Exploring the transformation mechanisms of matter at the nanoscale with computer simulations

  • Dipartimento di Fisica - Aula 500
  • Seminario

Relatori

Fabio Pietrucci
Sorbonne Universités – Université Pierre et Marie Curie

Dettagli

Condensed matter at the atomic scale transforms according to a multitude of ingenious, sometimes counter-intuitive mechanisms. A few examples are the nucleation of crystals from liquids, the formation of fullerenes from carbon fragments, the folding of proteins into a precise complex geometry, or the prebiotic reactions creating amino acids and nucleotides from much simpler molecules. The study of these transformation processes is a fascinating challenge, where computational methods play a major role since evanescent transition states usually escape experimental characterization. I will present some recently introduced strategies aimed to enhance molecular dynamics simulations and reconstruct free energy landscapes. The basic idea is to follow the changes of topology of the interatomic bond network using coordinates obtained from the adjacency matrix of the corresponding graph. Metadynamics and umbrella sampling are then exploited to explore and sample the space of possible topologies. The following case studies will be reviewed: carbon nanoclusters [1,2], poly(a)morphism in water ices [3], and chemical reactions in solution [4].

[1] F. Pietrucci and W. Andreoni. Graph theory meets ab initio molecular dynamics: atomic structures and transformations at the nanoscale. Phys. Rev. Lett., 107:085504, 2011.
[2] F. Pietrucci and W. Andreoni. Fate of a graphene flake: A new route toward fullerenes disclosed with ab initio simulations. J. Chem. Theory Comput. 10:913, 2014.
[3] F. Pietrucci and R. Martonak. Systematic comparison of crystalline and amorphous phases: charting the landscape of water structures and transformations. J. Chem. Phys. 142:104704, 2015.
[4] F. Pietrucci and A.M. Saitta. Formamide reaction network in gas phase and solution via a unified theoretical approach: toward a reconciliation of different prebiotic scenarios. Proc. Natl. Acad. Sci. U.S.A., 112:15030, 2015.