RESEARCH ACTIVITY
QUASY GAUSSIAN ENTROPY (QGE)
The QGE theory, Andrea Amadei has been applied to different systems in vacuum and in solution giving results in agreement whith theoretical prescriptions. Recently we applied the QGE theory to molecular dynamics simulations of ionic solutions in order to obtain statistical mechanical and thermodynamical predictions as a function of temperature. Results showed that the use of the Gamma state model provides an excellent theoretical description of the solution behavior in a wide range of temperature. It has been hence possible the evaluation of partial molar properties like free energy and entropy at relatively low computational cost.
COMPARISON OF THE MOST WIDELY USED TEMPERATURE COUPLING ALGORITHMS
I investigated molecular dynamics trajectories of a butane molecule, as obtained using different types of thermostats. Results show that the Nose'-Hoover thermostat fails to reproduce the statistical machanical behavior, even using simulation lenghts of millions of timesteps, whereas the Gaussian isokinetic (IG) thermostat reproduces quite well the expected statistical mechanical values. The Berendsen's (BC) coupling provides good results for basic properties but fails in reproducing the canonical fluctuations. Moreover the chaoticity analysis (see below) of the trajectories showed that the NH thermostat provides very slow divergence for the physical phase space, concentrating most of its chaoticity in the dynamics of the virtual added variable. On the contrary the IG thermostat provides always highly diverging trajectories in phase space and the BD one provides a moderate chaotic behavior for all the degrees of freedom.
COEXISTENCE OF ORDERED AND CHAOTIC DYNAMICS IN COMPLEX SYSTEMS.
I analyzed the dynamical behavior of simulated systems of many degrees of freedom, simulated with classical molecular dynamics. I developped some usefull diagnostic tools (Coherence Angles, CAs) to point out the difference in the dynamics of the single degrees of freedom. The CAs provide a measure in the tangent space of the phase space of the angular between any physically relevant direction and the direction of maximum expansion. They allow at the same time a detailed characterization and a synoptic view of the dynamical behavior of a system with many degrees of freedom. These tools have been applied to two- and three- dimensional Lennard-Jones lattice, to a butane molecule simulated in vacuum and now are being applied to a polipeptide, the contryphan, simulated in water.