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Luca Ferraro

Publications and source records attributed to Luca Ferraro.

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Dissecting the hydrogen bond: a Quantum Monte Carlo approach

We present a variational MonteCarlo (VMC) and lattice regularized diffusion MonteCarlo (LRDMC) study of the binding energy and dispersion curve of the water dimer. As a variation ansatz we use the JAGP wave function, an implementation of the resonating valence bond (RVB) idea. Actually one the aim of the present work is to investigate how the bonding of two water molecules, as a prototype of the hydrogen-bonded complexes, could be described within an JAGP approach. Using a pseudopotential for the inert core of the Oxygen, with a full optimization of the variational parameters, we obtain at the VMC level a binding energy of -4.5(0.1) Kcal/mol, while LRDMC calculations gives -4.9(0.1) Kcal/mol (experiment 5 Kcal/Mol). The calculated dispersion curve reproduces both at the VMC and LRDMC level the miminum position and the curvature.The quality of the WF gives us the possibility to dissect the binding energy in different contributions by appropriately switching off determinantal and Jastrow terms in the JAGP: we estimate the dynamical contribution to the binding energy to be of the order of 1.4(0.2) Kcal/Mol whereas the covalent contribution about 1.0(0.2) Kcal/Mol. JAGP reveales thus a promising WF for describing systems where both dispersive and covalent forces play an important role.

physics.chem-ph

Co-expression of statistically over-represented peptides in proteomes: a key to phylogeny ?

It is proposed that the co-expression of statistically significant motifs among the sequences of a proteome is a phylogenetic trait. From the co-expression matrix of such motifs in a group of prokaryotic proteomes a suitable definition of a phylogenetic distance is introduced and the corresponding distance matrix between proteomes is constructed. From the distance matrix a phylogenetic tree is inferred, following a standard procedure. It compares well with a reference tree deduced from a distance matrix obtained from the alignment of ribosomal RNA sequences. Our results are consistent with the hypothesis that biological evolution manifests itself with a modulation of basic correlations between shared peptides of short length, present in protein sequences. Moreover, the simple procedure we propose reconfirms that it is possible, sampling entire proteomes, to average the effects of lateral gene transfer and infer reasonable phylogenies.

q-bio.MN