Research interests
I graduated in Physics from the University of Rome "La Sapienza" in 2006, with a Master Thesis on Lattice Quantum Chromodynamics under the supervision of G. Martinelli. In the same year I enrolled in a PhD course in Statistical Physics at the International School for Advanced Studies (SISSA-ISAS) in Trieste. In 2010 I defended my PhD Thesis on Coarse-grained models of protein structure and interactions, supervised by C. Micheletti. In November 2010 I joined K. Kremer's group at MPIP as a postdoc, and became Project Leader in August 2013. In 2017 I was awarded an ERC starting grant for the VARIAMOLS project. In January 2018 I started to carry out this project in the Physics Dept. of the University of Trento, Italy.
My main research interest since during the PhD has been the development and application of coarse-grained models and coarse-graining strategies for soft matter, in particular biologically relevant systems. The two-sided, complementary goal of this approach are to understand the most fundamental and/or universal features of a system and, at the same time, to improve the computational efficiency of a simulation.
Curriculum Vitae
Publications
- Raffaele Fiorentini, Kurt Kremer, Raffaello Potestio, and Aoife C. Fogarty, Using force-based adaptive resolution simulations to calculate solvation free energies of amino acid sidechain analogues, J. Chem. Phys. 146, 244113 (2017)
- Paulo A. Netz, Raffaello Potestio and Kurt Kremer, Adaptive resolution simulation of oligonucleotides, J. Chem. Phys. 145, 23 (2016)
- Robinson Cortes-Huerto, Kurt Kremer and Raffaello Potestio, Communication: Kirkwood-Buff integrals in the thermodynamic limit from small-sized molecular dynamics simulations, J. Chem. Phys. 145, 141103 (2016)
- Aoife C. Fogarty, Raffaello Potestio and Kurt Kremer, A multi-resolution model to capture both global fluctuations of an enzyme and molecular recognition in the ligand-binding site, Proteins: Structure, Function, and Bioinformatics, DOI: 10.1002/prot.25173 (2016) [Selected by Faculty of 1000]
- Saeed Najafi, Rudolf Podgornik, Raffaello Potestio and Luca Tubiana, Role of Bending Energy and Knot Chirality in Knot Distribution and Their Effective Interaction along Stretched Semiflexible Polymers, Polymers 8 (10) (2016)
- Karsten Kreis and Raffaello Potestio, The relative entropy is fundamental to adaptive resolution simulations, J. Chem. Phys. 145 (2016)
- Saeed Najafi, Luca Tubiana, Rudolf Podgornik and Raffaello Potestio, Chirality modifies the interaction between knots, Europhys. Lett. 114 (5) (2016)
- Maziar Heidari, Robinson Cortes-Huerto, Davide Donadio and Raffaello Potestio, Accurate and general treatment of electrostatic interaction in Hamiltonian adaptive resolution simulation, Eur. Phys. J. Spec. Top. 225: 1505 (2016)
- Karsten Kreis, Raffaello Potestio, Kurt Kremer and Aoife C. Fogarty, Adaptive resolution simulations with self-adjusting high-resolution regions, J. Chem. Theory Comput. 12 (8), 4067-4081 (2016) [cover article]
- Jelle M. Boereboom, Raffaello Potestio, Davide Donadio, and Rosa E. Bulo, Toward Hamiltonian Adaptive QM/MM: Accurate Solvent Structures Using Many-Body Potentials, J. Chem. Theory Comput. 12 (8), 3441-3448 (2016)
- Karsten Kreis, Mark E. Tuckerman, Davide Donadio, Kurt Kremer, and Raffaello Potestio, From Classical to Quantum and Back: A Hamiltonian Scheme for Adaptive Multiresolution Classical/Path-Integral Simulations, J. Chem. Theory Comput. 12 (7), 3030-3039 (2016)
- Raffaello Potestio and Luca Tubiana, Discretized knot motion on a tensioned fiber induced by transverse waves, Soft Matter, 12, 669-673 (2015)
- Saeed Najafi and Raffaello Potestio, Folding of small knotted proteins: Insights from a mean field coarse-grained model, J. Chem. Phys. 143, 243121 (2015)
- Saeed Najafi and Raffaello Potestio, Two Adhesive Sites Can Enhance the Knotting Probability of DNA, PLoS ONE 10(7): e0132132 (2015)
- Aoife C. Fogarty, Raffaello Potestio, and Kurt Kremer, Adaptive resolution simulation of a biomolecule and its hydration shell: Structural and dynamical properties, J. Chem. Phys. 142, 195101 (2015)
- Karsten Kreis, Aoife C. Fogarty, Kurt Kremer, Raffaello Potestio, Advantages and challenges in coupling an ideal gas to atomistic models in adaptive resolution simulations, Eur. Phys. J. Special Topics, 224, 2289 (2015)
- Pep Espanol, Rafael Delgado-Buscalioni, Ralf Everaers, Raffaello Potestio, Davide Donadio and Kurt Kremer, Statistical mechanics of Hamiltonian adaptive resolution simulations, J. Chem. Phys. 142, 064115 (2015)
- Karsten Kreis, Davide Donadio, Kurt Kremer and Raffaello Potestio, A unified framework for force-based and energy-based adaptive resolution simulations, EuroPhysics Letters , 108(3) (2014)
- Raffaello Potestio, Computer simulation of particles with position-dependent mass, The European Physical Journal B , 87:245 (2014)
- Raffaello Potestio, Christine Peter, and Kurt Kremer, Computer Simulations of Soft Matter: Linking the Scales, Entropy special issue "Molecular Dynamics Simulations" , 16(8), 4199-4245 (2014)
- Sebastian Fritsch, Raffaello Potestio, Davide Donadio, and Kurt Kremer, Nuclear Quantum Effects in Water: A Multiscale Study, J. Chem. Theory Comput. , 10 (2), 816-824 (2014)
- Guido Polles, Giuliana Indelicato, Raffaello Potestio, Paolo Cermelli, Reidun Twarock, and Cristian Micheletti, Mechanical and Assembly Units of Viral Capsids Identified via Quasi-Rigid Domain Decomposition, PLoS Computational Biology 9(11): e1003331. doi: 10.1371/journal.pcbi.1003331 (2013) [cover article]
- R. Potestio, P. Español, R. Delgado-Buscalioni, R. Everaers, K. Kremer, and D. Donadio, Monte Carlo Adaptive Resolution Simulation of Multicomponent Molecular Liquids, Phys. Rev. Lett. 111, 060601 (2013)
- R. Potestio, S. Fritsch, P. Español, R. Delgado-Buscalioni, K. Kremer, R. Everaers, and D. Donadio, Hamiltonian Adaptive Resolution Simulation for Molecular Liquids, Phys. Rev. Lett. 110 , 108301 (2013)
- R. Potestio and K. Kremer, Theory and practice of adaptive resolution simulations, Proceedings of the HYBRID2013 workshop of the John von Neumann Institute for Computing, vol. 46 (2013)
- G. Morra, R. Potestio, C. Micheletti and Giorgio Colombo, Corresponding functional dynamics across the Hsp90 chaperone family: insights from amultiscale analysis of MD simulations, PLoS Computational Biology 8(3): e1002433. doi:10.1371/journal.pcbi.1002433 (2012)
- R. Potestio and L. Delle Site, Quantum locality and equilibrium properties in low-temperature parahydrogen: a multiscale simulation study, J. Chem, Phys. 136(5), 054101 (2012)
- R. Potestio, C. Micheletti and H. Orland, Knotted vs. Unknotted Proteins: Evidence of Knot-Promoting Loops, PlOS Computational Biology, 6(7) (2010) [Selected by Faculty of 1000]
- R. Potestio, F. Pontiggia, V. Carnevale and C. Micheletti, Bridging the atomic and coarse-grained descriptions of collective motions in proteins, invited contribution for the book Multiscale approaches to protein modeling: structure prediction, dynamics, thermodynamics and macromolecular assemblies, edited by A. Kolinski, Springer (2010)
- R. Potestio , T. Aleksiev, F. Pontiggia , S. Cozzini , and C. Micheletti, ALADYN: a web server for aligning proteins by matching their large-scale motion, Nucleic Acids Research - Web Server Issue, doi:10.1093/nar/gkq293 (2010) [go to ALADYN webserver]
- R. Potestio, F. Caccioli and P. Vivo, Random matrix approach to collective behavior and bulk universality in protein dynamics, Phys. Rev. Lett., 103, 268101 (2009)
- T. Aleksiev, R. Potestio , F. Pontiggia , S. Cozzini , and C. Micheletti, PiSQRD: a web server for decomposing proteins into quasi-rigid dynamical domains, Bioinformatics, DOI 10.1093/bioinformatics/btp512 (2009) [go to PiSQRD webserver]
- R. Potestio, F. Pontiggia and C. Micheletti, Coarse-grained description of proteins' internal dynamics: an optimal strategy for decomposing proteins in rigid subunits, Biophys. J., 96, 4993-5002 (2009)