Daniele Granata

Ai fini di pubblicazione B [email protected]

Personal information

Date of birth 18 April 1984 Place of birth Roma Nationality Italian Institution Temple University, Philadelphia, USA Phone number +1-215-410-0348 (mobile), +1-215-204-4221 (office) Email [email protected] , [email protected]

Scientific and research interest Computational Biophysics. Protein physics. Folding and structure prediction from experimental data. Molecular Dynamics simulation and enhanced sampling techniques. Knowledge-based potentials for native state discrimination and protein-protein interactions. Intrinsically disordered proteins. Ion channels. Sta- tistical mechanics. Bioinformatics and methods development.

Education 2014–Present Postdoctoral Researcher, Temple University, Philadelphia, USA. Department Institute for Computational Molecular Science, M.L. Klein’s group Topic Ion channels and application of statistical mechanics to bioinformatics and data analysis Supervisor Prof. M.L. Klein, Dr. V. Carnevale

2009–2013 Ph.D. Degree cum laude in Physics and Chemistry of Biological Systems, SISSA - International School for Advanced Studies, Trieste, Italy. Thesis Characterizing structure and free energy landscape of proteins by NMR-guided metadynamics Supervisor Prof. A. Laio, Prof. M. Vendruscolo Description A new enhanced sampling technique in Molecular Dynamics to study efficientely the structure and folding of globular and intrinsicaly disordered proteins exploiting experimental NMR data 2006–2009 Master’s Degree (Laurea Specialistica) cum laude in Physics, Università di Roma “La Sapienza”, Roma, Italy. Thesis Optimal states of human red blood cells metabolism. Supervisors Prof. A. Giansanti, Dr. A. De Martino Description Study of the fluxes, stability and responses to enzymopathies for red blood cell metabolic network, based on Von Neumann’s growth model 2003–2006 Bachelor’s Degree (Laurea Triennale) cum laude in Physics, Università di Roma “La Sapienza”, Roma, Italy. Thesis Analysis of the potential of a measure of the mean life difference between the two mass eigenstates of the Bs meson. Supervisor Prof. R. Faccini, Dr. M. Pierini

1/3 1998–2003 High School Scientific Diploma, LS “E.Torricelli”, Roma, Italy. grade 100/100

Teaching 2012 Physics Course for Sport and Motor Sciences, Università Cattolica Sacro Cuore, Milan, Italy. 2012 Tutorial on Statistical Analysis, Cecam Summer School on Atomistic Simulation Tech- niques for Material Science, Nanotechnology and Biophysics, SISSA, Trieste, Italy.

Grants and awards 2009 Ph.D. position and fellowship, SISSA, Trieste, Italy. 2006 Grant Award for Summer Student activity, SLAC, Stanford, CA, USA. A two months grant, given by the Department Of Energy of United States and INFN (Istituto Nazionale Fisica Nucleare) for research in High Energy Particles Physics laboratory of SLAC (Stan- ford Linear Accelerator Center), where I completed my Bachelor’s Degree Thesis .

Publications 1. Granata D, Camilloni C, Vendruscolo M, Laio A Characterisation of the free energy landscapes of proteins using NMR-guided metadynamics. PNAS, 110:17 (2013) 2. Cossio P, Granata D, Laio A, Seno F, Trovato A A simple and efficient statistical potential for scoring ensembles of protein structures. Scientific Report, 2: 351 (2012) 3. De Martino A, Granata D, Marinari E, Martelli C, Van Kerrebroeck V. Optimal fluxes, reaction replaceability, and response to enzymopathies in the human red blood cell. J Biomed Biotechnol, 2010 415148 (2010) 4. Granata D, Baftizadeh F, Habchi J, Galvagnion C, De Simone A, Camilloni C, Laio A, Vendruscolo M Free energy landscape of an intrinsically disordered peptide (submitted) 5. Sarti E, Granata D, Seno F, Trovato A, Laio A Native fold and docking pose discrimination by a single residue-based scoring function (submitted) Presentations at Conferences and Workshops Sep. 2013 CECAM workshop: Intrinsically Disordered Proteins. CECAM-ETHZ, Zurich - Switzerland Thermodynamics of an intrinsically disordered protein by atomistic simulation (Poster) Feb. 2013 Biophysical Society 57th Annual Meeting, Philadelphia, PA - USA. Thermodynamics of an intrinsically disordered protein by atomistic simulation (Poster) Sept. 2012 CECAM workshop: Exploring Protein Interactions through Theory and Experiments, Lausanne - Switzerland. BACH: A simple and efficient statistical potential for scoring ensembles of protein structures and complexes. (Oral presentation) Feb. 2012 2nd workshop on “Physics of Protein Folding and Aggregation", Bressanone (Bz) - Italy. Using NMR Chemical Shifts in Metadynamics for Protein Structure Determination and Free Energy Reconstruction. (Oral presentation)

2/3 Seminars Feb 2013 J. Onuchic, P. Wolynes and C. Clementi’s groups, BRC, Rice University, Houston, TX, US. Characterisation of the free energy landscapes of proteins using NMR-guided metadynamics. Feb 2013 L. Kavraki’s Lab, Computer Science Department, Rice University, Houston, TX, US. Two different computational insights on proteins: scoring functions and free energy reconstruction Feb 2013 Micheal L. Klein’s Group, ICMS, Temple University, Philadelphia, PA, US. Characterisation of the free energy landscapes of proteins using NMR-guided metadynamics. July 2011 Cecam Summer School on Atomistic Simulation Techniques for Material Science, Nanotechnology and Biophysics. SISSA, Trieste - Italy. Using NMR Chemical Shifts in Metadynamics for Protein Structure Determination. Computer skills OS Linux, Mac, Windows programming C, Fortran, matlab scripting Bash, Awk scientific Gnuplot, Xmgrace, VMD, simulations on clusters simulation Gromacs package and PLUMED (plu- gin for metadynamics simulation) Typesetting LATEX

Languages Italian Native English Fluent

Reference letters may be requested to Prof. Alessandro Laio SISSA - International School for Advanced Studies via Bonomea 265, 34136 Trieste - Italy. Email: [email protected] Prof. Michele Vendruscolo University of Cambridge, Department of Chemistry Lensfield Road, Cambridge CB2 1EW, UK Email: [email protected] Prof. Flavio Seno University of Padova, Department of Physics and Astronomy via Marzolo 8, I-35131 Padova, Italy Email: fl[email protected]

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