Luca Maragliano



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


 A PhD student position working on Molecular Dynamics simulations of biomolecules is available starting November 1st 2019. Please contact me before May 31 for info.


  • 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

IIT Publications

  • 2018
  • Chiodo L., Malliavin T.E., Giuffrida S., Maragliano L.iit, Cottone G.

    Closed-Locked and Apo-Resting State Structures of the Human α7 Nicotinic Receptor: A Computational Study

    Journal of Chemical Information and Modeling, vol. 58, (no. 11), pp. 2278-2293
  • Fassio A.iit, Esposito A.iit, Kato M., Saitsu H., Mei D., Marini C., Conti V., Nakashima M., Okamoto N., Olmez Turker A., Albuz B., Semerci Gunduz C.N., Yanagihara K., Belmonte E., Maragliano L.iit, Ramsey K., Balak C., Siniard A., Narayanan V., Ohba C., Shiina M., Ogata K., Matsumoto N., Benfenati F.iit, Guerrini R.

    De novo mutations of the ATP6V1A gene cause developmental encephalopathy with epilepsy

    Brain, vol. 141, (no. 6), pp. 1703-1718
  • Paz S.A., Maragliano L.iit, Abrams C.F.

    Effect of Intercalated Water on Potassium Ion Transport through Kv1.2 Channels Studied via On-the-Fly Free-Energy Parametrization

    Journal of Chemical Theory and Computation, vol. 14, (no. 5), pp. 2743-2750
  • Bramini M.iit, Alberini G., Colombo E., Chiacchiaretta M., DiFrancesco M. L., Maya-Vetencourt J. F., Maragliano L.iit, Benfenati F., Cesca F.iit

    Interfacing Graphene-Based Materials With Neural Cells

    Frontiers in Systems Neuroscience
  • Alberini G.iit, Benfenati F.iit, Maragliano L.iit

    Molecular Dynamics Simulations of Ion Selectivity in a Claudin-15 Paracellular Channel

    Journal of Physical Chemistry B, vol. 122, (no. 48), pp. 10783-10792
  • 2017
  • Chiodo L., Malliavin T.E., Maragliano L.iit, Cottone G.

    A possible desensitized state conformation of the human α7 nicotinic receptor: A molecular dynamics study

    Biophysical Chemistry, vol. 229, pp. 99-109
  • Alberini G.iit, Benfenati F.iit, Maragliano L.iit

    A refined model of claudin-15 tight junction paracellular architecture by molecular dynamics simulations

    PLoS ONE, vol. 12, (no. 9)
  • Eleftheriou C.iit, Cesca F.iit, Maragliano L.iit, Benfenati F.iit, Maya-Vetencourt J.F.iit

    Optogenetic modulation of intracellular signalling and transcription: Focus on neuronal plasticity

    Journal of Experimental Neuroscience, vol. 2017, (no. 11)
  • 2016
  • Rossi P., Sterlini B.iit, Castroflorio E.iit, Marte A., Onofri F., Valtorta F., Maragliano L.iit, Corradi A., Benfenati F.iit

    A novel topology of proline-rich transmembrane protein 2 (PRRT2): Hints for an intracellular function at the synapse

    Journal of Biological Chemistry, vol. 291, (no. 12), pp. 6111-6123
  • Paonessa F.iit, Criscuolo S.iit, Sacchetti S.iit, Amoroso D.iit, Scarongella H.iit, Bisogni F.P.iit, Carminati E.iit, Pruzzo G.iit, Maragliano L.iit, Cesca F.iit, Benfenati F.iit

    Regulation of neural gene transcription by optogenetic inhibition of the RE1-silencing transcription factor

    Proceedings of the National Academy of Sciences of the United States of America, vol. 113, (no. 1), pp. E91-E100
  • 2015
  • Chiodo L.iit, Malliavin T.E., Maragliano L.iit, Cottone G., Ciccotti G.

    A structural model of the human α7 nicotinic receptor in an open conformation

    PLoS ONE, vol. 10, (no. 7)
  • Fujisaki H., Moritsugu K., Matsunaga Y., Morishita T., Maragliano L.iit

    Extended phase-space methods for enhanced sampling in molecular simulations: A review

    Frontiers in Bioengineering and Biotechnology, vol. 3, (no. SEP)
  • Fossati S.M.iit, Candiani S., Nodl M.-T.iit, Maragliano L.iit, Pennuto M.iit, Domingues P., Benfenati F.iit, Pestarino M., Zullo L.iit

    Identification and Expression of Acetylcholinesterase in Octopus vulgaris Arm Development and Regeneration: a Conserved Role for ACHE?

    Molecular Neurobiology, vol. 52, (no. 1), pp. 45-56
  • Cortes-Ciriano I., Bouvier G., Nilges M., Maragliano L.iit, Malliavin T.E.

    Temperature Accelerated Molecular Dynamics with Soft-Ratcheting Criterion Orients Enhanced Sampling by Low-Resolution Information

    Journal of Chemical Theory and Computation, vol. 11, (no. 7), pp. 3446-3454
  • 2014
  • Maragliano L., Roux B., Vanden-Eijnden E.

    Comparison between mean forces and swarms-of-trajectories string methods

    Journal of Chemical Theory and Computation, vol. 10, (no. 2), pp. 524-533
  • Naveh Z.M.H., Malliavin T.E., Maragliano L.iit, Cottone G., Ciccotti G.

    Conformational changes in acetylcholine binding protein investigated by temperature accelerated molecular dynamics

    PLoS ONE, vol. 9, (no. 2)
  • Orlando M.iit, Lignani G.iit, Maragliano L.iit, Fassio A.iit, Onofri F., Baldelli P.iit, Giovedi S., Benfenati F.iit

    Functional role of ATP binding to synapsin I in synaptic vesicle trafficking and release dynamics

    Journal of Neuroscience, vol. 34, (no. 44), pp. 14752-14768
  • Selwa E., Huynh T., Ciccotti G., Maragliano L.iit, Malliavin T.E.

    Temperature-accelerated molecular dynamics gives insights into globular conformations sampled in the free state of the AC catalytic domain

    Proteins: Structure, Function and Genetics, vol. 82, (no. 10), pp. 2483-2496
  • 2012
  • Jiang W., Luo Y., Maragliano L., Roux B.

    Calculation of free energy landscape in multi-dimensions with hamiltonian-exchange umbrella sampling on petascale supercomputer

    Journal of Chemical Theory and Computation, vol. 8, (no. 11), pp. 4672-4680
  • Vashisth H., Maragliano L.iit, Abrams C.F.

    "dFG-Flip" in the insulin receptor kinase is facilitated by a helical intermediate state of the activation loop

    Biophysical Journal, vol. 102, (no. 8), pp. 1979-1987
  • Gentile F.iit, Moretti M.iit, Limongi T.iit, Falqui A.iit, Bertoni G.iit, Scarpellini A.iit, Santoriello S.iit, Maragliano L.iit, Proietti Zaccaria R.iit, Di Fabrizio E.iit

    Direct imaging of DNA fibers: The visage of double helix

    Nano Letters, vol. 12, (no. 12), pp. 6453-6458
  • Lacroix J.J., Pless S.A., Maragliano L., Campos F.V., Galpin J.D., Ahern C.A., Roux B., Bezanilla F.

    Intermediate state trapping of a voltage sensor

    Journal of General Physiology, vol. 140, (no. 6), pp. 635-652
  • 2010
  • Maragliano L., Cottone G., Ciccotti G., Vanden-Eijnden E.

    Mapping the network of pathways of CO diffusion in myoglobin

    Journal of the American Chemical Society, vol. 132, (no. 3), pp. 1010-1017
  • 2009
  • Maragliano L., Vanden-Eijnden E., Roux B.

    Free energy and kinetics of conformational transitions from voronoi tessellated milestoning with restraining potentials

    Journal of Chemical Theory and Computation, vol. 5, (no. 10), pp. 2589-2594
  • 2008
  • Maragliano L., Vanden-Eijnden E.

    Single-sweep methods for free energy calculations

    Journal of Chemical Physics, vol. 128, (no. 18)
  • 2007
  • Maragliano L., Vanden-Eijnden E.

    On-the-fly string method for minimum free energy paths calculation

    Chemical Physics Letters, vol. 446, (no. 1-3), pp. 182-190
  • 2006
  • Maragliano L., Vanden-Eijnden E.

    A temperature accelerated method for sampling free energy and determining reaction pathways in rare events simulations

    Chemical Physics Letters, vol. 426, (no. 1-3), pp. 168-175
  • Maragliano L., Fischer A., Vanden-Eijnden E., Ciccotti G.

    String method in collective variables: Minimum free energy paths and isocommittor surfaces

    Journal of Chemical Physics, vol. 125, (no. 2)
  • 2005
  • Maragliano L., Falconi M., Sergi A., Cioni P., Castelli S., Lania A., Stroppolo M.E., Strambini G., Ferrario M., Desideri A.

    Experimental and simulative dissociation of dimeric Cu,Zn superoxide dismutase doubly mutated at the intersubunit surface

    Biophysical Journal, vol. 88, (no. 4), pp. 2875-2882
  • 2004
  • Maragliano L., Cottone G., Cordone L., Ciccotti G.

    Atomic Mean-Square Displacements in Proteins by Molecular Dynamics: A Case for Analysis of Variance

    Biophysical Journal, vol. 86, (no. 5), pp. 2765-2772
  • Maragliano L., Ferrario M., Ciccotti G.

    Effective binding force calculation in dimeric proteins

    Molecular Simulation, vol. 30, (no. 11-12), pp. 807-816