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BRIEF
HISTORY OF THE GROUP Up to 1995 the Alfredo Di Nola's interests were mainly focussed in the field of molecular dynamics simulations of biomolecules and in developing new algorithms for the simulations. In 1995 he started a collaboration with Andrea Amadei who was working in the H.J.C. Berendsen's group, in the Netherlands, in the field of theoretical physical-chemistry. Andrea Amadei joined the Di Nola's group in 1996. In 1999 the group was also joined by Massimiliano Aschi whose experience was mainly in quantum chemistry.
RESEARCH Our research activities are mainly focussed in the field of molecular dynamics simulations, quantum mechanics and statistical mechanics of biomolecular systems (biopolymers, lipids etc.) and more in general of complex molecular systems (liquids, polyatomic molecules, etc.). The goal is the understanding and prediction of the macroscopic properties of such systems on the basis of their behaviour as obtained from computer simulations and theoretical models. The current research directions range from the study of biomacromolecules to electronic structure:
MECHANICS
AND DYNAMICS OF BIOMOLECULES This research area is mainly focussed on the understanding of biophysical-biochemical processes at molecular level. Our work concentrates on the study of biologically relevant molecules via molecular dynamics simulations, as well as on the development of tools such as simulation algorithms, and theoretical models. The final aim of such research is the prediction of biomolecular properties to be used in particular in conjunction with advanced experimental techniques such as time-resolved X-ray spectroscopy, NMR, EXAFS etc.
Our
current projects in this field concern basically molecular
recognition (protein folding, misfolding and ligand-receptor
binding), conformational equilibria (proteins conformational
behaviour) and biochemical activity (physical-chemical reactions). FLUID STATE STATISTICAL MECHANICS One of the most challenging area in theoretical physical chemistry is the modelling of fluid state physics and chemistry. In particular, the study of biochemical and biophysical systems requires the use of general reliable models for fluid state. Our activity in this field is mainly devoted to the development of theoretical models and simulation algorithms for fundamental studies as well as for supporting more specialized investigations (e.g. biomolecular research). Our current projects concern the extension of the statistical mechanical Fluctuation Theory, the Quasi-Gaussian Entropy theory (QGE), developed in collaboration with H.J.C. Berendsen in Groningen.
QUANTUM MECHANICS This research area is mainly focussed on the understanding of the quantum mechanical basis of physico-chemical processes ranging from molecular interactions to electronic structure. The research is aimed to the description of fundamental events as well as for supporting more specialized studies addressed to reactivity and spectroscopic properties of biomolecules. We are extending the Perturbed Matrix Method (PMM) developed in our group.PMM, in conjunction with classical molecular dynamics, has given excellent results in the prediction of spectroscopic properties (electronic, IR, ORD spectra), in the study of enzymatic reactions and in the study of the effects of an external perturbative field on electronic structure of proteins.
ALGORITHMS FOR MOLECULAR DYNAMICS SIMULATIONS The improvement of computational power nowadays makes it possible to rigorously describe the physical chemistry at molecular level, by means of computer simulations. However, such an advancement requires a continuous development of new algorithms based on a sound theoretical background. Our work in this field is mainly focussed on the following subjects: a) the improvement of the equations of motions for classical molecular dynamics MD simulations; b) the development of a new molecular force field, based on mixed quantum classical mechanical calculations, providing molecular polarizability.
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