"I've...seen things you people

 wouldn't believe"




2011-2016 Award ERC starting Grant Thermos

2010--present / Research at CNRS
2009--2010 / Fellow "P-G de Gennes Fundation", ENS, Paris, FR
2006--2008 / Research at High Performance Computing  CASPUR, Rome, IT
2004--2006 / Post-doc UT at Austin, TX, US
2000--2004 / PhD, UPMC and CEA, Saclay, FR
1999          / Laurea, Univ La Sapienza, Physics, Rome, IT


We are interested in the multi-scale modeling of biophysical processes. We apply and develop methods for studying protein stability and function in different conditions and environments. We move from quantum/classical to coarse-grained/nanoscale descriptions. 

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1. M.Kalimeri, O. Rahaman, S. Melchionna, F.Sterpone, "How Conformational Flexibility Stabilizes the Hyperthermophilic Elongation Factor G-Domain",JPCB (2013), 117, 13775-13785
2. F. Sterpone, P. Nguyen, M. Kalimeri, P. Derreumaux, "Importance of the Ion-Pair Interactions in the OPEP Coarse-Grained Force Field: Parametrization and Validation", JCTC(2013), 9, 4574-4584 
3. O. Rahaman, S. Melchionna, D. Laage, F. Sterpone, "The effect of protein composition on hydration dynamics", PCCP(2013), 15, 3570-3576
4. F. Sterpone and S. Melchionna,"Thermophilic proteins: insight and perspective from in silico experiments", CSR (2012), 41, 1665-1676


>> Thermal stability: A challenge for in silico study. We have proposed a approximate scheme for performing enhanced sampling and recovering the stability curve of small proteins via Hamiltonian Replica Exchange. "Recovering Protein Thermal Stability Using All-Atom Hamiltonian Replica-Exchange Simulations in Explicit Solvent"


>> Proteins in fluid. We provide an extended description of a novel simulation framework for including hydrodynamic interactions in protein simulations based on water-free coarse-grained models. "Protein Simulations in Fluids: Coupling the OPEP Coarse-Grained Force Field with Hydrodynamics"


>> Stay wet stay stable. A work recently accepted and to be published in Branka Ladanyi Festschrift JPCB. "Role of Internal Water on Protein Thermal Stability: The Case of Homologous G Domains"


>>> How thermophilic multi-domain proteins secure their fold at high T ? "Interface Matters: The Stiffness Route to Stability of a Thermophilic Tetrameric Malate Dehydrogenase"


>> A new work where the the coarse-grained model OPEP is used to investigate thermal stability: "Are coarse-grained models apt to detect protein thermal stability? The case of OPEP force field"


>> A review on the coarse-grained model OPEP is just out in Chem.Soc.Rev. "The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems"


>> The crew of ResearchMedia publishes an highlight of the project THERMOS in the International Innovation magazine: "Towards new thermostable proteins" 

...In the THERMOS project underway at the Laboratoire de Biochimie Théorique in France, original and diverse computational approaches aim to determine new strategies for bioengineering thermostable proteins for medical and industrial purposes. Interim findings point to new design paradigms….

 The contribution is available here and  the high resolution pdf can be downloaded from the publication page