Molecular Modeling Lab



Paolo Ruggerone
M.Sc. in Physics (University of Milan), Ph.D. in Physics (Scuola Normale, Pisa), currently Full Professor of Applied Physics. I focus my research on the following topics: i) computational study of bacterial efflux systems (MSF and RND families); ii) characterization of molecular properties of compounds of pharmachological interest; iii) identification of key interactions in the synapsis network; iv) dynamical properties of viral proteins and their inhibition by small molecules.
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Attilio Vittorio Vargiu
M.Sc. in Physics in 2003, Ph.D. in Physics in 2008, currently Associate Professor of Applied Physics. My main research interests are the following ones: i) development of computational protocols to improve the sampling of rare conformations of proteins and the predictive power of molecular docking and virtual screening; ii) computational investigation of the functioning and the inhibition of bacterial multidrug efflux transporters; iii) characterization and molecular rationalization of the self-assembly process of hydrogelling chiral peptides; iv) studies on molecular properties and inhibition of viral proteins by small molecules.
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Giuliano Malloci
M.Sc. (Ph.D) in Physics in 1999 (2003), Associate Professor of Condensed Matter Physics. Main scientific interests include molecular simulations, DFT calculations of molecules and nanostructures, molecular docking, molecular dynamics, data collection and sharing, teaching of physics, fun science experiments (Laboratorio Scienza - Museo di Fisica ).
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Andrea Bosin
M.Sc. in Physics in 1990, Ph.D. in Physics in 1995, currently Assistant Professor in Computer Science. Main research interests include software tools and data sharing (database and web-oriented) for bio-physics related systems, quantum simulations of electronic and optical properties of molecules and solids, molecular dynamics simulations, GPU and HPC computing and management, OS virtualization, Linux system management, micro-controller programming (Arduino).
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Silvia Gervasoni
M.Sc. in Pharmaceutical Biotechnologies and Ph.D. in Pharmaceutical Sciences (University of Milan, Italy). Currently Research Fellow in Computational Biophysics. My research topics are (1) simulations of metal-containing molecules such as radiopharmaceutical compounds; (2) the study of the interaction of antimicrobial compounds with bacterial efflux systems to tackle antimicrobial resistance.
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Mohd Athar
M.Sc. (Ph.D) in Chemistry in 2013 (2019), currently Researcher in Computational Biophysics. His research includes the study of efflux transporters of Gram-negative bacteria by means of bioinformatics, molecular mechanics, and various flavours of molecular dynamics simulations. In addition, he is involved in the development of computational methods to improve the accuracy of molecular docking and virtual screening
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Amit Kumawat
M.Sc. in Bioinformatics (2014), Ph.D. in Chemical Sciences (2019) and Postdoc at University of Milan, Italy (Prof. Carlo Camilloni), currently researcher in Computational Biophysics. Research interests include: (1) Drug design and development for rare genetic disorders. (2) Using molecular dynamics simulations and rare event sampling techniques to gain molecular insights into protein-ligand systems, with a specific focus on membrane proteins.
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Işılay Öztürk
M.Sc. (Ph.D) in Physical Chemistry in 2016 (2022), currently Post-doctoral researcher in Computational Biophysics. Her main research topic is the investigation of radiopharmaceutical compounds. Her interests include i) DFT calculations and benchmarking ii) investigating molecular, electronic properties and non-bonded interactions iii) data collection for molecular design.
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Ke Zuo
Ke Zuo got his bachelor’s degree in Pharmaceutical Engineering in 2015 and master’s degree in Medicinal Chemistry in 2018 at Chengdu University, China. He received his European Joint Ph.D. in computational biophysics at the RWTH Aachen University, Germany, the Hebrew University of Jerusalem, Israel, and the University of Ferrara, Italy, in 2023, under the supervision of Paolo Carloni, Rachel Nechushtai, and Fabio Schifano. The same year, he joined the University of Cagliari as a postdoctoral researcher. His current work focuses on the molecular simulation of protein-protein interaction networks in autism spectrum disorder.
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PhD Students

Camilla Guccione
M.Sc. in Physics in 2022, currently Ph.D. student in Computational Biophysics. Her project focuses on the study of systems involving radiopharmaceuticals using molecular dynamics simulations. The aim is to unravel new insights contributing to drug discovery and design.

Han Kurt
M.Sc. in Biomedical Engineering and Bioinformatics in 2019, currently Ph.D. student in Computational Biophysics. His project focuses development of computational methods to improve drug design.

CONTACTS Giuliano Malloci Andrea Bosin Attilio Vittorio Vargiu Paolo Ruggerone