Effect of the fluorinated solvents on the stability of secondary structure forming peptides

The effect of 2,2,2-trifluoroethanol (TFE) as a cosolvent on the stability of three different secondary structure-forming peptides, the Melittin, the Betanova, and the β-hairpin II from the bacterial protein GB1 (see the crystal structures in Figure 1), was studied using molecular dynamics simulations.  Continue reading

Application of Quasi-Gaussian entropy theory to predict the properties of simple fluids and biomolecules in solution

The Quasi-Gaussian Entropy theory (QGE) is a new statistical mechanics theory (Amadei et al., J. Chem. Phys. (1996), 104, 1560-1574), that can be used to predict the physical-chemistry properties of real and simulated systems in a very wide temperature range. A new expression of the Clausius-Clapeyron equation, based on the QGE, for the evaluation of the liquid-vapor equilibrium pressure of pure liquids, was developed [1]. The new equation is able to predict the liquid-vapor equilibrium pressure curve, with high accuracy, over a large temperature range and for different fluids like water, methanol, and mercury.

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Molecular Dynamics Simulations Combined to X-Ray Spectroscopies XANES and EXAFS

In Laurea thesis (equivalent to M.Sc. Diploma Thesis, discussed in 1992), I have for the first time investigated and attempted the combination Molecular Dynamics (MD) simulations and theoretical spectra calculation for the interpretation of experimental XANES (X-ray Absorption Near-Edge Spectroscopy) [4]. The method was used to study the aquatrisimidazole copper (II) sulfate complex’s crystal structure, but the results not yet published. The thesis is in Italian, and it is available on request to the interested reader.

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Parallel computing and molecular dynamics simulations

The recent technical developments in parallel computing have made available large parallel computing facilities at relatively contained costs that have stimulated an intense developing activity to realize efficient parallel programs for the scientific and technical calculation. One of the scientific fields that most benefit from these developments is computational chemistry and in particular Molecular Dynamics (MD). The reason of that is related to the increasing interest in the study, with this technique, larger molecular systems for long simulation times. Continue reading