Biomedical subjects

Alessandro Tani

Publications and source records attributed to Alessandro Tani.

7 recordsLinked to original sources

PubMed2006

Solvation dynamics by computer simulation: coumarin C153 in 1,4-dioxane.

Computer simulation results are presented for an atomistic pair potential model of 1,4-dioxane which takes into account molecular flexibility. The model has been conceived to be applied to the study of solvatochromism and solvation dynamics in the presence of the polar probe coumarin C153. Computer simulations on the pure liquid have produced thermodynamical, structural, and dynamical data in good agreement with available experimental measures. This constitutes a valuable test of the 1,4-dioxane all-atom model employed. The study of solute-solvent interactions for C153 in 1,4-dioxane has been motivated by the aim of casting light, through simulations, on the interesting experimental findings according to which such a solvent behaves as a "polar" solvent with respect to dynamic solvation properties. Molecular dynamics is particularly suitable to model the process and provides an interpretation of the so-called "dioxane anomaly". An investigation of the structure of the solvation shell and of the dynamics of solvation is presented and discussed. In particular, the satisfactory accordance between simulated and experimental solvation response implies that the simulations give a reliable description of both solute and solvent at a molecular level and reinforces the idea that the explicit inclusion of discrete solvent molecules is needed for a realistic treatment of solvation phenomena in which the local structure of the liquid plays a key role.

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PubMed2006

Modeling a liquid crystal dynamics by atomistic simulation with an ab initio derived force field.

Atomistic molecular dynamics (MD) simulations of 4-n-pentyl 4'-cyano-biphenyl (5CB) have been performed, adopting a specific ab initio derived force field. Two state points in the nematic phase and three in the isotropic phase, as determined in a previous work, have been considered. At each state point, at least 10 ns have been produced, allowing us to accurately calculate single-molecule properties. In the isotropic phase, the values of the translational diffusion coefficient, and even more so the activation energy for the process, agree well with experimental data. Qualitatively, also the dynamic anisotropy of the nematic phase is correctly accounted for. Rotational diffusion coefficients, which describe spinning and tumbling motions, fall well within the range of experimental values. The reorientational dynamics of our model 5CB covers diverse time regimes. The longest one is strongly temperature dependent and characterized by a relaxation time in accord with experimental dielectric relaxation data. Shear viscosity and Landau-de Gennes relaxation times, typically collective variables, reproduce the experimental results very well in the isotropic phase. In the nematic phase, despite a large statistical uncertainty due to the extremely slow relaxation of the correlation functions involved, our simulation yields the correct relative order of the three experimental Miesowicz viscosities.

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PubMed2005

Orientational dynamics in the isotropic phase of a calamitic liquid-crystal model.

We report a molecular dynamics simulation study on the isotropic phase of an idealized calamitic liquid crystal model with a length-to-width ratio of approximately 5-6. The study focuses on the characterization of single-particle and collective orientational dynamics on approaching the phase transition to the nematic phase. Recent experimental and simulation works have suggested that a power law behavior exists at relatively short times in the decay of the time derivative of the orientational correlation functions. Qualitatively, our simulation data are consistent with these findings. Both single-particle and collective time correlation function derivatives possess, in their respective log-log plots, a linear region at very short times, whose slope is essentially independent from the thermodynamic state. Nevertheless, the single-particle orientational correlation functions are better described by a function which is the sum of a fast exponential, an intermediate stretched-exponential and a slow exponential, while the collective orientational correlation functions are satisfactorily described by a sum of two exponentials, at higher density, or by just one exponential, at lower density.

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PubMed2005

Diffusion and viscosity of a calamitic liquid crystal model studied by computer simulation.

We report a molecular dynamics simulation study on an ensemble of rod-like particles, each composed of nine soft spheres held rigidly along a line. We have calculated translational mean square displacements and velocity autocorrelation functions in the fluid phases exhibited by the model, i.e., smectic A, nematic and isotropic. These quantities have then been used to compute diffusion coefficients. In addition, we have calculated viscosities in the nematic and isotropic phases. Despite its crude nature, the model is capable of providing a faithful reproduction of many features of the transport behavior observed in real liquid-crystalline materials. The simulation results have been compared with the predictions of the modified affine transformation theory, finding only a fair agreement.

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PubMed2005

Numerical study of a calamitic liquid-crystal model: phase behavior and structure.

We have studied an idealized calamitic liquid-crystal model, consisting of a linear rigid array of nine soft repulsive spheres, employing both theory and molecular dynamics simulation. The phase behavior (which includes crystalline, smectic, nematic, and isotropic phases) and structure of a collection of these rodlike particles have been determined by molecular dynamics simulation in an isothermal-isobaric ensemble. The liquid crystalline part of the phase diagram has been compared to that emerging from an Onsager-type density-functional theory. We have found a fair agreement between theory and computer simulation results, with a similar accuracy for the smectic to nematic and nematic to isotropic phase transitions.

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PubMed2005

Atomistic simulation of a nematogen using a force field derived from quantum chemical calculations.

Bulk phase atomistic computer simulations of 4-n-pentyl-4'-cyanobiphenyl (5CB) were performed with a specific force field obtained from ab initio and DFT calculations. The intermolecular potential was previously derived through the fragmentation reconstruction method (FRM), developed in our group. The description of some intramolecular interactions, like the torsional potential between the phenyl rings and at the aryl-alkyl linkage, is achieved through accurate DFT studies. Lengthy ( approximately 40 ns) molecular dynamics (MD) simulations were then carried out at constant atmospheric pressure and different temperatures. The system was stable in the experimental crystalline structure up to 285 K, where the early stage of the melting process appears with the loss of positional order. At higher temperatures (between 290 and 305 K) a kinetically stable, orientationally ordered phase is obtained. This nematic phase was reached starting with three initial configurations, differing in their orientational order parameter. The calculated values of thermodynamic and structural properties of each phase were in fairly good agreement with the relevant experimental data.

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PubMed2004

Computer simulation of solid and liquid benzene with an atomistic interaction potential derived from ab initio calculations.

Molecular dynamics atomistic simulations of solid and liquid benzene have been performed, employing a model intermolecular potential derived from quantum mechanical calculations. The ab initio database includes approximately 200 geometries of the benzene dimer with interaction energies computed at the MP2 level of theory. The accuracy of the modeled force field results is satisfactory. The thermodynamic and structural properties, calculated in the condensed phases, are compared with experimental data and previous simulation results. Single particle and collective dynamical properties are also investigated through the calculation of translational and rotational diffusion coefficients, reorientational dynamics, and viscosities. The agreement of these data with experimental measurements confirms the reliability of the proposed force field.

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