Silvio a Beccara

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We investigate the folding mechanism of the WW domain Fip35 using a realistic atomistic force field by applying the Dominant Reaction Pathways approach. We find evidence for the existence of two folding pathways, which differ by the order of formation of the two hairpins. This result is consistent with the analysis of the experimental data on the folding(More)
Silicon carbide (SiC) has unique chemical, physical, and mechanical properties. A factor strongly limiting SiC-based technologies is the high-temperature synthesis. In this work, we provide unprecedented experimental and theoretical evidence of 3C-SiC epitaxy on silicon at room temperature by using a buckminsterfullerene (C(60)) supersonic beam. Chemical(More)
In this work, we investigate the processes leading to the room-temperature growth of silicon carbide thin films by supersonic molecular beam epitaxy technique. We present experimental data showing that the collision of fullerene on a silicon surface induces strong chemical-physical perturbations and, for sufficient velocity, disruption of molecular bonds,(More)
The local thermal behavior of the Ag(2)O framework structure has been studied by extended x-ray absorption fine structure. The average Ag-O nearest-neighbor distance expands upon heating, while the Ag-Ag next-nearest-neighbor distance contracts. An original implementation of the cumulant analysis shows that the Ag-O expansion is a joint effect of potential(More)
Protease inhibition by serpins requires a large conformational transition from an active, metastable state to an inactive, stable state. Similar reactions can also occur in the absence of proteases, and these latency transitions take hours, making their time scales many orders of magnitude larger than are currently accessible using conventional molecular(More)
Using the dominant reaction pathways method, we perform an ab initio quantum-mechanical simulation of a conformational transition of a peptide chain. The method we propose makes it possible to investigate the out-of-equilibrium dynamics of these systems, without resorting to an empirical representation of the molecular force field. It also allows to study(More)
We introduce a framework to investigate ab initio the dynamics of rare thermally activated reactions, which cannot be studied using the existing techniques. The electronic degrees of freedom are described at the quantum-mechanical level in the Born-Oppenheimer approximation, while the nuclear degrees of freedom are coupled to a thermal bath, through a(More)
We introduce a variational approximation to the microscopic dynamics of rare conformational transitions of macromolecules. Within this framework it is possible to simulate on a small computer cluster reactions as complex as protein folding, using state of the art all-atom force fields in explicit solvent. We test this method against MD simulations of the(More)
In this work we demonstrate that core level analysis is a powerful tool for disentangling the dynamics of a model polypeptide undergoing conformational changes in solution and disulphide bond formation. In particular, we present computer simulations within both initial and final state approximations of 1s sulphur core level shifts (S1s CLS) of the CYFC(More)
We introduce an iterative algorithm to efficiently simulate protein folding and other conformational transitions, using state-of-the-art all-atom force fields. Starting from the Langevin equation, we obtain a self-consistent stochastic equation of motion, which directly yields the reaction pathways. From the solution of this set of equations we derive a(More)