Publications

Scientific Publications


  1. G. Stirnemann, F. Sterpone, «Recovering Protein Thermal Stability Using All-Atom Hamiltonian Replica-Exchange Simulations in Explicit Solvent», J. Chem. Theory Comput. (2015), 11, 5573–5577
  2. D.Chakraborty, A. Taly, F. Sterpone, «Stay Wet, Stay Stable? How Internal Water Helps the Stability of Thermophilic Proteins», J. Phys. Chem. B (2015) 119 (40), 12760–12770.
  3. B. Tarus , T. T. Tran , J. Nasica-Labouze , F. Sterpone , P. H. Nguyen , and P. Derreumaux, «Structures of the Alzheimer’s Wild-Type Aβ1-40 Dimer from Atomistic Simulations», J. Phys.Chem. B (2015) 119, 10478–1048.
  4. F. Sterpone, P. Derreumaux, S. Melchionna «Protein simulations in fluids: coupling the OPEP coarse-grained force field with hydrodynamics», J. Chem. Theory Comput. (2015) 11, 1843-1853.
  5. J. Nasica-Labouze et al., « Amyloid β Protein and Alzheimer’s Disease: When Computer Simulations Complement Experimental Studies», Chem. Rev. (2015), 115, 3518–3563.
  6. M. Kalimeri, P. Derreumaux, F. Sterpone «Are coarse-grained models apt to detect protein thermal stability? The case of OPEP force field », J. Non-Cryst. Solids (2015), 407, 494-501.
  7. O. Rahaman, M. Kalimeri, S. Melchionna, J. Henin, F. Sterpone  «Role of Internal Water on Protein Thermal Stability: The Case of Homologous G Domains», J. Phys. Chem. B (2015),119, 8939-49.
  8. M. Kalimeri, E.Girard, D. Madern, F. Sterpone «Interface Matters: The Stiffness Route to Stability of a Thermophilic Tetrameric Malate Dehydrogenase», Plos ONE (2014), 9, e113895. [Free at PlosONE] 
  9. F. Sterpone et al. « The OPEP coarse-grained protein model: from single molecules, amyloid formation, role of macromolecular crowding and hydrodynamics to RNA/DNA complexes», Chem.Soc.Rev. (2014), 43, 4871-4893. 
  10. M. Kalimeri, S. Melchionna, F. Sterpone, « Inquiring Protein Thermostability: Is Resistance to Temperature Stress a Rigidity/Flexibility Trade-off? », Proceedings of the European Conference on Complex Systems 2012, Springer Proceedings in Complexity 2013, pp 535-541.
  11. M. Kalimeri, O. Rahaman, S. Melchionna, F. Sterpone, « How Conformational Flexibility Stabilizes the Hyperthermophilic Elongation Factor G-Domain », J. Phys. Chem . B (2013), 117, 13775-13785. [Free at Europe PMC]
  12. F. Sterpone, P. Nguyen, M. Kalimeri, P. Derreumaux, « Importance of the Ion-Pair Interactions in the OPEP Coarse-Grained Force Field: Parametrization and Validation », J. Chem. Theory Comput. (2013), 9, 4574-4584. [Free at Europe PMC]
  13. A. Fogarty, E. Duboue-Dijon, F.Sterpone, J.T. Hynes, D. Laage, « Biomolecular hydration dynamics: a jump model perspective », Chem. Soc. Rev.(2013), 42, 5672-5683
  14. O. Rahamn, S. Melchionna, D. Laage, F. Sterpone « Effect of protein composition on hydration dynamics », PCCP (2013), 15, 3570-3576. [Free at Europe PMC]
  15. M. Montagna, F. Sterpone, L. Guidoni, « Structural and Spectroscopic Properties of Water around Small Hydrophobic Solutes », J. Phys. Chem. B (2012), 116, 11695-11700. [Free at Europe PMC] 
  16. F. Sterpone, S. Bonella, S. Meloni, « Exploring dehydrogenation process in Alanates via Temperature Accelerated ab initio Molecular dynamics », J. Phys. Chem. C (2012), 116, 19636-19643
  17. F. Sterpone,  G. Stirnemann, D. Laage, « Magnitude and molecular origin of water slowdown next to protein », J. Am. Chem. Soc. (2012), 134, 4116-4119.
  18. F. Sterpone and S. Melchionna, «Thermophilic proteins : insight and perspective from in silico experiments », Chem.Soc.Rev. (2012), 41, 1665-1676. [Free at Europe PMC]
  19. D. Laage, G. Stirnemann, F. Sterpone, J.T. Hynes, « Water Jump Reorientation : From Theoretical Prediction to Experimental Observation », Acc. Chem. Res. (2012), 45, 53-62. 
  20. F. Sterpone, R. Martinazzo, A.N. Panda, I. Burghardt, « Coherent Excitation Transfer Driven by Torsional Dynamics: a Model Hamiltonian for PPV Type Systems », Zeitschrift für Physikalische Chemie (2011), 255, 541-551.
  21. F.Sterpone, S.Melchionna, « Role of packing, hydration and fluctuation on Thermostability”, Chapter for “Thermostable proteins: Structural stability and design ». CRC Press- Taylor and Francis. L. Nilsson and S.Sen Eds.
  22. G. Stirnemann, F. Sterpone,  D. Laage, « Dynamics of water in concentrated solutions of amphiphiles: key roles of local structure and aggregation » J. Phys. Chem . B (2011), 115, 3254-3262. 
  23. D. Laage , G.Stirnemann, F.Sterpone, R. Rey, J.T. Hynes, «Reorientation and allied dynamics in water and aqueous solution », Ann. Rev. Phys. Chem.( 2011), 62, 395-416.
  24. M. Bedard-Hearn, F. Sterpone, P.J. Rossky, « Non adiabatic simulations of exciton dissociation in poly-p-phenylenevinylene oligomers ». J.Phys.Chem. A (2010), 114, 7661–7670.
  25. F. Sterpone, C. Bertonati, G. Briganti, S. Melchionna, “Water around thermophilic proteins: the role of charged and polar atoms », J. of Physics: Condensed Matter (2010), 22, 28413.
  26. F.Sterpone, G.Stirnemann, J.T. Hynes, D. Laage, “Water Hydrogen bond dynamics around amino acids: The key role of hydrophilic hydrogen-bond acceptor groups », J. Phys. Chem. B (2010), 114, 2083-2089.
  27. F. Sterpone, G. Briganti and C. Pierleoni, « Sphere vs Cylinder: The effect of packing on the structure on non ionic C12E6 micelles ». Langmuir (2009), 25, 8960-8967.
  28. F. Sterpone, M. Bedard-Hearn, P.J. Rossky, « Non adiabatic mixed quantum-classical simulation of p-stacked PPV oligomers in the groud state and excited states ». J.Phys.Chem. A (2009), 113, 3427–3430. 
  29. F. Sterpone, C. Bertonati, G. Briganti, S. Melchionna « Key role of proximal water on protein thermostability ». J.Phys.Chem.B. (2009), 113, 131-137.
  30. F. Sterpone, L. Spanu, L. Ferraro, S. Sorella, L. Guidoni « Water-water hydrogen bond studied by QMC ». J. Chem.Theory and Comput. (2008), 4, 1428-1432.
  31. F. Sterpone, G. Briganti, S. Melchionna, C. Pierleoni « Pressure induced core packing and interfacial dehydration in nonionic C12E6 micelle in acqueous solution ». Langmuir (2008), 24, 6067-6071. 
  32. F. Sterpone, P.J. Rossky, « Molecular modeling and simulation of conjugated polymer oligomers: Ground and excited state chain dynamics of PPV in the gas phase ». J. Phys. Chem. B (2008), 112, 4983-4993.
  33. F. Pizzitutti, M. Marchi, F. Sterpone, P.J. Rossky, « How Protein Surfaces Induce Anomalous Dynamics of Hydration Water ».  J. Phys. Chem. B. (2007), 111, 7584-7590.
  34. F. Sterpone, C. Pierleoni, G. Briganti, M. Marchi, « Structure and dynamics of hydrogen bonds in the interface of a C12E6 spherical micelle in water solution: A MD study at various temperatures ».  J. Phys. Chem. B. (2006), 110, 18254-18261.
  35. F. Sterpone, G. Marchetti, C. Pierleoni, M. Marchi, « Molecular modeling and simulation of water near model micelles : Diffusion, rotational relaxation and structure at the hydration interface ». J. Phys. Chem. B. (2006), 110, 11504-11510. 
  36. G.Briganti, G.D’Arrigo, M.Maccarini, C.Pierleoni, F. Sterpone, « Hydration and thermodynamic equilibrium of nonionic surfactant solution », Colloids and Surfaces (2005), 261, 93-99.
  37. S.Abel, F.Sterpone, S. Bandyopadhyay, M.Marchi, « Molecular modeling and simulation of AOT-water reverse Micelles in iso-octane: structural and dynamic properties », J. Phys. Chem. B. (2005), 108, 19458-19466. 
  38. F.Sterpone, C.Pierleoni, G.Briganti, M.Marchi, « Temperature dehydration of C12E6 micelle », Langmuir (2004), 20, 4311-4314. 
  39. F.Sterpone, M.Ceccarelli, M.Marchi, « Linear response and electron transfer in complex biomolecules systems and Reaction Center Protein », J. Phys. Chem. B (2003), 107, 11208-11215.
  40. M.Marchi, F.Sterpone, M.Ceccarelli, « Water rotational relaxation and diffusion in hydrated Lysozyme », J. Am. Chem. Soc. (2002), 124, 23, 6787-6791.
  41. F.Sterpone, M.Ceccarelli, M.Marchi, « Dynamics of hydration in Hen Egg White Lysozyme », J.Mol.Biol. (2001), 311, 429-439.
  42. F.Sterpone, G.Briganti, C.Pierleoni, « Molecular Dynamics study of spherical aggregates of chain molecules at different degree of hydrophilicity in water solution », Langmuir (2001), 17, 5103-5110.

 


PhD Thesis


Maria KALIMERI :: "Are thermophilic proteins rigid or flexible?" [here]


Science & Society



 


TOWARD NEW THERMOSTABLE PROTEINS


The RESEARCH MEDIA crew publishes an highlight of the project THERMOS on the magazine International Innovation, N. 136


The contribution is available below (Courtesy of International Innovation) and is published under the Creative Common License.


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With the crew LASER ( think thank for discussing the horizons in Science, Epistemology and Research), I am coauthor of


 



FREE KNOWLEDGE (Il sapere liberato)


Feltrinelli (2005).


LASER. (publisher's catalog)


The book is freely available here and published under the Creative Common License (cc


The free-software movement and its philosophy could inspire practices in the broad arena of the scientific research?   


 


 


 


 



SCIENCE SPA


Derive&Approdi (2002). 


LASER. (publisher's catalog


A quest for an appropriate description of the scientific workers in the "post-FORD" new-economy era. When science is more and more at the crossroad of business and technology, how science and society talk each others?


 


 


Contribution as Editor to 


SCIENCE and TECHNOLOGY ENCYCLOPAEDIA


Results and perspectives of science frontiers presented in a innovative, extraordinary and fascinating dissemination [read more]   


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