Luca Maragliano



Center for Synaptic Neuroscience (NSYN) Largo Rosanna Benzi 10, Padiglione IST Nord, Torre D
+39 010 5558 382




  • 11/2011-present - Researcher, Istituto Italiano di Tecnologia, Center for Synaptic Neuroscience (NSYN)
  • 1/2008-10/2011 - Postdoc (Research Associate), Department of Biochemistry and Molecular Biology, University of Chicago
  • 1/2005-12/2007 - Postdoc (Research Associate), Courant Institute of Mathematical Sciences, New York University 
  • 3/2004-10/2004 - Postdoc (Research Engineer), CECAM-ENS, Lyon


  • 2004 Ph.D. Physics, Università degli Studi di Modena e Reggio Emilia
  • 2000 Laurea (B.Sc.+M.Sc.) Physics, Università degli Studi di Roma La Sapienza



Structural modeling and Molecular Dynamics simulations of neuronal proteins

Rare events sampling in biomolecular simulations

Selected Publications

30) Molecular Dynamics Simulations of Ion Selectivity in a Claudin-15 Paracellular Channel
G. Alberini, F. Benfenati and L. Maragliano 
J. Phys. Chem. B, 2018, Journal
29) Closed-Locked and Apo-Resting State Structures of the Human α7 Nicotinic Receptor: A Computational Study
L. Chiodo, T. E. Malliavin, S. Giuffrida, L. Maragliano and G. Cottone
J. Chem. Inf. Model., 2018, Journal
28) De novo mutations of the ATP6V1A gene cause developmental encelopathy with epilepsy
A. Fassio et al.
Brain, 2018, 141, 1703-1718. Journal
27) Effect of intercalated water on potassium ion transport through Kv1.2 channels studied via On-the-Fly Free-Energy Parametrization
S.A. Paz , L. Maragliano and C.F. Abrams 
J. Chem. Theory Comp., 2018, 14, 2743-2750 Journal
26) A refined model of claudin-15 tight junction paracellular architecture by molecular dynamics simulations
G. Alberini, F. Benfenati and L. Maragliano
PLOS ONE, 2017, 12, e0184190. Journal 
25) A possible desensitized state conformation of the human α7 nicotinic receptor: A molecular dynamics study.
L. Chiodo, T.E. Malliavin, L. Maragliano and G. Cottone
Biophys. Chem., 2017, 229, 99-109. Journal 
24) Optogenetic Modulation of Intracellular Signalling and Transcription: Focus on Neuronal Plasticity. (Review)
C. Eleftheriou, F. Cesca, L. Maragliano, F. Benfenati, J.F. Maya-Vetencourt
J. Exp. Neurosci., 2017, 11, 1179069517703354. Journal  
23) A novel topology of proline-rich transmembrane protein 2 (PRRT2): hints for an intracellular function at the synapse
P. Rossi, B. Sterlini, E. Castroflorio, A. Marte, F. Onofri, F. Valtorta, L. Maragliano, A. Corradi and F. Benfenati
J. Biol. Chem., 2016, 291, 6111-23. Journal
22) Regulation of neural gene transcription by optogenetic inhibition of the RE1-silencing transcription factor
F. Paonessa, S. Criscuolo, S. Sacchetti, D. Amoroso, H. Scarongella, F. Pecoraro Bisogni, E. Carminati, G. Pruzzo, L. Maragliano, F. Cesca and F. Benfenati
Proc. Natl. Acad. Sci. U.S.A., 2016, 113, E91-100. Journal
21) Extended phase-space methods for enhanced sampling in molecular simulations: a review
H. Fujisaki, K. Moritsugu, Y. Matsunaga, T. Morishita and L. Maragliano
Front. Bioeng. Biotechnol., 2015, 3, 125. Journal  
20) A structural model of the human α7 nicotinic receptor in an open conformation 
L. Chiodo, T.E. Malliavin, L. Maragliano, G. Cottone and G. Ciccotti
PLOS ONE, 2015, 10, e0133011. Journal
19) Temperature accelerated molecular dynamics with soft-ratcheting criterion orients enhanced sampling by low-resolution information
I. Cortes-Ciriano, G. Bouvier, M. Nilges, L. Maragliano and T.E. Malliavin
J. Chem. Theory Comp., 2015, 11, 3446–3454. Journal
18) Identification and expression of acetylcholinesterase in Octopus vulgaris arm development and regeneration: a conserved role for AChE?
S.M. Fossati, S. Candiani, M.-T. Nodl, L. Maragliano, M. Pennuto, P. Domingues, F. Benfenati, M. Pestarino and L. Zullo 
Mol. Neurobiol., 2015, 52, 45-56 Journal
17) Functional role of ATP binding to Synapsin I in synaptic vesicle trafficking and release dynamics
M. Orlando, G. Lignani, L. Maragliano, A. Fassio, F. Onofri, P. Baldelli, S. Giovedì and F. Benfenati
J. Neurosci., 2014, 34, 14752-14768. Journal

16) Temperature Accelerated Molecular Dynamics gives insights into globular conformations sampled in the free state of the AC catalytic domain
E. Selwa, T. Huynh, G. Ciccotti, L. Maragliano and T.E. Malliavin
Proteins, 2014, 82, 2483–2496Journal
15) Conformational changes in acetylcholine binding protein investigated by Temperature Accelerated Molecular Dynamics
Z. M. Hoseyni, T.E. Malliavin, L. Maragliano, G. Cottone and G. Ciccotti
PLOS ONE, 2014, 9, e88555. Journal
14) Comparison of mean forces and swarms-of-trajectories string methods
L. Maragliano, B. Roux and E. Vanden-Eijnden
J. Chem. Theory Comp., 2014, 10, 524-533. Journal
13) Direct imaging of DNA fibers: the visage of double helix
F. Gentile, M. Moretti, T. Limongi, A. Falqui, G. Bertoni, A. Scarpellini, S. Santoriello, L. Maragliano, R. Proietti Zaccaria and E. Di Fabrizio
Nano Lett., 2012, 12, 6453–6458. Journal
12) Intermediate state trapping of a voltage sensor
J.J. Lacroix, S.A. Pless, L. Maragliano, F.V. Campos, J.D. Galpin, C.A. Ahern, B. Roux and F. Bezanilla
J. Gen. Physiol., 2012, 140, 635-652. Journal (Cover article)
11) Calculation of free energy landscape in multi-dimensions with hamiltonian-exchange Umbrella Sampling on petascale supercomputer
W. Jiang, Y. Luo, L. Maragliano and B. Roux
J. Chem. Theory Comp., 2012, 8, 4672-4680. Journal
10) “DFG-flip" in the insulin receptor kinase is facilitated by a helical intermediate state of the activation loop
H. Vashisth, L. Maragliano and C. F. Abrams
Biophys. J., 2012 , 102, 1979-1987. Journal
9) Mapping the network of pathways of CO diffusion in myoglobin
L. Maragliano, G. Cottone, G. Ciccotti and E. Vanden-Eijnden
J. Am. Chem. Soc., 2010, 132, 1010-1017. Journal
8) Free energy and kinetics of conformational transitions from Voronoi tessellated milestoning with restraining potentials 
L. Maragliano, E. Vanden-Eijnden and B. Roux
J. Chem. Theory Comp., 2009, 5, 2589-2594. Journal 
7) Single-sweep methods for free energy calculations
L. Maragliano, and E. Vanden-Eijnden
J. Chem. Phys., 2008, 128, 184110. Journal
6) On-the-fly string method for minimum free energy paths calculation
L. Maragliano and E. Vanden-Eijnden
Chem. Phys. Lett., 2007, 446, 182-190. Journal 
5) A temperature accelerated method for sampling free energy and determining reaction pathways in rare events simulations
L. Maragliano and E. Vanden-Eijnden
Chem. Phys. Lett., 2006, 426, 168-175. Journal
4) String method in collective variables: minimum free energy paths and isocommittor surfaces
L. Maragliano, A. Fischer, E. Vanden-Eijnden, and G. Ciccotti
J. Chem. Phys., 2006, 125, 024106. Journal
3) Experimental and simulative dissociation of dimeric Cu,Zn Superoxide Dismutase doubly mutated at the intersubunit surface
L. Maragliano, M. Falconi, A. Sergi, P. Cioni, S. Castelli, A. Lania, G. Strambini, M. Ferrario, and A. Desideri
Biophys. J., 2005, 88, 2875-2882. Journal
2) Effective binding force calculation in dimeric proteins
L. Maragliano, M. Ferrario, and G. Ciccotti
Mol. Sim., 2004, 30, 807-816. Journal

1) Atomic mean square displacements in proteins by Molecular Dynamics: a case for analysis of variance
L. Maragliano, G. Cottone, L. Cordone, and G. Ciccotti
Biophys. J., 2004, 86, 2765-2772. Journal