Structure, Dynamics and Thermodynamics of Nanostructured and Biophysical Systems

Cluster

Theoretical Physics

Description

The Research group concerning “Structure, dynamics and thermodynamics of nanostructured and biophysical systems” is active both in the field of theoretical-computational simulations and in the field of experimental techniques, in particular Nuclear Magnetic Resonance (NMR) in collaboration with prof. G. Esposito (New York University at Abu Dhabi, UAE).

The group's numerical simulation activity deals with a wide range of timescales, dimensions and levels of theory and accuracy. The simulations from prime principles based on the theory of the density functional (such as the Car-Parrinello molecular dynamics) are the most accurate and the most demanding, in terms of computational resources. In this field, P.G. is active in the development of new methodologies and the related software, in particular as to the distributed open-source Quantum ESPRESSO, used by many groups all over the world, whose development he coordinates, in cooperation with the European MaX Project. The systems studied by P.G. in recent works include: organic-inorganic heterostructures for photovoltaic devices and applications; aggregation of models of peptide chains due to metal ions; catalytic properties and gas absorption on graphene and carbon nanotubes.

The simulations of biomolecules with classical force fields provide atomic-level information as to molecular dynamics and on the differences in the free energy in conformational fields and in the biomolecular interactions. The group developed methods for electrostatics calculations and for free energy calculations from simulations. On the experimental side, the NMR spectroscopy allows the detailed study at the atomic level of the structure, interactions and kinetics of biomolecular processes. The group (when headed by Prof. G. Esposito) developed an experiment (BLUU-Tramp) in which the hydrogen-deuterium exchange is monitored as a function of time and temperature. The passing of time is coupled with the increase in temperature. In this way, it is possible to achieve in one session the information that would require weeks or months by means of traditional exchange experiments.Specific programs have also been developed for the calculation of conformational (PDB2ENTROPY), rotational/translational (PDB2TRENT) entropies and for electrostatics calculations in biosystems in solution (BLUUES). Simulations and experiments are applied to different biological systems including proteins, drugs and nanoparticles.

Research subjects

New developments, validation and porting of scientific software for first-principles calculations to exascale
New catalysers obtained by deposition on graphene and self-organization of biomimetic molecules
Quantum transport with non-equilibrium Green's function with electron-phonon interaction from first principles
Calculations of free energy through simulations
Biomolecular electrostatics
Biomolecular Nuclear Magnetic Resonance, thermodynamics and local and global dynamics
Biocatalysis in deep eutectic solvents