, Lausanne, Switzerland
  • Institut de Biologie Structural, September 2013, Grenoble, France
  • 3rdMeeting on Structure and Dynamics of Water and Aqueous Solutions in Materials Science, June 2013 University of California, Davis, USA
  • 14thInternational Congress of Quantum Chemistry Symposium on Computational Chemistry at the Petascale, July 2012 Urbana, Illinois, USA