Fabio Pietrucci

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Related publications (25)

Fate of a Graphene Flake: A New Route toward Fullerenes Disclosed with Ab Initio Simulations

Wanda Andreoni, Fabio Pietrucci

The top-down formation of a fullerene from a graphene flake is investigated via extensive ab initio molecular dynamics simulations in the range 300-3000 K, accelerated by metadynamics. Topological (SPRINT) coordinates are used to ensure a prejudice-free ex ...

Amer Chemical Soc2014

DFT-Derived Reactive Potentials for the Simulation of Activated Processes: the Case of CdTe and CdTe:S

Wanda Andreoni, Fabio Pietrucci, Riccardo Ciaglia

We introduce a new ab initio derived reactive potential for the simulation of CdTe within density functional theory (DFT) and apply it to calculate both static and dynamical properties of a number of systems (bulk solid, defective structures, liquid, surfa ...

Amer Chemical Soc2014

Characterizing and Understanding Divalent Adsorbates on Carbon Nanotubes with Ab Initio and Classical Approaches: Size, Chirality, and Coverage Effects

Wanda Andreoni, Fabio Pietrucci, Alessandro Curioni

The study of oxygen chemisorption on single-walled carbon nanotubes generally relies on simple atomistic models and hence hampers the possibility to understand whether nanotube size or adduct concentration have a role in determining the surface adsorbate i ...

Amer Chemical Soc2014

Atomic Oxygen Chemisorption on Carbon Nanotubes Revisited with Theory and Experiment

Wanda Andreoni, Fabio Pietrucci, Alessandro Curioni

Density-functional-theory based calculations of two single-walled carbon nanotubes of different chirality settle open issues on the sidewall chemisorption of atomic oxygen at low concentrations. Ether groups are the thermodynamically favored configurations ...

Amer Chemical Soc2013

Structural cluster analysis of chemical reactions in solution

Fabio Pietrucci

We introduce a simple and general approach to the problem of clustering structures from atomic trajectories of chemical reactions in solution. By considering distance metrics which are invariant under permutation of identical atoms or molecules, we demonst ...

Amer Inst Physics2013

The Fate of a Zwitterion in Water from ab Initio Molecular Dynamics: Monoethanolamine (MEA)-CO2

Wanda Andreoni, Fabio Pietrucci

Understanding the fundamental reactions accompanying the capture of carbon dioxide in amine solutions is critical for the design of high-performance solvents and requires an accurate modeling of the solute-solvent interaction. As a first step toward this g ...

Amer Chemical Soc2013

Mapping the Native Conformational Ensemble of Proteins from a Combination of Simulations and Experiments: New Insight into the src-SH3 Domain

Fabio Pietrucci

The biological function of a protein is strongly tied to the ensemble of three-dimensional conformations populated at physiological temperature, and dynamically transforming into each other. Experimental techniques such as nuclear magnetic resonance spectr ...

Amer Chemical Soc2013

Nucleation Process of a Fibril Precursor in the C-Terminal Segment of Amyloid-beta

Fabio Pietrucci

By extended atomistic simulations in explicit solvent and bias-exchange metadynamics, we study the aggregation process of 18 chains of the C-terminal segment of amyloid-beta, an intrinsically disordered protein involved in Alzheimer's disease and prone to ...

Amer Physical Soc2013

METAGUI. A VMD interface for analyzing metadynamics and molecular dynamics simulations

Fabio Pietrucci

We present a new computational tool, METAGUI, which extends the VMD program with a graphical user interface that allows constructing a thermodynamic and kinetic model of a given process simulated by large-scale molecular dynamics. The tool is specially des ...

2012

Multidimensional View of Amyloid Fibril Nucleation in Atomistic Detail

Fabio Pietrucci

Starting from a disordered aggregate, we have simulated the formation of ordered amyloid-like beta structures in a system formed by 18 polyvaline chains in explicit solvent, employing molecular dynamics accelerated by bias-exchange metadynamics. We exploit ...

2012

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