Biomedical subjects

E Allahyarov

Publications and source records attributed to E Allahyarov.

5 recordsLinked to original sources

PubMed2002

Mesoscopic solvent simulations: multiparticle-collision dynamics of three-dimensional flows.

A recently developed mesoscopic solvent model with multiparticle-collision dynamics is applied to three-dimensional solvent flows in a channel with and without a spherical obstacle. The advantage of a gravitationally driven flow of the solvent over the flow induced by a pressure gradient in the calculation of the solvent viscosity is demonstrated. Three different algorithms for stochastic collision steps are investigated and compared. In particular, we have examined an alternative algorithm with relative velocities drawn from a Maxwell-Boltzmann distribution at each collision step. This algorithm increases the numerical efficiency of the mesoscopic model for solvent flows with low and intermediate Reynolds numbers. Our simulation results for the recirculation length of stationary vortices behind a spherical obstacle are in good agreement with the previous experimental measurements.

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PubMed2002

Effective forces in colloidal mixtures: from depletion attraction to accumulation repulsion.

Computer simulations and theory are used to systematically investigate how the effective force between two big colloidal spheres in a sea of small spheres depends on the basic (big-small and small-small) interactions. The latter are modeled as hardcore pair potentials with a Yukawa tail which can be either repulsive or attractive. For a repulsive small-small interaction, the effective force follows the trends as predicted by a mapping onto an effective nonadditive hardcore mixture: both a depletion attraction and an accumulation repulsion caused by small spheres adsorbing onto the big ones can be obtained depending on the sign of the big-small interaction. For repulsive big-small interactions, the effect of adding a small-small attraction also follows the trends predicted by the mapping. But a more subtle "repulsion through attraction" effect arises when both big-small and small-small attractions occur: upon increasing the strength of the small-small interaction, the effective potential becomes more repulsive. We have further tested several theoretical methods against our computer simulations: The superposition approximation works best for an added big-small repulsion, and breaks down for a strong big-small attraction, while density functional theory is very accurate for any big-small interaction when the small particles are pure hard spheres. The theoretical methods perform most poorly for small-small attractions.

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PubMed2001

Influence of solvent granularity on the effective interaction between charged colloidal suspensions.

We study the effect of solvent granularity on the effective force between two charged colloidal particles by computer simulations of the primitive model of strongly asymmetric electrolytes with an explicitly added hard-sphere solvent. Apart from molecular oscillating forces for nearly touching colloids that arise from solvent and counterion layering, the counterions are attracted towards the colloidal surfaces by solvent depletion providing a simple statistical description of hydration. This, in turn, has an important influence on the effective forces for larger distances which are considerably reduced as compared to the prediction based on the primitive model. When these forces are repulsive, the long-distance behavior can be described by an effective Yukawa pair potential with a solvent-renormalized charge. As a function of colloidal volume fraction and added salt concentration, this solvent-renormalized charge behaves qualitatively similar to that obtained via the Poisson-Boltzmann cell model, but there are quantitative differences. For divalent counterions and nanosized colloids, on the other hand, the hydration may lead to overscreened colloids with mutual attraction while the primitive model yields repulsive forces. All these new effects can be accounted for through a solvent-averaged primitive model (SPM) which is obtained from the full model by integrating out the solvent degrees of freedom. The SPM was used to access larger colloidal particles without simulating the solvent explicitly.

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PubMed2000

Effective interaction between helical biomolecules.

The effective interaction between two parallel strands of helical biomolecules, such as deoxyribose nucleic acids (DNA), is calculated using computer simulations of the "primitive" model of electrolytes. In particular we study a simple model for B-DNA incorporating explicitly its charge pattern as a double-helix structure. The effective force and the effective torque exerted onto the molecules depend on the central distance and on the relative orientation. The contributions of nonlinear screening by monovalent counterions to these forces and torques are analyzed and calculated for different salt concentrations. As a result, we find that the sign of the force depends sensitively on the relative orientation. For intermolecular distances smaller than 6 A it can be both attractive and repulsive. Furthermore, we report a nonmonotonic behavior of the effective force for increasing salt concentration. Both features cannot be described within linear screening theories. For large distances, on the other hand, the results agree with linear screening theories provided the charge of the biomolecules is suitably renormalized.

Computer Simulation↗

PubMed1999

Effect of geometrical confinement on the interaction between charged colloidal suspensions.

The effective interaction between charged colloidal particles confined between two planar like-charged walls is investigated using computer simulations of the primitive model describing asymmetric electrolytes. In detail, we calculate the effective force acting onto a single macroion and onto a macroion pair in the presence of slitlike confinement. For moderate Coulomb coupling, we find that this force is repulsive. Under strong-coupling conditions, however, the sign of the force depends on the distance to the plates and on the interparticle distance. In particular, the particle-plate interaction becomes strongly attractive for small distances which may explain the occurrence of colloidal crystalline layers near the plates observed in recent experiments.

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