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Walter Rocchia Write a Message

Senior Researcher TT (TT2)

Contacts

Via Morego 30
+39 010 71781 552

About

Walter Rocchia graduated cum laude in Electronic Engineering on July 1996, with a thesis on Quantum Computing. In February 2000, he got a PhD in Electronic Devices at the University of Trento. He then was a Research Scholar at the Biochemistry Department of the Columbia University, developing models to calculate the electrostatic field generated by biological macromolecules in solution. As a consultant in the Corporate Technology Centre at Honeywell Int (NJ, USA), and then at the Bioengineering Research Centre "E. Piaggio" of University of Pisa he studied the modeling of the physical properties of actuating polymers and nanotubes in a wet environment. In 2003 he joined the Molecular Biophysics group of National Enterprise for nanoScience and Nanotechnology (NEST-INFM-CNR), at Scuola Normale Superiore of Pisa, working on molecular recognition and targeting. There, he extended his interests from algorithms for speeding up and making more accurate the calculation of the electrostatic interaction energy of biomolecules to Bioinformatic and Biostatistical techniques aimed at identifying targets and engineering molecules involved in biochemical pathways of medical relevance.

In 2008, he moved to the Drug Discovery and Development Department of the Italian Institute of Technology (IIT), working on computational approaches to ligand-protein binding free energy estimation. In 2010 he was awarded, together with the Clemson University, a NIH 5-years grant entitled: DelPhi: Software for Electrostatic Modeling of Biomolecules and Objects.

In late 2014, he created the Computational mOdelling of NanosCalE and bioPhysical sysTems (CONCEPT) Lab.

He is author of more than 50 publications including International Journals, book contributions and Proceedings.

Selected Publications

Mollica L., Decherchi S., Zia S. R., Gaspari R., Cavalli A. and Rocchia W., "Kinetics of protein-ligand unbinding via smoothed potential molecular dynamics simulations", Scientific Reports, 5, 2015

S. Decherchi, A. Berteotti, G. Bottegoni, W. Rocchia and A. Cavalli, “The ligand binding mechanism to purine nucleoside phosphorylase elucidated via molecular dynamics and machine learning”, Nat. Communic. 6, art. N. 6155, 2015

Decherchi S, Rocchia W (2013) A general and Robust Ray-Casting-Based Algorithm for Triangulating Surfaces at the Nanoscale. PLoS ONE 8(4): e59744. doi:10.1371/journal.pone.0059744

S. Decherchi, J. Colmenares, C. E. Catalano, M. Spagnuolo, E. Alexov, and W. Rocchia, “Between algorithm and model: different Molecular Surface definitions for the Poisson-Boltzmann based electrostatic characterization of biomolecules in solution”,  Communications in Computational Physics, 13(1), 61-89, 2013.

 

Other Publications

INTERNATIONAL JOURNALS:

W. Rocchia and S. Bonella “A Statistical Mechanics handbook for protein-ligand binding simulation” Frontiers in Bioscience, Scholar, 5, 478-495, January 1, 2013 

S. Sarkar, S. Witham, Jie Zhang, Maxim Zhenirovsky, Walter Rocchia and Emil Alexov DelPhi Web Server: A comprehensive online suite for electrostatic calculations of biological macromolecules and their complexes Communications in Computational Physics 13(1), 269-284, 2013.

L. Wang, Z. Zhang, W. Rocchia and E. Alexov, Using DelPhi capabilities to mimic protein's conformational reorganization with amino acid specific dielectric constants, Communications in Computational Physics, 13(1), 13-30 , 2013.

J. Fu, G. Bottegoni, O. Sasso, R. Bertorelli, W. Rocchia, M. Masetti, A. Guijarro, A. Lodola, A. Armirotti, G. Garau, T. Bandiera, A. Reggiani, M. Mor, A. Cavalli & D. Piomelli “A catalytically silent FAAH-1 variant drives anandamide transport in neurons” Nature Neurosci. 15, 64–69 (2012)

G. Bottegoni, W. Rocchia, M. Rueda, R. Abagyan, and A. Cavalli “Systematic exploitation of Multiple Receptor Conformations for Virtual Ligand Screening”, PLoS ONE, 6(5), e18845 (1-15), 2011

J. Patel, D. Branduardi, W. Rocchia, and A. Cavalli “Insights into ligand-protein binding from local mechanical response”, Journal of Chemical Theory and Computation, 2011, 7 (10), pp 3368–3378

S. Bonella, W. Rocchia, P. Amat, R. Nifosì and V. Tozzini “SDPhound, a mutual information-based method to investigate specificity-determining positions” accepted in Algorithms 2, 764-789, ISSN 1999-4893, 2009

A. Di Fenza, W. Rocchia, V. Tozzini “Complexes of HIV-1 integrase with HAT proteins: Multiscale models, dynamics, and hypotheses on allosteric sites of inhibition”, Proteins: Structure, Function, and Bioinformatics, in press ISSN 1097-0134, 2009

A. Mazzoldi, M. Tesconi, A.Tognetti, W. Rocchia, G. Vozzi, G. Pioggia, A. Ahluwalia, D. De Rossi, “Electroactive Carbon Nanotube Actuators: Soft-Lithographic Fabrication and Electro-chemical Modelling”, Material Science and Engineering C 28 1057-1064, ISSN 0928-4931, 2008

W. Rocchia and G. Neshich, “Electrostatic Potential Calculation for biomolecules – creating a database of pre-calculated values reported on a per residue basis for all PDB protein structures”, Genet. Mol. Res. 6 (4): 923-936, ISSN 1676-5680, 2007

R. Bizzarri, R. Nifosì, S. Abbruzzetti, W. Rocchia, S. Guidi, D. Arosio, G. Garau, B. Campanini, E. Grandi, F. Ricci, C. Viappiani, and F. Beltram, “Green Fluorescent Protein ground states: the influence of a second protonation site near the chromophore”, Biochemistry 46 (18): 5494-5504, ISSN 0006-2960, 2007

S. Giordano and W. Rocchia, “Predicting the dielectric nonlinearity of anisotropic composite materials via tensorial analysis”, J. Phys.: Condens. Matter 18, pp. 10585–10599, ISSN: 0953-8984, 2006

G. Bottegoni, W. Rocchia, M. Recanatini and A. Cavalli, “AClAP, Autonomous hierarchical agglomerative Cluster Analysis based Protocol to partition conformational datasets”, Bioinformatics 22(14) pp. e58-e65, ISSN: 1367-4803, 2006

V. Tozzini, W. Rocchia and J. A. McCammon, “Mapping All-Atom Models onto One-Bead Coarse-Grained Models: General Properties and Applications to a Minimal Polypeptide Model” J. Chem. Theory and Comput. 2(3), 667-673, ISSN: 1549-9618, 2006

S. Giordano and W. Rocchia, “Shape dependent effects of dielectrically nonlinear inclusions in heterogeneous media”, Journal of Applied Physics 98, 104101, ISSN: 0021-8979, 2005

W. Rocchia, “Poisson-Boltzmann equation boundary conditions for biological applications” Mathematical and Computer Modelling, 41/10: 1109-1118, ISSN: 0895-7177, 2005

G. Neshich, W. Rocchia, A. L. Mancini, M. E. B. Yamagishi, P. R. Kuser, R. Fileto, C. Baudet, I. P. Pinto, A. J. Montagner, J. F. Palandrani, J. N. Krauchenco, M. C. Vianna, S. Souza, R. C. Togawa and R. H. Higa, “JavaProtein Dossier: a novel web-based data visualization tool for comprehensive analysis of protein structure”, Nucleic Acid Research Vol. 32, Web Server Issue, ISSN: 0305-1048, 2004

Pioggia G., Ahluwalia A., Carpi F., Marchetti A., Ferro M., Rocchia W., De Rossi D., “FACE: Facial Automaton for Conveying Emotions”, Applied Bionics and Biomechanics 1 (2) ISSN: 1176-2322, 2004

W. Rocchia, L. Zoppi and L. Colombo, “Combined atomistic and continuum methods to map electric properties of nanostructured carbon films”, Computational Material Science, 30: 150-154, ISSN: 0927-0256, 2004

F. Lorussi, W. Rocchia, E.P. Scilingo, A. Tognetti, D. De Rossi, “Redundant fabric-based sensor arrays for reconstruction of body posture”, IEEE Sensors Journal, vol. 4, No. 6, ISSN: 1530-437X, 2004

W. Rocchia, S. Sridharan, A. Nicholls, E. Alexov, A. Chiabrera and B. Honig, “Rapid Grid-based Construction of the Molecular Surface for both Molecules and Geometric Objects: Applications to the Finite Difference Poisson-Boltzmann Method”, J. Comp. Chem. 23:128-137 ISSN 0192-8651, 2002

W. Rocchia, E. Alexov and B. Honig, “Extending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dielectric constants and multivalent ions”, J. Phys. Chem. B Vol. 105, n. 28, pp.6507-6514, ISSN 1520-6106, 2001

B. Bianco, E. Moggia, S. Giordano, W. Rocchia, A. Chiabrera, “Friction and noise in quantum mechanics: a model for the interactions between a system and a thermal bath”, Nuovo Cimento B 116, n.2, ISSN 1594-9982, 2001

BOOK CONTRIBUTIONS:

W. Rocchia, M. Masetti, A. Cavalli, “Theoretical approaches for the prediction of binding affinities” Chapter of the Book: Physico-Chemical and Computational Approaches to Drug Discovery; RSC publishing

G. Bottegoni, W. Rocchia, and A. Cavalli, “The application of cluster analysis to conformational sampling and protein-ligand docking.” Book Chapter in the Volume: Computer-Aided Drug Design , Methods in Molecular Biology series, Humana Press, USA (Springer).

Parodi M.T., Rocchia W., Chiabrera A., Di Zitti E., Ricci D., \\"Structural properties of mixed ultrathin organic films investigated by scanning probe microscopy\\", Sensors and Microsystems, C. Di Natale, A. D\\'Amico, F. Davide Eds, World Scientific Publ., Singapore, pp.181-185, ISBN 981-02-4199-2, Jan. 2000

M.T. Parodi, D. Ricci, W. Rocchia, F. Sbrana, E. Di Zitti \\"Assembling gold nanoparticle patterns for molecular electronics applications\\", in Sensors and Microsystems, C. Di Natale, A. D\\'Amico, P. Siciliano (Eds), World Scientific Publ., Singapore, pp. 66-70, ISBN 981-02-4487-8, Dec. 2000.

S. Bruna, W. Rocchia, B. Bianco, J. J. Kaufman, A. Chiabrera, “The state of the science for the Langevin-Lorentz model”, in Electricity and Magnetism in Medicine and Biology, F. Bersani Ed., Plenum Press Publ. Co, New York, ISBN 030-64-6041-6, Aug.1999

S. Bruna, W. Rocchia, E. Moggia, B. Bianco, J. J. Kaufman, A. Chiabrera, “Prediction of e. m. susceptibility at radio frequencies of ligand binding to hydrophobic metalloproteins”, in Electricity and Magnetism in Biology and Medicine, F. Bersani Ed., Kluwer Ac./Plenum Press Publ. Co, New York, ISBN 030-64-6041-6, Aug.1999

M. Zago, W. Rocchia, A. Palombo, E. Moggia, G. D\\'Inzeo, B. Bianco, A.Chiabrera, “Validation of the quantum Z-S model by means of the interaction between mw fields and Zn-protoporphyrin system” , in Electricity and Magnetism in Biology and Medicine,\\'\\' edited by F. Bersani, Kluiwer Academic/Plenum Publisher, New York, pp. 379-382. ISBN 030-64-6041-6, 1999

PROOCEEDINGS:

D'Agostino D., Decherchi S., Galizia A., Colmenares J., Quarati A., Rocchia W. and Clematis A. CUDA Accelerated Blobby Molecular Surface Generation 2011 Lecture Notes in Computer Science Parallel Processing and Applied Mathematics 2011

R. Bizzarri, R. Nifosì, S. Abbruzzetti, W. Rocchia, S. Guidi, D. Arosio, G. Garau, B. Campanini, E. Grandi, F. Ricci, C. Viappiani, and F. Beltram, “Thermodynamic and kinetic characterization of protonation exchanges in GFPs: a way to mutants with tailored optical properties”, 2007 Biophysical Society Meeting Abstracts. Biophysical Journal, Supplement, 329a, Abstract, 1548-Pos., ISSN: 0006-3495

W. Rocchia, A. Mazzoldi, G. Serra, and D. DeRossi, “Exploiting conducting polymer fiber radial expansion for bioinspired actuation” Proc. SPIE 5051: 453-457, ISSN 0277-786X, March 2003

R. Mosca, F. Queirolo, W. Rocchia, F. Tonelli, “Designed simulation (DOE) of complex systems: new frontiers in using neural networks for R.S. research, part two: assessment of the new approach”, Proc. of SCSC 2002, San Diego, California (USA), 15-17 July 2002.

D. DeRossi, F. Lorussi, A. Mazzoldi, W. Rocchia, P. Scilingo, “A Strain Amplified Electroactive polymer actuator” Proc. SPIE 4329, pp. 43-53, ISSN 0277-786X, March 2001

S. Giordano, W. Rocchia, B.Bianco, A. Chiabrera “Quantum lifetimes and classical collision frequency of a ligand under e.m. exposure”, 1998 Annual Meeting of the Bioelectromagnetic Society, June 7-11, St.Petersburg Beach, Florida, USA, 1998

A. Bonfiglio, M. T. Parodi, E. Di Zitti, W. Rocchia, B. Bianco, A. Chiabrera, “An experimental study on the structural and electrical properties of pyrrole derivatives Langmuir-Blodgett films”, 18th Ann. Conf. IEEE Engineering in Biology and Medicine, Amsterdam, The Netherlands, Proceedings 5, pp. 2067-2068, ISSN: 0589-1019, 1996

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I numeri di IIT

L’Istituto Italiano di Tecnologia (IIT) è una fondazione di diritto privato - cfr. determinazione Corte dei Conti 23/2015 “IIT è una fondazione da inquadrare fra gli organismi di diritto pubblico con la scelta di un modello di organizzazione di diritto privato per rispondere all’esigenza di assicurare procedure più snelle nella selezione non solo nell’ambito nazionale dei collaboratori, scienziati e ricercatori ”.

IIT è sotto la vigilanza del Ministero dell'Istruzione, dell'Università e della Ricerca e del Ministero dell'Economia e delle Finanze ed è stato istituito con la Legge 326/2003. La Fondazione ha l'obiettivo di promuovere l'eccellenza nella ricerca di base e in quella applicata e di favorire lo sviluppo del sistema economico nazionale. La costruzione dei laboratori iniziata nel 2006 si è conclusa nel 2009.

Lo staff complessivo di IIT conta circa 1440 persone. L’area scientifica è rappresentata da circa l’85% del personale. Il 45% dei ricercatori proviene dall’estero: di questi, il 29% è costituito da stranieri provenienti da oltre 50 Paesi e il 16% da italiani rientrati. Oggi il personale scientifico è composto da circa 60 principal investigators, circa 110 ricercatori e tecnologi di staff, circa 350 post doc, circa 500 studenti di dottorato e borsisti, circa 130 tecnici. Oltre 330 posti su 1400 creati su fondi esterni. Età media 34 anni. 41% donne / 59 % uomini.

Nel 2015 IIT ha ricevuto finanziamenti pubblici per circa 96 milioni di euro (80% del budget), conseguendo fondi esterni per 22 milioni di euro (20% budget) provenienti da 18 progetti europei17 finanziamenti da istituzioni nazionali e internazionali, circa 60 progetti industriali

La produzione di IIT ad oggi vanta circa 6990 pubblicazioni, oltre 130 finanziamenti Europei e 11 ERC, più di 350 domande di brevetto attive, oltre 12 start up costituite e altrettante in fase di lancio. Dal 2009 l’attività scientifica è stata ulteriormente rafforzata con la creazione di dieci centri di ricerca nel territorio nazionale (a Torino, Milano, Trento, Parma, Roma, Pisa, Napoli, Lecce, Ferrara) e internazionale (MIT ed Harvard negli USA) che, unitamente al Laboratorio Centrale di Genova, sviluppano i programmi di ricerca del piano scientifico 2015-2017.

IIT: the numbers

Istituto Italiano di Tecnologia (IIT) is a public research institute that adopts the organizational model of a private law foundation. IIT is overseen by Ministero dell'Istruzione, dell'Università e della Ricerca and Ministero dell'Economia e delle Finanze (the Italian Ministries of Education, Economy and Finance).  The Institute was set up according to Italian law 326/2003 with the objective of promoting excellence in basic and applied research andfostering Italy’s economic development. Construction of the Laboratories started in 2006 and finished in 2009.

IIT has an overall staff of about 1,440 people. The scientific staff covers about 85% of the total. Out of 45% of researchers coming from abroad 29% are foreigners coming from more than 50 countries and 16% are returned Italians. The scientific staff currently consists of approximately 60 Principal Investigators110 researchers and technologists350 post-docs and 500 PhD students and grant holders and 130 technicians. External funding has allowed the creation of more than 330 positions . The average age is 34 and the gender balance proportion  is 41% female against 59% male.

In 2015 IIT received 96 million euros in public funding (accounting for 80% of its budget) and obtained 22 million euros in external funding (accounting for 20% of its budget). External funding comes from 18 European Projects, other 17 national and international competitive projects and approximately 60 industrial projects.

So far IIT accounts for: about 6990 publications, more than 130 European grants and 11 ERC grants, more than 350 patents or patent applications12 up start-ups and as many  which are about to be launched. The Institute’s scientific activity has been further strengthened since 2009 with the establishment of 11 research nodes throughout Italy (Torino, Milano, Trento, Parma, Roma, Pisa, Napoli, Lecce, Ferrara) and abroad (MIT and Harvard University, USA), which, along with the Genoa-based Central Lab, implement the research programs included in the 2015-2017 Strategic Plan.