Biomedical subjects

Josep Bonet Avalos

Publications and source records attributed to Josep Bonet Avalos.

6 recordsLinked to original sources

PubMed2005

Histogram reweighting method for dynamic properties.

The histogram reweighting technique, widely used to analyze Monte Carlo data, is shown to be applicable to dynamic properties obtained from molecular dynamics simulations. The theory presented here is based on the fact that the correlation functions in systems in thermodynamic equilibrium are averages over initial conditions of trajectory functions, the latter depending on the volume of the system, the total number of particles, and the classical Hamiltonian. Thus, the well-known histogram reweighting method can be almost straightforwardly applied to reconstruct the probability distribution of initial states at different thermodynamic conditions, without extra computational effort. Correlation functions and transport coefficients are obtained with this method from few simulation data sets.

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PubMed2005

Transport coefficients and dynamic properties of hydrogen sulfide from molecular simulation.

Molecular-dynamics simulation results on thermodynamic and transport properties of pure H2S under conditions of practical interest are presented. Our data are in very good quantitative agreement with the scarce experimental data and estimates on thermophysical properties of this substance. Our results serve as a test of the validity of the intermolecular potential used in the simulations as well as the consistency of the existing data in the studied range. New simulation data on thermal conductivity at low temperature as well as in supercritical states are also reported. Furthermore, we present a comparative analysis between the local order in the liquid phase of pure hydrogen sulfide and water, due to the molecular analogies between both substances, and its relation with the formation of H=S bonds. Our results indicate that under the same corresponding thermodynamic states, H2S is a much less structured substance, with a first solvation shell with a dodecahedral order instead of the tetrahedral order observed in water.

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PubMed2005

Computing the Soret coefficient in aqueous mixtures using boundary driven nonequilibrium molecular dynamics.

We have computed the Soret coefficient in aqueous mixtures using a boundary driven nonequilibrium molecular dynamics algorithm and standard molecular force fields. The choice of this specific approach is justified by the nature of the mixtures studied here. Four aqueous solutions, including methanol, ethanol, acetone, and dimethyl-sulfoxide (DMSO) have been studied at ambient conditions for different compositions. The experimental behavior of water-alcohol mixtures was reproduced, including the change of sign of the Soret coefficient with composition, in excellent agreement with existing experimental data. The methodology has been applied to obtain pure predictions for water-acetone and water-DMSO where no experimental data are accessible. A change of sign is also observed in the same range of composition as in water-alcohol mixtures. It is suggested that the nature and strength of the molecular interactions, rather than the mass or shape ratio of the components, dominates the behavior of the Soret coefficient versus composition for the aqueous associating mixtures studied here.

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PubMed2005

Prediction of the critical micelle concentration in a lattice model for amphiphiles using a single-chain mean-field theory.

A single-chain mean-field theory is used to predict the properties of binary surfactant solutions including the critical micelle concentration (cmc). In particular, the cmc of two symmetric nonionic amphiphiles is calculated as a function of temperature in order to analyze the validity of the ideal mixing assumption, often employed in the mass action model. On comparing against literature Monte Carlo results for the same lattice model we find that although it is applicable at low temperatures and hence cmcs at low amphiphile concentrations, at higher temperatures it becomes necessary to correct for the nonideal mixing of the free chain-free chain bulk interaction. We find that a simplistic model taking into account only the repulsive interaction is sufficient to restore the excellent quantitative agreement found between a single-chain mean-field theory calculations and literature molecular simulation results at the low temperature limit.

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PubMed2005

Polyoxometalates in solution: Molecular dynamics simulations on the alpha-PW12O40(3-) Keggin anion in aqueous media.

The Keggin anion, PW12O40(3-), is one of the most representative polyoxometalates (POMs). In recent years increasing theoretical work focused on this family of compounds has explained or even predicted some of their properties using quantum mechanics methods. In this report we applied for the first time molecular dynamics (MD) to the title compound to analyze its interactions with water. We used three atomic charge definitions (Mulliken, ChelpG, and formal charges) to carry out MD simulations. The results show that the terminal oxygens of the cluster are invariably most effectively solvated by water because of their prominent position within the framework. On the other hand, bridging oxygens, which are confined in more internal positions, concentrate a smaller portion of the whole solvation. We investigated the hydrogen bonds existing between water and the cluster, confirming that the terminal positions form more contacts with H2O than any other site of the cluster. In the end, the lifetime of such contacts is longer with bridging oxygens, presumably due to their higher atomic charge.

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PubMed2004

Dynamical and structural properties of benzene in supercritical water.

We have employed an anisotropic united atom model of benzene (R. O. Contreras, Ph.D. thesis, Universitat Rovira i Virgili 2002) that reproduces the quadrupolar moment of this molecule through the inclusion of seven point charges. We show that this kind of interaction is required to reproduce the solvation of these molecules in supercritical water. We have computed self-diffusion coefficient and Maxwell-Stefan coefficients as well as the shear viscosity for the mixture water-benzene at supercritical conditions. A strong density and composition dependence of these properties is observed. In addition, our simulations are in qualitative agreement with the experimental evidence that, at medium densities (0.6 g/cm(3) and 673 K), almost half of the benzene molecules have one hydrogen bond with water molecules. We also observe that these bonds are longer lived than the corresponding hydrogen bonds between water molecules. Similarly, we obtain an important reduction of the dielectric constant of the mixture with the increment of the amount of benzene molecules at medium and high densities.

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