Biomedical subjects

José Alejandre

Publications and source records attributed to José Alejandre.

12 recordsLinked to original sources

PubMed2006

Electrostatic interactions in dissipative particle dynamics using the Ewald sums.

The electrostatic interactions in dissipative particle dynamics (DPD) simulations are calculated using the standard Ewald [Ann. Phys. 64, 253 (1921)] sum method. Charge distributions on DPD particles are included to prevent artificial ionic pair formation. This proposal is an alternative method to that introduced recently by Groot [J. Chem. Phys. 118, 11265 (2003)] where the electrostatic field was solved locally on a lattice. The Ewald method is applied to study a bulk electrolyte and polyelectrolyte-surfactant solutions. The structure of the fluid is analyzed through the radial distribution function between charged particles. The results are in good agreement with those reported by Groot for the same systems. We also calculated the radius of gyration of a polyelectrolyte in salt solution as a function of solution pH and degree of ionization of the chain. The radius of gyration increases with the net charge of the polymer in agreement with the trend found in static light scattering experiments of polystyrene sulfonate solutions.

Journal Article↗

PubMed2006

Molecular dynamics simulations of aqueous solutions of ethanolamines.

We report on molecular dynamics simulations performed at constant temperature and pressure to study ethanolamines as pure components and in aqueous solutions. A new geometric integration algorithm that preserves the correct phase space volume is employed to study molecules having up to three ethanol chains. The most stable geometry, rotational barriers, and atomic charges were obtained by ab initio calculations in the gas phase. The calculated dipole moments agree well with available experimental data. The most stable conformation, due to intramolecular hydrogen bonding interactions, has a ringlike structure in one of the ethanol chains, leading to high molecular stability. All molecular dynamics simulations were performed in the liquid phase. The interaction parameters are the same for the atoms in the ethanol chains, reducing the number of variables in the potential model. Intermolecular hydrogen bonding is also analyzed, and it is shown that water associates at low water mole fractions. The force field reproduced (within 1%) the experimental liquid densities at different temperatures of pure components and aqueous solutions at 313 K. The excess and partial molar volumes are analyzed as a function of ethanolamine concentration.

Computer Simulation↗

PubMed2006

The intrinsic structure of the water surface.

An operational procedure to obtain the intrinsic structure of liquid surfaces is applied here to a molecular dynamics simulation of water, with a model of point charges for the molecular interactions. The method, which had been recently proposed and used for simple fluids, is successfully extended to a molecular liquid with the complex bond structure of water. The elimination of the capillary wave fluctuations, in the intrinsic density and orientation profiles, gives a new overall view of the water surface, at the sharpest molecular level, and without the size-dependent broadening observed in the mean profiles. The molecules belonging to the outer liquid layer are clearly identified, and we find that only these molecules exhibit a clear preferential orientation to lie flat on the surface. Moreover, there is a strong correlation between the dipolar structure and the local curvatures of the intrinsic surface, so that at the extrusions of the intrinsic surface the molecular dipoles point preferentially toward the vapor side of the interface. Finally, we have found an intrinsic density layering structure, although the inner structure is strongly damped beyond the second layer.

Journal Article↗

PubMed2006

Finite-size effects in dissipative particle dynamics simulations.

We have performed dissipative particle dynamics (DPD) simulations to evaluate the effect that finite size of transversal area has on stress anisotropy and interfacial tension. The simulations were carried out in one phase and two phases in parallelepiped cells. In one-phase simulations there is no finite-size effect on stress anisotropy when the simulation is performed using repulsive forces. However, an oscillatory function of stress anisotropy is found for attractive-repulsive interactions. In the case of liquid-liquid interfaces with repulsive interaction between molecules, there is only a small effect of surface area on interfacial tension when the simulations are performed using the Monte Carlo method at constant temperature and normal pressure. An important but artificial finite-size effect of interfacial area on surface tension is found in simulations in the canonical ensemble. Reliable results of interfacial tension from DPD simulations can be obtained using small systems, less than 2000 particles, when they interact exclusively with repulsive forces.

Journal Article↗

PubMed2005

Computer simulations of surfactant monolayers at solid walls.

A series of molecular dynamics simulations to study the structure of a surfactant monolayer near real surfaces was carried out. A comparison of two different surfaces, TiO2 and SiO2, with the same monolayer was performed. Moreover, each surface was modeled by two different approaches, the first model considers the complete structure of a TiO2 (or SiO2) wall, whereas the second model is a continuous solid wall with an effective potential. Both wall models give essentially the same monolayer configuration suggesting that the explicit form of the wall does not play a relevant role to study the structure of surfactant monolayers close to planar surfaces.

Journal Article↗

PubMed2005

Oscillatory surface tension due to finite-size effects.

The simulation results of surface tension at the liquid-vapor interface are presented for fluids interacting with Lennard Jones and square-well potentials. From the simulation of liquids we have reported [M. González-Melchor et al., J. Chem. Phys. 122, 4503 (2005)] that the components of pressure tensor in parallelepiped boxes are not the same when periodic boundary conditions and small transversal areas are used. This fact creates an artificial oscillatory stress anisotropy in the system with even negative values. By doing direct simulations of interfaces we show in this work that surface tension has also an oscillatory decay at small surface areas; this behavior is opposite to the monotonic decay reported previously for the Lennard Jones fluid. It is shown that for small surface areas, the surface tension of the square-well potential artificially takes negative values and even increases with temperature. The calculated surface tension using a direct simulation of interfaces might have two contributions: one from finite-size effects of interfacial areas due to box geometry and another from the interface. Thus, it is difficult to evaluate the true surface tension of an interface when small surface areas are used. Care has to be taken to use the direct simulation method of interfaces to evaluate the predicted surface tension as a function of interfacial area from capillary-wave theory. The oscillations of surface tension decay faster at temperatures close to the critical point. It is also discussed that a surface area does not show any important effect on coexisting densities, making this method reliable to calculate bulk coexisting properties using small systems.

Journal Article↗

PubMed2005

Molecular dynamics simulations of the surface tension of ionic liquids.

We report molecular dynamics computer simulations of the surface tension and interfacial thickness of ionic liquid-vapor interfaces modeled with a soft core primitive model potential. We find that the surface tension shows an anomalous oscillatory behavior with interfacial area. This observation is discussed in terms of finite size effects introduced by the periodic boundary conditions employed in computer simulations. Otherwise we show that the thickness of the liquid-vapor interface increases with surface area as predicted by the capillary wave theory. Data on the surface tension of size-asymmetric ionic liquids are reported and compared with experimental data of molten salts. Our data suggest that the surface tensions of size-asymmetric ionic liquids do not follow a corresponding states law.

Journal Article↗

PubMed2005

Stress anisotropy induced by periodic boundary conditions.

Finite size effects due to periodic boundary conditions are investigated using computer simulations in the canonical ensemble. We study liquids with densities corresponding to typical liquid coexistence densities, and temperatures between the triple and critical points. The components of the pressure tensor are computed in order to analyze the finite size effects arising from the size and geometry of the simulation box. Two different box geometries are considered: cubic and parallelepiped. As expected the pressure tensor is isotropic in cubic boxes, but it becomes anisotropic for small noncubic boxes. We argue this is the origin of the anomalous behavior observed recently in the computation of the surface tension of liquid-vapor interfaces. Otherwise, we find that the bulk pressure is sensitive to the box geometry when small simulation boxes are considered. These observations are general and independent of the model liquid considered. We report results for liquids interacting through short range forces, square well and Lennard-Jones, and also long range Coulombic interactions. The effect that small surface areas have on the surface tension is discussed, and some preliminary results at the liquid vapor-interface for the square well potential are given.

Journal Article↗

PubMed2005

Liquid-vapor equilibrium and surface tension of nonconformal molecular fluids.

Molecular dynamics simulations at constant temperature have been performed on the liquid-vapor interface for fluids characterized by a recently introduced three-parameter potential. This potential is a modification of the well-known spherical Kihara interaction and is termed approximate nonconformal (ANC). It has been used successfully to describe many real molecules in the gaseous phase. Besides the usual molecular energy and size, the ANC potential introduces a third parameter s, called softness, to measure the form of the potential profile. Study of these systems shows that their critical and interfacial properties follow very closely those of four selected substances: argon, methane, propane, and hexane. Deviations of the properties predicted from the experimental values are analyzed and their probable causes are determined. The critical properties of ANC fluids and their dependence on s are also obtained via first-order perturbation theory in the form of an augmented van der Waals model. Analysis of the results shows that ANC potential functions can be used as reliable effective interactions for real dense fluids.

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PubMed2004

Liquid-vapor interface of square-well fluids of variable interaction range.

Properties of the liquid-vapor interface of square-well fluids with ranges of interaction lambda=1.5, 2.0, and 3.0 are obtained by Monte Carlo simulations and from square-gradient theories that combine the Carnahan-Starling equation of state for hard spheres with the second and third virial coefficients. The predicted surface tensions show good agreement with the simulation results for lambda=2 and for lambda=3 in a temperature range reasonably close to the critical point, 0.8</=T/T(c)</=0.95. As expected, the surface tension increases with the range of interaction and decreases monotonically with temperature. A comparison between theory and simulation results is also given for the width of the interface and for the coexistence curves for the different interaction ranges.

Journal Article↗

PubMed2004

Surface tension of associating fluids by Monte Carlo simulations.

Canonical Monte Carlo (NVT-MC) simulations were performed to obtain surface tension and coexistence densities at the liquid-vapor interface of one-site associating Lennard-Jones and hard-core Yukawa fluids, as functions of association strength and temperature. The method to obtain the components of the pressure tensor from NVT-MC simulations was validated by comparing the equation of state of the associative hard sphere system with that coming from isothermal-isobaric Monte Carlo simulations. Surface tension of the associative Lennard-Jones fluid determined from NVT-MC is compared with previously reported results obtained by molecular dynamics simulations of a pseudomixture model of monomers and dimers. A good agreement was found between both methods. Values of surface tension of associative hard-core Yukawa fluids are presented here for the first time.

Journal Article↗

PubMed2003

Surface tension of the restrictive primitive model for ionic liquids.

Hybrid molecular dynamics and Monte Carlo simulations are performed to study the liquid-vapor interface of the restricted primitive model (RPM) of ionic fluids. We report for the first time simulation results of the surface tension associated to this interface. The RPM accurately predicts experimental surface tensions of ionic salts and good agreement with theoretical predictions that include the idea of ion association is found. The simulation results indicate that the structure of an ionic liquid-vapor interface is rather rough. This is reflected in the interfacial thickness, larger than that observed in simple fluids and water.

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