Fabio Pietrucci

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Bridging Static and Dynamical Descriptions of Chemical Reactions: An ab Initio Study of CO2 Interacting with Water Molecules

Wanda Andreoni, Fabio Pietrucci

Extracting reliable thermochemical parameters from molecular dynamics simulations of chemical reactions, although based on ab initio methods, is generally hampered by difficulties in reproducing the results and controlling the statistical errors. This is a ...

Amer Chemical Soc2012

Exohedral Hydrogen Chemisorption on a Carbon Nanotube: The Clustering Effect

Wanda Andreoni, Fabio Pietrucci, Alessandro Curioni

Density functional theory-based calculations of the (10,0) zigzag single-walled carbon nanotube with hydrogen chemisorbed exohedrally show that electron pairing and strain minimization lead hydrogen atoms to cluster and preferentially sit in axial configur ...

2012

Which similarity measure is better for analyzing protein structures in a molecular dynamics trajectory?

Fabio Pietrucci

An important step in the computer simulation of the dynamics of biomolecules is the comparison of structures in a trajectory by exploiting a measure of distance. This allows distinguishing structures which are geometrically similar from those which are dif ...

2011

Graph Theory Meets Ab Initio Molecular Dynamics: Atomic Structures and Transformations at the Nanoscale

Wanda Andreoni, Fabio Pietrucci

Social permutation invariant coordinates are introduced describing the bond network around a given atom. They originate from the largest eigenvalue and the corresponding eigenvector of the contact matrix, are invariant under permutation of identical atoms, ...

2011

CdTe surfaces: Characterizing dynamical processes with first-principles metadynamics

Wanda Andreoni, Fabio Pietrucci, Guido Gerra

We study dynamical processes at CdTe surfaces using ab initio metadynamics simulations. The c(2X2) to (2X1) transition of the Te-terminated (001) surface is found to involve a "c(2X2) + (2X1)" intermediate, consistent with experiment, and crossing of simil ...

AIP American Institute of Physics2010

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Exohedral Hydrogen Chemisorption on a Carbon Nanotube: The Clustering Effect

Wanda Andreoni, Fabio Pietrucci, Alessandro Curioni

2012

Graph Theory Meets Ab Initio Molecular Dynamics: Atomic Structures and Transformations at the Nanoscale

Wanda Andreoni, Fabio Pietrucci

2011

Bridging Static and Dynamical Descriptions of Chemical Reactions: An ab Initio Study of CO2 Interacting with Water Molecules

Wanda Andreoni, Fabio Pietrucci

Amer Chemical Soc2012

Which similarity measure is better for analyzing protein structures in a molecular dynamics trajectory?

Fabio Pietrucci

2011

CdTe surfaces: Characterizing dynamical processes with first-principles metadynamics

Wanda Andreoni, Fabio Pietrucci, Guido Gerra

AIP American Institute of Physics2010