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Simone Melchionna, PhD
Curriculum Vitae
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Curriculum Vitae

Professional Address:

IPCF – CNR, Dipartimento di Fisica – Università La Sapienza

P.le A. Moro 2, 00185 Rome, Italy

Phone:

+39 06 4991 4239 (office)

+39 06 4957 697 (fax)

+39 339 7565 600 (mobile phone)

Professional Profile:

Computational physicist of biological and physiological systems

Education

• Master degree in Physics (1993), University of Rome La Sapienza. Title of the thesis: Molecular Dynamics methods for solid mixtures at constant temperature and pressure. Application to the solution of deuterium in palladium. Advisors: Prof. G. Ciccotti and Prof. A. Tenenbaum.

• PhD in Chemistry (1997), University of Rome La Sapienza. Title of the thesis: Structural study of monomeric microperoxidases in water and water/methanol solution by molecular dynamics simulations. Advisor Prof. M. Barteri. Thesis accepted without amendments.

Employment

• Ecole Polytechnique Fédérale de Lausanne, Switzerland (Research Scientist, 2009-2010)
• Harvard University, School of Engineering and Applied Sciences (Research Scientist, 2007-2009)
• National Research Council, Italy (Senior Research Scientist, Permanent Position, 2005-)
• Ylichron Ltd., Italy (2004-2005)
• National Research Council, Italy (Junior Research Scientist, 2003-2004)
• Institute for Condensed Matter  (INFM, CNR), Italy (Post-doc, 2002)
• University of Cambridge, department of Chemistry (Post-doc, 1998-2001)
• University of Rome La Sapienza, department of Physics (Post-doc, 1998)
• Ecole Polytechnique Fédérale de Lausanne, IRRMA (Post-doc, 1998)

Work experience

• Multiscale cardiovascular response

1. Plasma and cellular dynamics from micrometric to millimetric scales
2. Microrheology at varying hematocrit level, vessel morphology and pulsatility

• Soft materials at molecular level: proteins, oligopeptides, DNA, lipids, membranes

1. Structure and dynamics at varying conditions (hydration, thermodynamic point, etc)
2. Electronic structure and function of biomolecules
3. Sampling analysis and enhancement
4. DNA translocation for sequencing in solid-state nanopores

• Water, colloids and ionic solvents

1. Phase coexistence and intermittency of water under confinement
2. Non-equilibrium loads and ratchet effect
3. Electro-osmotic and dielectric forces
4. Depletion interactions

Methodological expertise

• Multi-scale modeling and simulations

1. Hybrid methods for suspended bodies of finite size
2. Synthetic models via Lattice Boltzmann and Lattice Fokker-Planck methods
3. Structure, thermodynamics and dynamics of inhomogeneous fluids
4. Statistical foundations for particle-based and field-based numerical methods
5. Electrostatics and polarizable media

• Particle-based simulations via Molecular Dynamics and Monte Carlo

1. Deterministic and stochastic simulation methods
2. Constrained and multiple time-step molecular dynamics
3. Kinetic methods for correlated atomic systems
4. Ensemble transformations via feed-backs
5. Enhanced sampling of rare events
6. Force field modeling and statistical inversion

• General-purpose numerical analysis

1. Complexity, robustness and feasibility
2. Truncation and finite-precision control
3. Optimization and algorithmic design

High Performance Computing

• Design and deployment of large scale software packages (DLPROTEIN, IMAGE, MUPHY)
• Parallel Programming with message passing and shared memory paradigms
• Distributed clusters and highly scalable platforms (Blue Gene)
• HPC on General Purpose Graphical Processing Units (GP-GPU)
• Objected-oriented, procedural, scripting programming and scientific visualization

Consultancy and Collaborations

• Harvard Medical School, Brigham and Women’s Hospital, USA
• University of Cambridge, UK
• Council for New Technologies, Energies and Environment (ENEA), Italy
• ENI R&D, Donegani Institute, Italy
• Institute for Applied Mathematics IAC, CNR, Italy
• University of Trento, Italy
• University of Rome 2, Italy
• University of Rome 1, Italy
• Université Libre de Bruxelles, Belgium

Awards and Fellowships

• Gordon Bell Honorable Mention, Supercomputing Conference, Seattle (2011)
• Finalist at the Gordon Bell Award, Supercomputing Conference, New Orleans (2010)
• Best Invited Talk, International Conference on Computational Science, Beijing  (2007)
• Research Fellowship, CINECA Supercomputing center, Casalecchio di Reno (2001)
• Research Fellowship, Leverhulme Trust, UK (1998)
• INFM Prize for Junior Research, Italy (1997)
• Research fellowship of the European Human Capital Mobility Program, EU (1997)
• Silicon Graphics Prize for Junior Research, Italy (1996)
• PhD Fellowship in Chemistry, Italy (1994)

Teaching and Educational Activity

• Academic Years 2004-2006: Course “Computational methods for biological applications”, Graduate Level, Faculty of Engineering, University of Rome La Sapienza, Italy.

• Years 2001-2002: Course “Biosimulation with DLPROTEIN”. University of Rome la Sapienza.

• Years 2000-2001: “HPC simulation methods in biology”. Supercomputing Center Cineca, Italy.

• Academic Years 1996-1998: Course “Computer Programming, Architectures and Algorithmic Design”, Undergraduate Level, Faculty of Environmental Science, University of Tuscia, Italy.

• Joint supervision of the graduate students:

1. Marcello Sega, Department of Physics, University of Trento. 1998-2002
2. Michelle Borkin, School of Engineering and Applied Sciences, Harvard University, 2008-
3. Amanda Peters, School of Engineering and Applied Sciences, Harvard University, 2008-

• 2005-2006: Joint supervision of the master students:

1. Raffaele Sinibaldi, Department of Physics, University of Rome La Sapienza. 2001-2002
2. John Russo, Department of Physics, University of Rome La Sapienza. 2002-2003

Supervision of 6 undergraduate students, University of Cambridge.

Grants

Co-Principal Investigator of the Grant from the Swiss Competence Centre for Materials Science and Technology “Biocompatible films, foams, fabrics and surfaces from poly(isobutylene)-oligopeptide conjugates”, 2010-2012.

Co-Principal Investigator of the Italian National Grant (PRIN) “Physical properties in nanosized bio-matrices based on polymers”, 2007-2008.

Co-Principal Investigator of the Italian National Grant (PRIN) “Structural, dynamical and functional properties of proteins in non-liquid systems containing residual water”, 2005-2006.

Principal Investigator of the industrial grant from ENI R&D “Multi-lamellar structure of binary and ternary polymer blends via computer modelling and small angle neutron scattering” 2002-2003.

Co-Principal Investigator of the Italian National Grant (PRIN) “Dynamical processes in self-organized structure of polysaccharides in aqueous solvents.” 2003-2004.

Organizational activities

CECAM Workshop on “Trends in computational hemodynamics”, 10-12 May 2010. Organizers: S. Melchionna, E. Kaxiras, A. Quarteroni

CECAM Workshop on “Common trends between kinetic theory, dynamic density functional theory and mesoscopic methods based on effective free energy models”, 2-5 October 2008. Organizers: S. Melchionna, U. Marini Bettolo Marconi, I. Pagonabarraga

International Conference “Computational Physics CCP2004”, Genova 1-4 September 2004. Scientific secretaries: S. Melchionna, C. Pierleoni, M. Ferrario

Euroconference “Monte Carlo and Molecular Dynamics of Condensed Matter Systems”, Como, July 1995. Organizers: K. Binder, G. Ciccotti.

Keynotes and invited talks

Invited talk “Cardiovascular blood flows with suspended red blood cells via computer simulation”, Conference Micro and Nano flows, Thessaloniki, 2011.

Invited talk “Thermal response of proteins and hydration water”, CECAM Workshop on Models for bulk, confined water and aqueous solutions upon supercooling, Lausanne, 2011.

Invited talk “Dynamics of charged fluids in nanospaces: the effect of excluded volume interactions”, CECAM Workshop on New Challenges for the simulation of electrokinetic phenomena, Paris, 2011.

Keynote talk, “Multiscale cardiovascular hemodynamics: heart-size circulation at red blood cell resolution”, Workshop on Multiscale fluid mechanics with the Lattice Boltzmann method, Leiden, 2011.

Invited talk “Multiscale cardiovascular hemodynamics: heart-size circulation at red blood cell resolution”, SuperComputing, New Orleans, 2010.

Invited talk “Cardiovascular blood flows with suspended red blood cells via computer simulation”, Nanomedicine, Beijing, 2010.

Invited talk “Hydrokinetic approach to hemodynamics: a showcase for anisotropic suspended particles”, International workshop: Novel simulation approaches to soft matter systems, Dresden, 2010.

Invited talk “Blood flows via suspended particles and the Lattice Boltzmann method”, World Congress on Computational Mechanics ECCOMAS – CFD Minisymposium, Lisbon, 2010.

Invited talk “Multi-scale modeling of blood flows in large scale coronary systems”, 5^th Conference “From Solid State to Biophysics: from Physics to Life Sciences”, Dubrovnik, 2010.

Invited talk “DNA translocation in nanopores: departure from scaling behavior”, XII International Workshop on Complex Systems, Andalo, 2010.

Invited talk “Multi-scale simulations of blood flow in realistic coronary arteries”, 5^th MIT Conference on Computational Fluid and Solid Mechanics, Boston, 2009.

Invited talk “Multi-scale methods for mesoscopic flows with application to hemodynamics”, Black Forest Focus on Soft Matter, Freiburg, 2009.

Invited talk “Role of water in stabilizing thermophilic proteins”, CECAM Workshop, Lausanne, 2009.

Invited talk “Multi-scale simulations of DNA and arterial systems”, BECAT-IBM Symposium on High Performance Computational Science and Engineering, University of Connecticut, 2008.

Invited talk “Recent advances in multi-scale modeling of DNA translocation and hemodynamics”, Conference on Discrete Simulation in Fluid Dynamics, Florianopolis, 2008.

Invited talk “Multi-scale simulations with a combined Lattice Boltzmann/Molecular Dynamics approach” World Congress on Computational Mechanics ECCOMAS – WCCM Minisymposium, Venice, 2008.

Invited talk “Multi-scale simulations of complex materials for engineering and biological applications” 6^th International Congress on Industrial and Applied Mathematics, Minisimposium, Zurich, 2007.

Invited talk “Multiscale modeling of biopolymer translocation through nanopores”, International Conference on Computational Science, Beijing, 2007.

Invited talk “Multiscale modeling of DNA translocation: a Lattice Boltzmann-Molecular Dynamics study”, 3^rd International Conference on Multiscale Materials Modeling, Freiburg, 2006.

Plenary talk “Multiscale modeling of DNA translocation and colloids in presence of hydrodynamics”, Conference on Discrete Simulation in Fluid Dynamics, Geneva, 2006.

Invited talk “Electrorheology in nanopores via Lattice Boltzmann methods”, Europhysics Conference in Computational Physics, Genova, 2004.

Keynote lecture ”Rare events and constrained statistical mechanics”, Congress of the Italian Mathematical Society, Chia Laguna. 2002.

Invited talk “Thermal response and glass-like behavior of a protein” 16^th congress on Theoretical Physics and Condensed Matter, Fai della Paganella, 1997.

Invited talk “Structure and dynamics of Microperoxidases in solution”, National School in Biophysics, Bressanone,1995.

Invited talk “Isothermal and isobaric methods for Molecular Dynamics”, Congress of the Italian Chemical Society, Rome,1993.