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  1. 1. CCB – ComputationalChemistry and Biologygroup<br />Stefano Piotto, PhD - Assistant Professor<br />DepartmentofPharmaceuticalSciences– Research Centre for Nanomaterials and Nanotechnology NANOMATES<br />Universityof Salerno<br />
  2. 2. Methods vs applications<br />
  3. 3. What modeling is for?<br />
  4. 4. Researchstreams<br />Self-assembly in confined systems<br />applications<br />Model cell membranes<br />Polymer – membrane interaction<br />Force fields, coarse graining, analysis tool<br />coding<br />Bioinformatics algorithms<br />ideas<br />Ideas for smart drug release<br />
  5. 5. Self-assembly in confinedsystems<br />
  6. 6. What we can learn from the biology lesson?<br />to design new material, we need to know the rules behind folding, self-assembly…<br />6<br />Self-assembly in confined systems<br />
  7. 7. 7<br />Self-assembly in confined systems<br />
  8. 8. 8<br />Self-assembly in confined systems<br />
  9. 9. 9<br />Self-assembly in confined systems<br />Dynamics of V10S10V10S10V10 in vacuum and water<br />Vacuum<br />In water<br />
  10. 10. 10<br />polar<br />apolar<br />polar<br />
  11. 11. <ul><li>Catalysis
  12. 12. Sensors
  13. 13. Separation technologies
  14. 14. Electronics (Q computer)
  15. 15. Information storage (magnetic, electronic, optical, electrooptical devices or switches…)
  16. 16. Adhesives and Coatings
  17. 17. Medicine (drug delivery systems...)
  18. 18. Materials (ceramics, ...)
  19. 19. Energy (batteries, fuel cells, solar cells, ...)
  20. 20. Optics
  21. 21. Paints and Dyes
  22. 22. Cosmetics</li></ul>11<br />What’s the purpose of novel exotic nanomorphologies?<br />
  23. 23. Infiltration of Macromolecules into Nanoporous Silica ParticlesWang, Y., Angelatos, A.S., Dunstan, D.E., and Caruso, F. Macromolecules, 2007,<br />Schematic representation of two extreme cases: (a) low pH and/or high ionic strength (resulting in infiltration of coiled PAA molecules in the nanopores) and (b) high pH and/or low ionic strength (resulting in exclusion of extended PAA molecules from the nanopores).<br />12<br />
  24. 24. Fundamentalvariables:<br />– Densities of polymer beads of type i at point r ρI(r)<br />Dynamics:<br />– StochasticdiffusionequationsforρI(r)<br />– M is a bead mobility, v is the molar volume, η is a random noise term, and the chemical potentials μ are determined from F[ρI(r)] which is based on a chain representation<br />13<br />DDFT: Fundamentals<br />
  25. 25. Parameterization<br />V230Å3<br />0.76 nm<br />12 nm<br />14<br />
  26. 26. after 200s after 500s<br />15<br />PAN-PS system under PBC<br />
  27. 27. 16<br />PAN-PS 50-50% varying the size of the sphere<br />
  28. 28. 17<br />PAN-PS 50-50% changing the polymer length<br />
  29. 29. 18<br />
  30. 30. TEM images of nanospheres of PAN-PS system cutted and shadowed with RuO4, revealing the inner organization (in collaboration with Dr. Massimo Lazzari, Univ. Turin).<br />19<br />Comparison between simulations and experiments<br />
  31. 31. 20<br />3 component: A-B-selective solvent<br />
  32. 32. 21<br />Confinement in P* surface (Im3m)<br />
  33. 33. 22<br />Confinement in G* surface (Ia3d)<br />
  34. 34. Model cell membranes<br />
  35. 35. Model cell membranes<br />
  36. 36. Polymer – membrane interaction<br />Docking on model membranes. Docking and subsequent molecular dynamics permit to determine the interaction mechanisms of antimicrobial peptides/polymers<br />
  37. 37. Polymer – membrane interaction<br />
  38. 38. Membrane fluidity<br />Docking on membranes<br />Interactive molecular dynamics on GPUs<br />Force field parameters for exotic lipids<br />Peptido mimetick copolymers<br />Force fields, coarse graining, analysis tool<br />
  39. 39. Bioinformatics algorithms<br />ECOLI<br />SALTY<br />THET8<br />METJA<br />ARCFU<br />PYRFU<br />ERITRO<br />BACSU<br />STAAN<br />
  40. 40. Ideas for smart drug release<br />
  41. 41. Publications cited in Slide 2<br />Piotto, S., Concilio, S. Iannelli, P., Lazzari, M. “Copolymer organization in confined systems”, Exp. Pol. Lett., submitted<br />Bianchino, E., Piotto, S. “Design of novel amphiphilic antimicrobial peptides”, Prot. Pept. Lett., submitted<br />Amenitsch H, Bombelli C, Borocci S, Ceccacci F, La Mesa C, Piotto S, Mancini G, Rappolt M, submitted to JACS, Segregation into Domains Observed in Liquid Crystal Phases<br />Bianchino E, Piotto S, Concilio S, Striccoli M, Mavelli F, Curri Ml, (in press), DPD simulations of PMMA-Oleic acid mixture behaviour in organic capped nanoparticle based polymer nanocomposites, Macromol. Symposia<br />Piotto S, Concilio S, Iannelli P, Mavelli F, (in press), Computer simulations of natural and synthetic polymers in confined systems, Macromol. Symposia<br />Piotto S, Concilio S, Iannelli P, Mavelli F, (2008) DDFT Simulations of the Assembly of Block Copolymers in Confined Systems, IV INTERNATIONAL CONFERENCE TIMES OF POLYMERS (TOP) AND COMPOSITES. AIP Conference Proceedings, Volume 1042, pp. 44-45.<br />Bianchino E, Piotto S, Concilio S, Sciancalepore C, Curri Ml, Agostiano A, Striccoli M, Mavelli F, (2008) Investigation of morphology of nanocrystal based nanocomposites. Theoretical and computational analysis, IV INTERNATIONAL CONFERENCE TIMES OF POLYMERS (TOP) AND COMPOSITES. AIP Conference Proceedings, Volume 1042, pp. 261-262<br />Urbani P., Ramunno A., Filosa R., Pinto A., Popolo A., Bianchino E., Piotto S., Saturnino C., De Prisco R., Nicolaus B., Tommonaro G., “Antioxidant Activity of Diphenylpropionamide Derivatives: Synthesis, Biological Evaluation and Computational Analysis” Molecules2008, 13, 749-761 <br />Piotto, S., Bianchino, E., “QSAR analysis on antimicrobial peptides”, Chem. Phys. Lipids (2007); 149, 87<br />Vigh L, Torok Z, Balogh G, Glatz A, Piotto S, Horvath I., “Membrane-regulated stress response: a theoretical and practical approach”, Adv Exp Med Biol.2007; 594: 114-31<br />Piotto, S., Concilio, S., Iannelli, P., “Modelling of lipid membranes and membrane interacting compounds”, Chem. Phys. Lipids, (2006), 143(1-2), 62<br />Vigh,L., Balogh,G., Török, Z., Piotto, S. & Horváth, I. “A practical and theoretical approach to membrane-regulated stress response”, in “Molecular aspects of the stress response: chaperones, membranes and networks”, Csermely, P. & Vigh, L. , Eds., (2006) Georgetown, TX, Landes Bioscience.<br />F. Mavelli, S. Piotto, Stochastic simulations of homogeneous chemically reacting systems, Journal of Molecular Structure: THEOCHEM 771 (2006) 55–64<br />V. Bugatti, S. Concilio, P. Iannelli, S. Piotto, S. Bellone, H.C. Neitzert, L. Ferrara, A. Rubino, P. Vacca, D. Della Sala, Synthesis and characterization of new electroluminescent molecules containing carbazole and oxadiazole units, Synt. Metals, (2006), 156, 13<br />L. Vigh, J. Harwood, S. Piotto et al., The significance of lipid composition for membrane activity: new concepts and ways of assessing function, Prog Lipid Res. 2005Sep;44(5):303-44<br />G. Caracciolo, S. Piotto, C. Bombelli, G. Mancini, R. Caminiti, Segregation and phase transition in mixed lipid films, Langmuir, (2005), 21, 9137-9142<br />S. Piotto, R. Nesper, CURVIS: a program to study and analyze crystallographic structures and phase transitions, J. Appl. Cryst., (2005), 38, 223-227.<br />D. Acierno, E. Amendola, V. Bugatti, S. Concilio, L. Giorgini, P. Iannelli, S.P. Piotto, Synthesis and Characterization of Segmented Liquid Crystalline Polymers with the Azo Group in the Main Chain. Macromolecules (2004), 37(17), 6418-6423.<br />S.P. Piotto, F. Mavelli, Monte Carlo simulations of vesicles and fluid membranes transformations, Origins Life Evol. Biosph., (2004), 34, 225-235<br />S.P. Piotto, Lipid aggregates inducing symmetry breaking in prebiotic polymerizations, Origins Life Evol. Biosph., (2004), 34, 123-132<br />A. Zürn, S. Piotto, R. Nesper, Teaching Chemistry: The Challenge to Visually Communicate Complex Systems, E-Learn 2003AACE, (2003), 150-153<br />S. Piotto, A. Zürn, R. Nesper, Novel tools for combining research and teaching: inorganic and structural chemistry, E-Learn 2003AACE, (2003), 2372-2376<br />M.B. Nielsen, J-P. Gisselbrecht, N. Thorup, S.P. Piotto, C. Boudon, M. Gross, Synthesis and characterisation of alkene-extended tetrathiafulvalenes with lateral alkyne appendages, Tetrahedron Letters, (2003), 40, 6721- 6723<br />S. Concilio, I. Biaggio, P. Günter, S.P. Piotto, M. J. Edelmann, J.-M. Raimundo, F. Diederich, Third order nonlinear optical properties of in-backbone substituted Oligo(triacetylene) Chromophores, J. Opt. Soc. Am. B, (2003), 20 (8), 1656-1660<br />S.P. Piotto, A. Zuern, W. Uhlig, C. Mensing, B. Ruettiman, R. Nesper, New media for teaching and communicating inorganic chemistry, Chimia (2003), 57, 94-98 <br />A. Zuern, S.P. Piotto, C. Mensing, B. Ruettiman, W. Uhlig, R. Nesper, New media for teaching inorganic chemistry, Chimia (2002), 56, 7/8, 406<br />S.P. Piotto, A. Zuern, R. Nesper, CURVIS – a computer program to analyze phase transitions, Chimia (2002), 56, 7/8, 349<br />D. Acierno, S. Concilio, A. Diodati, P. Iannelli, S.P. Piotto, P. Scarfato, Synthesis and liquid crystalline properties of low molecular mass compounds containing the 1,4-bis(5-phenyl-1,3,4-oxadiazolyl)benzene unit. Liquid Crystals (2002), 29(11), 1383-1392<br />M.B. Nielsen, N.F. Utesch, N.N.P. Moonen, C. Boudon, J-P. Gisselbrecht, S Concilio, S.P. Piotto, P. Seiler, P. Günter, M. Gross, F. Diederich,, Novel Extended Tetrathiafulvalenes Based on Acetylenic Spacers: Synthesis and Electronic Properties, Chem. Eur. J. (2002), 8-16<br />S.P. Piotto: Novel mathematical description of surfactants macroaggregates. Coll. Surf, A (2001), 177, 3-21.<br />S.P. Piotto, P.L. Luisi, L. Morettini: Origin of Life. Edited by Vismedia, Zürich; (2000). (scientific movie)<br />S.P. Piotto, Diss. Naturwiss. ETH Zürich, Nr. 13953, (2000)<br />
  42. 42. CCB – ComputationalChemistry and Biologygroup<br />