Article Index
Simone Melchionna, PhD
Curriculum Vitae
Publications
All Pages

Publications

 

Soft Matter, Electrochemistry and Biomolecules

 

1.     C.W. Hsu, M. Fyta, G. Lakatos, S. MELCHIONNA, E. Kaxiras, Ab initio determination of coarse-grained interactions in double-stranded DNA, J. Chem. Phys., in press (2012).

2.     U. Marini Bettolo Marconi, S. MELCHIONNA,Charge transport in nanochannels: a molecular theory, Langmuir, in press (2012).

3.     F. Sterpone, S. MELCHIONNA, Thermophilic proteins: insight and perspective from in silico experiments, Chem. Soc. Rev., 41, 1665 (2012).

4.     S. MELCHIONNA, G. Pontrelli, M. Bernaschi, M. Bisson, I. Halliday, T.J. Spencer, S. Succi, The Lattice Boltzmann method as a general framework for blood flow modeling and simulations, book chapter in Nano and Micro Flow Systems for Bioanalysis, M.W. Collins and C. Koenig eds, Springer (2012).

5.     S. MELCHIONNA, U. Marini Bettolo Marconi, Electro-osmotic flows under nanoconfinement: a self-consistent approach, Europhys. Lett., 95, 44002 (2011).

6.     U. Marini Bettolo Marconi, S. MELCHIONNA, Multicomponent diffusion in nanosystems, J. Chem. Phys., 044104, 135 (2011).

7.     M. Fyta, S. MELCHIONNA, S. Succi, Translocation of biomolecules through solid-state nanopores: theory meets experiments, Polymer Phys., 49, 985 (2011).

8.     S. MELCHIONNA, E. Kaxiras, M. Bernaschi, S. Succi, Endothelial shear stress from large-scale blood flow simulations, Phil. Trans. A Royal Soc., 369, 2354 (2011).

9.     F. Sterpone, S. MELCHIONNA, Role of packing, hydration and fluctuations on thermostability, book chapter in Thermostable Proteins: Structural stability and design, L. Nilsson and S. Sen Eds., Taylor and Francis (2011).

10.  A. Gizzi, M. Bernaschi, D. Bini, C. Cherubini, S. Filippi, S. MELCHIONNA, S. Succi, Three-band decomposition analysis of wall shear stress in pulsatile flows, Phys. Rev. E, 83, 032902 (2011).

11.  U. Marini Bettolo Marconi, S. MELCHIONNA, Dynamics of fluid mixtures in nanospaces, J. Chem. Phys., 134, 064118 (2011).

12.  F. Sterpone, C. Bertonati, G. Briganti, S. MELCHIONNA, Water around thermophilic proteins: the role of charged and apolar atoms, J. Phys.: Condens. Matter, 22, 284113 (2010).

13.  S. MELCHIONNA, M. Bernaschi, M. Fyta, E. Kaxiras, S. Succi, Quantized biopolymer translocation through nanopores: departure from simple scaling, Phys.Rev.E 79, 030901 (2009).

14.  M. Fyta, S. MELCHIONNA, M. Bernaschi, E. Kaxiras, S. Succi, Numerical simulation of conformational variability in biopolymer translocation through wide nanopores, J. Stat. Mech. Theo. Expt., P06009 (2009).

15.  F. Sterpone, C. Bertonati, G. Briganti, S. MELCHIONNA, Key role of proximal water in regulating thermostable proteins. J. Phys. Chem. B, 113, 131 (2009).

16.  M. Fyta, S. MELCHIONNA, S. Succi, E. Kaxiras, Hydrodynamic correlations in the translocation of a biopolymer through a nanopore: theory and multiscale simulations, Phys. Rev. E 78, 036704 (2008).

17.  M. Chinappi, S. MELCHIONNA, C.M. Casciola, S.Succi, Mass flux through asymmetric nanopores: microscopic versus hydrodynamic motion, J.Chem.Phys. 129, 124717 (2008).

18.  F. Sterpone, C. Pierleoni, S. MELCHIONNA, G. Briganti, Pressure induced core packing and interfacial dehydration in nonionic C12E6 micelle in aqueous solution, Langmuir 26, 6067 (2008).

19.  M. Bernaschi, S. MELCHIONNA, S. Succi, M. Fyta, E. Kaxiras, Quantized current blockade and hydrodynamic correlations in biopolymer translocation through nanopores: evidence from multiscale simulations, Nanoletters 8, 1115 (2008).

20.  M. Sega, R. Vallauri, P. Brocca, L. Cantù, S. MELCHIONNA, Short range structure of a GM3 ganglioside membrane: comparison between experimental WAXS and computer simulation results, J. Phys. Chem. B, 111, 10965 (2007).

21.  M. Fyta, S. MELCHIONNA, S. Succi, E. Kaxiras, Multiscale modeling of biopolymer translocation through a nanopore, Lecture Notes in Computer Science, 4487, 786 (2007).

22.  J. Russo, S. MELCHIONNA, F. De Luca, C. Casieri, Water confined in nanopores: spontaneous formation of microcavities, Phys.Rev. B, 76, 195403 (2007) Cond-mat/0705.2348v1.

23.  S. MELCHIONNA, M. Fyta, E. Kaxiras, S. Succi, Exploring DNA translocation through a nanopore via a multiscale Lattice-Boltzmann Molecular Dynamics methodology, Intl. J. Mod. Phys. C, 18, 685 (2007).

24.  M. Fyta, S. MELCHIONNA, E. Kaxiras, S. Succi, Multiscale coupling of molecular dynamics and hydrodynamics: application to DNA translocation through a nanopore, MultiScale Modelling and Sim., 5, 1156 (2006).

25.  M. Chinappi, E. De Angelis, S. MELCHIONNA, C.M. Casciola, S.Succi, R. Piva, Molecular dynamics simulation of ratchet motion in an asymmetric nanochannel, Phys. Rev. Lett., 97, 144509 (2006).

26.  S. MELCHIONNA, R. Sinibaldi, G. Briganti, Explanation of the stability of thermophilic proteins based on unique micromorphology, Biophys. J. 90, 4204 (2006).

27.  R. Sinibaldi, C. Casieri, S. MELCHIONNA, G. Onori, A.L. Segre, S. Viel, L.Mannina, F.De Luca, The role of water coordination in binary mixtures. A study of two model amphiphilic molecules in aqueous solutions by Molecular Dynamics and NMR , J. Phys. Chem. B, 110, 8885 (2006).

28.  M. Sega, R. Vallauri, S. MELCHIONNA, Diffusion of water in confined geometry: The case of a multilamellar bilayer, Phys. Rev. E, 72, 41201 (2005).

29.  M. Sega, P. Brocca, S. MELCHIONNA, R. Vallauri, Molecular dynamics simulation of a GM3 ganglioside bilayer, J. Phys. Chem. B, 108, 20322 (2004).

30.  S. MELCHIONNA, G. Briganti, P. Londei, P. Cammarano, Water induced effects on the thermal response of a protein, Phys.Rev.Lett., 92, 158101 (2004).

31.  R. Allen, J.-P. Hansen, S. MELCHIONNA, A Molecular Dynamics investigation of water permeation through nanopores, J.Chem.Phys., 119, 3905 (2003). Reprinted in Virtual Journal of Biological Physics Research, August 1, 2003 and Virtual Journal of Nanoscale Science & Technology, August 11, 2003.

32.  R. Allen, J.-P. Hansen, S. MELCHIONNA, Permeation of nanopores by water: the effects of channel polarization, J.Phys.Cond.Matt. 15, S297 (2003).

33.  R. Allen, J.-P. Hansen, S. MELCHIONNA, Intermittent permeation of cylindrical nanopores by water, Phys.Rev.Lett. 89, 175502-1 (2002). Reprinted in Virtual Journal of Biological Physics Research, October 15, 2002 and Virtual Journal of Nanoscale Science & Technology, October 21, 2002.

34.  D. Goulding, S. MELCHIONNA, Accurate calculation of three-body depletion interactions, Phys. Rev. E 64, 11403 (2001).

35.  D. Goulding, S. MELCHIONNA, J.-P. Hansen, Entropic selectivity of microporous materials, Phys.Chem.Chem.Phys. 3, 1644 (2001).

36.  S. Makholizo, S. MELCHIONNA, Molecular Characterization of a laminin-derived oligopeptide with implications in biomimetic applications, Biophys.Chem. 89, 129 (2001).

37.  G. Briganti, R. Giordano, S. MELCHIONNA, L. Abis, G. Marra, C. Giannotta, A. Gennaro, Small Angle Neutron Scattering from isotopic mixtures of binary and ternary polymer blends, J. of Colloids and Surfaces A, 176, 161 (2001).

38.  G.-M. Rignanese, F. De Angelis, S. MELCHIONNA, A. De Vita, Glutathione S-Transferase: a First-Principles Study of the Active Site, J.Am.Chem.Soc. 122, 11963 (2000).

39.  D. Goulding, S. MELCHIONNA, J.-P. Hansen, Size selectivity of narrow pores, Phys. Rev. Lett. 85, 1132 (2000).

40.  S. MELCHIONNA, J.-P. Hansen, Triplet depletion forces from density functional optimization, Phys.Chem.Chem.Phys. 2, 3465 (2000).

41.  M. Falconi, S. MELCHIONNA, A. Desideri, Molecular dynamics simulations of Cu, Zn superoxide dismutase: Effect of temperature on dimer asymmetry, Biophys. Chem. 81, 197 (1999).

42.  S. MELCHIONNA, A. Desideri, Origin of the low-frequency modes of globular proteins, Phys.Rev.E 60, 4664 (1999).

43.  L. Stella, S. MELCHIONNA, Equilibration and sampling in molecular dynamics simulations of biomolecules, J. Chem. Phys. 109, 10115 (1998).

44.  S. MELCHIONNA, M. Falconi, A. Desideri, Effect of temperature and hydration on protein fluctuations: molecular dynamics simulation of Cu,Zn superoxide dismutase at six different temperatures. Comparison with neutron scattering data, J. Chem. Phys. 108, 6033 (1998).

45.  S. MELCHIONNA, M. Falconi, A. Desideri, Molecular dynamics simulation of Cu,Zn superoxide dismutase as a function of temperature, in Biological Macromolecular Dynamics, edited by Cusack, S., Buttner, H., Ferrand, M., Langan, P., Timmins, P. (Adenine Press, 1997).

46.  S. MELCHIONNA, M. Barteri, G. Ciccotti, Molecular dynamics study of microperoxidases in aqueous and non-aqueous solutions, J.Phys.Chem. 100, 19241 (1996).

47.  S. MELCHIONNA, M. Barteri, G. Ciccotti, Molecular dynamics study of monomeric heme undecapeptide of Cytochrome c, J. Comp. Aided Mat. Des. 2, 9 (1995).

 

Computational methodology: Multi-­‐Scale and Kinetic approaches

 

1.     H. Basagaoglu, S. MELCHIONNA, S. Succi, V. Yakot, Fluctuation-dissipation relation for a FLB-BGK model, Europhys. Lett. 99, 64001 (2012).

2.     S. MELCHIONNA, U. Marini Bettolo Marconi, Stabilized Lattice Boltzmann-Enskog method for compressible flows and its application to one and two-component fluids in nanochannels, Phys. Rev. E, 85 ,036707 (2012).

3.     G. Pontrelli, I. Halliday, S. MELCHIONNA, T.J. Spencer, S. Succi,  The Lattice Boltzmann method and Multiscale hemodynamics: recent advances and perspectives,  book chapter in Nano and Micro flow systems for bioanalysis, M.W. Collins and C.S. Konig eds, Springer Verlag (2012).

4.     I. Mazzitelli, M. Venturoli, S. MELCHIONNA, S. Succi, Towards a mesoscopic model of water-like fluids with hydrodynamic interactions, J. Chem. Phys., 135, 124902 (2011).

5.     S. MELCHIONNA, A model for red blood cells in simulations of large-scale blood flows, Macromol. Theory & Simul., 20, 548 (2011).

6.     S. MELCHIONNA, Incorporation of smooth spherical particles in the Lattice Boltzmann method, J. Comput. Phys., 230, 3966 (2011).

7.     U. Marini Bettolo Marconi, S. MELCHIONNA, Dynamic density functional theory and Kinetic theory of simple fluids, J. Phys.: Condens. Matt., 22, 364110 (2010).

8.     S. MELCHIONNA, M. Bernaschi, S. Succi, E. Kaxiras, F.J. Rybicki, D. Mitsouras, A.U. Coskun, C.L. Feldman, Hydrokinetic approach to large-scale cardiovascular blood flow, Comput. Phys. Comm., 181, 462 (2010).

9.     U. Marini Bettolo Marconi, S. MELCHIONNA, Kinetic theory of correlated fluids: from dynamic density functional to Lattice Boltzmann methods, J. Chem. Phys., 131, 014105 (2009).

10.  F.J. Rybicki, S. MELCHIONNA, D. Mitsouras, A.U. Coskun, A.G. Whitmore, M. Steigner, L. Nallamshetty, F. Welt, M. Bernaschi, M., Borkin, J. Sircar, E. Kaxiras, S. Succi, P.H. Stone, C.L. Feldman, Prediction of coronary artery plaque progression and potential rupture from 320-detector row prospectively ECG-gated single heart beat CT angiography: Lattice Boltzmann evaluation of endothelial shear stress. Intl. J. of Cardiovasc. Imaging, DOI 10.1007/s10554-008-9418-x (2009).

11.  M. Fyta, S. MELCHIONNA, E. Kaxiras, S. Succi, Multiscale simulation of nanobiological flows, Computing in Science and Engineering, 10, 10 (2008).

12.  S. MELCHIONNA, F.J. Rybicki, D. Mitsouras, A.U. Coskun, S. Succi, M. Bernaschi, E. Kaxiras, P.H. Stone, C.L. Feldman, Non-invasive Prediction of Localization and Progression of Coronary Disease in Man Using Shear Stress Profiles Derived from 320-Row Detector Computed Tomography: Implications for Widespread Screening, Circ., S845, 118 (2008).

13.  S. MELCHIONNA, U. Marini Bettolo Marconi, Lattice Boltzmann method for inhomogeneous fluids, Europhys. Lett., 81 34001 (2008).

14.  U. Marini Bettolo Marconi, P. Tarazona, F. Cecconi, S. MELCHIONNA, Beyond dynamic density functional theory: the role of inertia. J. Phys.: Condens. Matter  20, 494233 (2008).

15.  U. Marini Bettolo Marconi, S. MELCHIONNA, Phase-space approach to dynamical density functional theory, J. Chem. Phys., 126, 184109 (2007).

16.  S. MELCHIONNA, Design of quasi-symplectic propagators for Langevin dynamics, J. Chem. Phys. 127, 044108 (2007).

17.  M. Fyta, S. MELCHIONNA, E. Kaxiras, S. Succi, Multiscale coupling of molecular dynamics and hydrodynamics: application to DNA translocation through a nanopore, MultiScale Modelling and Sim., 5, 1156 (2006).

18.  S. MELCHIONNA, Numerical integration of projective Hamiltonian dynamics, Mol. Phys., 104, 3045 (2006).

19.  D. Moroni, B. Rotenberg, J.-P. Hansen, S. MELCHIONNA, S. Succi, Solving the Fokker-Planck kinetic equation on a lattice, Phys. Rev. E, 73, 066707 (2006).

20.  D. Moroni, J.-P. Hansen, S. MELCHIONNA, S. Succi, On the use of the lattice Fokker-Planck schemes for hydrodynamics, Europhys.  Phys. Lett., 75, 399 (2006).

21.  S. MELCHIONNA, S. Succi, J.-P. Hansen, Simulation of single-file ion transport with the lattice Fokker-Planck equation, Phys. Rev. E 73, 107701 (2006).

22.  S. Succi, S. MELCHIONNA, J.-P. Hansen, Lattice Fokker-Planck equation, Intl. J. Mod. Phys. C, 17, 459 (2006).

23.  S. MELCHIONNA, S. Succi, Lattice Boltzmann-Poisson method for electrorheological nanoflows in ion channels, Comp.Phys.Comm., 169 203 (2005).

24.  S. MELCHIONNA, Altered inertial response of generic degrees of freedom, J. Chem. Phys., 121, 4534 (2004).

25.  S. MELCHIONNA, Molecular Dynamics simulation of biosystems: perspectives and open problems, Mem. S.A.It., 4, 75 (2004).

26.  S. MELCHIONNA, S. Succi, Electro-rheology in nanopores via Lattice Boltzmann, J.Chem.Phys., 120, 4492 (2003).

27.  R.  Allen, J.-P. Hansen, S. MELCHIONNA, Electrostatic potential inside ionic solutions confined by dielectrics: a variational approach, Phys. Chem. Chem. Phys. 3, 4177 (2001).

28.  G. Ciccotti, G.J. Martyna, S. MELCHIONNA, M.E. Tuckerman, Constrained isothermal-isobaric molecular dynamics with full atomic virial, J.Phys.Chem.B 105, 6710 (2001).

29.  J.-P. Ryckaert, G. Arialdi, S. MELCHIONNA, Molecular dynamics of polymers with explicit but frozen hydrogens, Mol.Phys. 99, 155 (2001).

30.  S. MELCHIONNA, Enhanced sampling of rare events, Phys. Rev. E 62, 8762 (2000).

31.  S. MELCHIONNA, Constrained systems and statistical distribution, Phys. Rev. E 61, 6165 (2000). Phys.Rev.E 62, 5864 (2000).

32.  S. MELCHIONNA, G. Ciccotti, Atomic stress isobaric scaling for systems subjected to holonomic constraints, J.Chem.Phys. 106, 195 (1997).

33.  S. MELCHIONNA, G. Ciccotti, B.L. Holian, Comment on constant pressure molecular dynamics algorithms, J.Chem.Phys. 105, 346 (1996).

34.  S. MELCHIONNA, G. Ciccotti, B.L. Holian, Hoover NpT dynamics for systems varying in shape and size, Mol.Phys. 78, 533 (1993).

High-­‐Performance Computing

 

1.     M. Bernaschi, M. Bisson, M. Fatica, S. MELCHIONNA, S. Succi, Petaflop hydrokinetics simulations of complex flows on massive GPU clusters, Comm. Comput. Phys., in press (2012).

2.     M. Bisson, M. Bernaschi, S. MELCHIONNA, S. Succi, E. Kaxiras, Multiscale hemodynamics using GPUs, Comm. Comput. Phys., 11, 48 (2012).

3.     M. Bernaschi, M. Bisson, T. Endo, M. Fatica, S. Matsuoka, S. MELCHIONNA, S. Succi,Petaflop biofluidics simulations on a two-million cores system, Proc. ACM/IEEE Intl. Conference for High Performance Computing, SC11 (2011).

4.     M. Bisson, M. Bernaschi, S. MELCHIONNA, Parallel Molecular Dynamics with irregular domains, Comm. Comput. Phys., 10, 1071 (2011).

5.     M. Borkin, Z. Gajos, A. Peters, D. Mitsouras, S. MELCHIONNA, F.J. Rybicki, C.L. Feldman, H. Pfister, Evaluation of artery visualizations for heart disease diagnosis, IEEE Transactions on visualization and Computer Graphics (Proc. of Information Visualization 2011), 17, 12 (2011).

6.     A. Peters, S. MELCHIONNA, E. Kaxiras, J. Latt, J. Sircar, M. Bernaschi, M. Bisson, S. Succi,Multiscale simulation of cardiovascular flows on the IBM Bluegene/P: Full heart-circulation system at red blood cell resolution, Proc. ACM/IEEE Intl. Conference for High Performance Computing, SC10 (2010).

7.     M. Bernaschi, M. Fatica, S. MELCHIONNA, S. Succi, E. Kaxiras, A flexible high-performance Lattice Boltzmann GPU code for the simulations of fluid flows in complex geometries, Concurrency & Comput., 22, 1 (2010).

8.     M. Bernaschi, S. MELCHIONNA, S. Succi, M. Fyta, E. Kaxiras, J.K. Sircar. MUPHY: a parallel MUlti PHYsics/scale code for high performance bio-fluidic simulations, Comput. Phys. Comm., 180, 1495 (2009).

9.     M. Fyta, J. Sircar, E. Kaxiras, E. MELCHIONNA, M. Bernaschi, S. Succi, Parallel multiscale modeling of biopolymer dynamics with hydrodynamic correlations. Intl. J. Multiscale Comput. Eng. 6, 25 (2008).

10.  R. Casilli, A. Marongiu, S. MELCHIONNA, P. Palazzari, R. Paparcone, V.Rosato IMAGE: a new tool for the prediction of the Transcription Factor binding sites, Bioinfo. Biol. Insights, 2, 363 (2008).

11.  S. MELCHIONNA, A. Luise, M. Venturoli, S. Cozzini, DLPROTEIN : A Molecular Dynamics package to simulate biomolecules, in Science and Supercomputing at Cineca, edited by M.Voli (Cineca, 1997). 

Edited Proceedings and Technical Reports

 

1. S. MELCHIONNA, Large-scale simulations of blood flow with coarse-grained cells, book chapter in Hierarchical methods for dynamics of complex molecular systems, Juelich, March (2012).
2. S. Mechionna, Simulazioni ad alte prestazioni di biofluidica per la diagnostica cardiovascolare, Sapere Magazine, Jan/Feb issue (2012).
3. M. Borkin, S. MELCHIONNA, C. Feldman, E. Kaxiras, H. Pfister, Multidimensional Visualization of Hemodynamic Data, Proceedings of the IEEE Visualization Conference, Atlantic City (NJ) (2009).
4. M. Bernaschi, S. Succi, M. Fyta, E. Kaxiras, S. MELCHIONNA, J.K. Sircar. MUPHY: a parallel high/performance MUlti PHYsics/scale code, Parallel and Distributed Processing, 1 (2009).
5. S. MELCHIONNA, Coupling of atomistic and mesoscopic scales: multiscale modeling of DNA translocation through nanopores, Proc. Appl. Math. Mech. , 7, 1030809-1030810 (2007).
6. M. Fyta, S. Melchionjna, E. Kaxiras, S. Succi, Multiscale modelling of biopolymer translocation through a nanopore, Seventh Intl., Symposium on Computational Science and Simulation, Beijing, China (2007).
7. S. MELCHIONNA et al., Non-invasive prediction of localization and progression of coronary disease, Meeting of the American Heart Association (2008).
8. S. MELCHIONNA, Methods for biosimulations, Report, University of Rome La Sapienza (2005)
9. G. Lavorgna, A. Marongiu, S. MELCHIONNA, P. Palazzari, V. Rosato, P. Verrecchia, Statistical Methods for the Discovery of Co-operative Transcription Factors: the Co-bind code revised, Proceedings of the 4th IEEE International Workshop on High Performance Computational Biology, (2005) 
10. Proceedings of the Europhysics Conference on Computational Physics 2004, Computer Physics Communications 169, issues 1-3, M. Ferrario, S. MELCHIONNA and C. Pierleoni Editors (2004).
11. R. Casilli, A. Marongiu, S. MELCHIONNA, P. Palazzari, R. Paparcone, V. Rosato Predicting Transcription Factor binding sites with the innovative software IMAGE, Internal Report, Ylichron Ltd (2003).
12. S. MELCHIONNA, S. Cozzini, The DLPROTEIN User Manual, University of Rome La Sapienza (2001).