Molecular Modeling Lab

Peptide on graphene

Poster for CRESCO Meeting (May 2008), pdf file
A small peptide of 12 amminoacid, selected by phage display for its high affinity to
carbon nanotubes, has been folded in solution by using MD simulation
with classical force fields. A best folded structure has been obtained by selecting, on the
basis of the potential Energy, all folded structures appearing during two independent
MD simulations of 20 ns. each.
The resulting structure was subsequently docked on two different, carbon-based substrates,
namely a single-wall carbon nanotube (SWNT) and a flat graphene sheet. The docking of the
peptide on the different substrates has been performed in two steps: firstly, a rigid
docking has been performer by using the AUTODOCK tool by following a
steepest-descent force relaxation. The resulting lowest-energy configuration of the total system
(peptide plus substrate) has been equilibrated, at room temperature, by using MD simulations
with classical force fields in water.
The resulting configuration is then the object of electronic structure calculations, based on ab initio
Car-Parrinello molecular dynamics, to evaluate the electronic structure of the peptide as
relaxed by classical molecular dynamics simulations. Interaction with the SWNT will be
considered and characterized in terms of charge densities and polarizability.

Collaboration with:

MgH2-Mg interface: a first principle
molecular dynamics characterization

Poster for CRESCO Meeting (May 2008), pdf file

Nanostructured magnesium hydride MgH2, prepared by a mechanical milling method,
is considered an attractive hydrogen storage material. In particular, MgH2 shows interesting
properties such as high H2 gravimetric storage capacity (7.6 wt%), low cost and high abundance.
However, this material displays too high temperatures of decomposition, mainly owing to high
thermodynamic stability and slow decomposition kinetics, so that several routes have been
proposed in order to enhance the reaction and to reduce the decomposition temperature.
These processes are based on the introduction of an high density of crystal defects or by
ball-milling with intermetallic compounds with lower hydrogen desorption temperature than magnesium.

Since the desorption mechanism is strongly influenced by the chemical and mechanical
properties at the interface between MgH2 and Mg, a detailed study of this interface is
needed. From an experimental point of view there is not a clear evidence of which interfaces
are involved in the hydrogen diffusion and which is the atomic dynamics at the interfaces.
However, extensive first-principle molecular dynamics simulations of the interface MgH2-Mg give
clear indications of both the equilibrium properties and the behaviour of the Mg and H atoms
in terms of total energy calculations. The interface and the hydrogen desorption are studied as
functions of the temperature. The atomic environment of the Mg atoms at the interface and
hydrogen paths for desorption are characterized and studied. Furthermore some indications
of the rearrangement of the magnesium atoms after desorption are provided to characterize the phase transition.

Collaboration with:

Icosaehdral order in undercooled metals
Poster (June 2006), pdf file

We elucidate the role played by defective icosahedra on the stability of
undercooled copper by using molecular-dynamics simulations. Our approach is
substantiated by the level of agreement with experiments on a variety of structural properties.
We show that not only perfect but also defective icosahedra, embedded in a disordered matrix,
lower the local cohesive energy. This has the effect of stabilizing the liquid structure against
crystallization. Our work rationalizes experimental findings by identifying the nature of those
icosahedral subunits that contribute to the stability of the undercooled liquid.

Collaboration with:
prof. Andrea di Cicco, University of Camerino, Italy

Intermediate range order in disordered materials

We elucidate the structural properties of amorphous SiSe2 by first-principles molecular dynamics.
The calculated structure factor is in very good agreement with experiments, as well as the number
of corner- and edge-sharing tetrahedra. By focusing on the sequences of Si atoms linked via
 intra- and intertetrahedral bonds, we identify the predominant structural motifs.
The sequences involving both corner- and edge-sharing connections are significantly more
frequent than those formed exclusively by edge-shared Si atoms. Our results clarify a
longstanding controversy on the structure of this prototypical disordered network-forming material.

Collaboration with:
dr. Carlo Massobrio, IPCMS-CNRS, Strasbourg, France