Dr Paolo Raiteri

Research Interests

Learning to predict polymorphism through simulation of nucleation and nanoparticle evolution

(ARC discovery grant)

Nature is able to demonstrate remarkable control over the assembly of molecules to form highly specific chemical structure. Selection of the ultimate structural form is often already decided while the material is still at the nanoscale, thought details of how the choice occurs are limited. This project seeks to advance the latest computer simulation methods in order to understand the complex structures of these nanoparticles, and resolve the apparent contradiction of how they can be disordered, yet at the same time different, while containing the nascent information as the the chemical form they will ultimately take. Through this scientist will be bette able to miimic the natural selectivity and thereby design technological materials.

Molecular Studies of the Aggregation of β-Amyloid Peptides and its Inhibition in the Treatment of Alzheimer’s Disease

(Collaboration with R. Mancera – Curtin University)

Protein aggregation lies at the heart of the molecular origin of several neurodegenerative diseases, such as Alzheimer’, Parkinson’s, Huntington’s and prion diseases. These diseases constitute a significant and growing burden on healthcare systems in Australia and many other countries as the world’s population continues to age. Consequently there is an urgent need to understand at the most essential level the molecular mechanisms responsible for protein aggregation and how they can be inhibited by small molecules of potential therapeutic value. This project will develop fundamental insight into the molecular factors that govern protein aggregation and its inhibition in neurodegenerative disease states.

Solubility of organic compounds with accurate molecular dynamics simulations

(Collaboration with P. Karamertzanis – Imperial College UK)

A big obstacle in predicting the crystal structure of organic molecules is to choose which of the multitude of almost equi-energetic computationally generated minima will really appear in nature. What is clearly missing is the ability to re-rank the lattice enthalpy minima by reliably computing their Gibbs free energy at all temperatures up to the melting point using highly accurate, non-empirical models for the inter- and intra-molecular contributions to the lattice energy. There is clear evidence that methodological improvements in the thermodynamic models increase the number of experimental structures that correspond to the global minimum and hence enhance the reliability of the predictions. This part of my research will deal with the development of cutting-edge methodologies to reliably compute the Gibbs free energy of the organic solid state that underpins several crystal engineering applications.

Development of a portable plugin for free energy calculations: PluMeD

http://merlino.mi.infn.it/~plumed

PLUMED is a plugin for free energy calculation in molecular systems which works together with some of the most popular molecular dynamics engines (GROMACS 3.3/4.0, NAMD2.6, DL_POLY 2, AMBER9-sander module, LAMMPS). Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The present software, written in ANSI-C language, can be easily interfaced with both fortran and C/C++ codes.

Selected Publications

• M. Bonomi, D. Branduardi, G. Bussi, C. Camilloni, D. Provasi, P. Raiteri, D. Donadio, F. Marinelli, F. Pietrucci, R. Broglia, and M. Parrinello, “PLUMED: a portable plugin for free energy calculations with molecular dynamics”, Comp. Phys. Comm., 180, 1961 (2009).
• C. S. Cucinotta, G. Miceli, P. Raiteri, M. Krack, T. D. Kuehne1 , M. Bernasconi, M. Parrinello “Superionic conduction in substoichiometric LiAl alloy: an ab-initio study”, Phys. Rev. Lett., 103, 125901 (2009).
• T. Zykova-Timan, P. Raiteri, M. Parrinello, “Investigating the Polymorphism in PR179: A Combined Crystal Structure Prediction and Metadynamics Study”, J. Phys. Chem B, 112, 13231-13237 (2008).
• D. Donadio, R. Martoňák, P. Raiteri, M. Parrinello, “Influence of Temperature and Anisotropic Pressure on the Phase Transitions in α-Cristobalite”, Phys. Rev. Lett., 100, 165502 (2008).
• P. Raiteri, G. Bussi, C.S. Cucinotta, A. Credi, J.F. Stoddart and M. Parrinello, “Unravelling the Shuttling Mechanism in a Photoswitchable Multicomponent Bistable Rotaxane”, Angew. Chem. In. Ed., 47, 3536-3539 (2008).
• P.G. Karamertzanis, P. Raiteri, M. Parrinello, M. Leslie, S.L. Price, “The Thermal Stability of Lattice Energy Minima of 5-Fluorouracil: Metadynamics as an Aid to Polymorph Prediction”, J. Chem. Phys. B, 112, 4298 -4308 (2008).
• P. Raiteri, A. Laio, F.L. Gervasio, C. Micheletti, M. Parrinello, “Efficient reconstruction of complex free energy landscapes by multiple walkers metadynamics”, J. Chem. Phys. B, 110, 3533-3539 (2006).
• A.R. Oganov, R. Martonak, A. Laio, P. Raiteri, M. Parrinello, “Anisotropy of Earth’s D" layer and stacking faults in the MgSiO3 post-perovskite phase”, Nature, 438 1142-1144 (2005).
• P. Raiteri, R. Martonak, M. Parrinello, “Exploring polymorphism: The case of benzene”, Angew. Chem. Int. Ed., 44, 3769-3773 (2005).
• R. Martonak, A. Laio, M. Bernasconi, C. Ceriani, P. Raiteri, F. Zipoli, M. Parrinello, “Simulation of structural phase transitions by metadynamics”, Zeitscrift fur Krist. 220, 489-498 (2005).
• D. Donadio, P. Raiteri, M. Parrinello, “Topological defects and bulk melting in hexagonal ice”, J. Phys. Chem. B, 109, 5421-5424 (2005).
• F. Montalenti, P. Raiteri, D.B. Migas, H. von Kanel, A. Rastelli, C. Manzano, G. Costantini, U. Denker, O.G. Schmidt, K. Kern, K; L. Miglio, “Atomic-scale pathway of the pyramid-to-dome transition during Ge growth on Si(001)” Phys. Rev. Lett., 93, 216102 (2004).
• P. Raiteri, A. Laio, M. Parrinello, “Correlations among hydrogen bonds in liquid water”, Phys. Rev. Lett., 93, 087801 (2004).
• D.B. Migas, P. Raiteri, L. Miglio, A. Rastelli, H. von Kanel, “Evolution of the Ge/Si(001) wetting layer during Si overgrowth and crossover between thermodynamic and kinetic behavior”, Phys. Rev. B, 69, 235318 (2004).
• L. Martinelli, A. Marzegalli, P. Raiteri, M. Bollani, F. Montalenti, L. Miglio, D. Chrastina, G. Isella, H. von Kanel, “Formation of strain-induced Si-rich and Ge-rich nanowires at misfit dislocations in SiGe: A model supported by photoluminescence data” Appl. Phys. Lett., 84, 2895-2897 (2004).
• A. Rastelli, H. von Kanel, G. Albini, P. Raiteri, D.B. Migas, L. Miglio, “Morphological and compositional evolution of the Ge/Si(001) surface during exposure to a Si flux” Phys. Rev. Lett., 90, 216104 (2003).
• P. Raiteri, L. Miglio, “Energy distribution in Ge islands on Si(001): A spectral and site-resolved analysis versus size and morphology”, Phys. Rev. B, 66, 235408 (2002).
• M. Iannuzzi, P. Raiteri, M. Celino, L. Miglio, “Point defects and stacking faults in TiSi2 phases by tight binding molecular dynamics”, J. Phys. Cond. Matt., 14, 9535-9553 (2002).
• F. Rosei, P. Raiteri, “Stress induced surface melting during the growth of the Ge wetting layer on Si(001) and Si(111)”, Appl. Surf. Sci., 195, 16-19 (2002).
• P. Raiteri, D.B. Migas, L. Miglio, A. Rastelli, H. von Kanel, “Critical role of the surface reconstruction in the thermodynamic stability of {105} Ge pyramids on Si(001)”, Phys. Rev. Lett., 88, 256103 (2002).
• P. Raiteri, L. Miglio, F. Valentinotti, M. Celino, “Strain maps at the atomic scale below Ge pyramids and domes on a Si substrate”, Appl. Phys. Lett., 80, 3736-3738 (2002).
• P. Raiteri, F. Valentinotti, L. Miglio, “Stress, strain and elastic energy at nanometric Ge dots on Si(001)”, Appl. Surf. Sci., 188, 4-8 (2002).
• P. Raiteri, M. Celino, F. Valentinotti, L. Miglio, “2D versus 3D competition at the early stages of growth for Ge on Si(001) by molecular dynamics”, Mat. Sci. Eng. B, 89, 157-159 (2002).
• L. Miglio, M. Iannuzzi, P. Raiteri, M. Celino, “Silicon diffusion in competitive TiSi2 phases by molecular dynamics simulations”, Microel. Eng., 55, 83-92 (2001).
• M. Iannuzzi, P. Raiteri, L. Miglio, “Self-diffusion of silicon in TiSi2 competing phases by tight-binding molecular dynamics”, Comp. Mat. Sci., 20, 394-400 (2001).