Biomedical subjects

E Allahyarov

Publications and source records attributed to E Allahyarov.

8 recordsLinked to original sources

PubMed2004

Attraction between DNA molecules mediated by multivalent ions.

The effective force between two parallel DNA molecules is calculated as a function of their mutual separation for different valencies of counterion and salt ions and different salt concentrations. Computer simulations of the primitive model are used and the shape of the DNA molecules is accurately modeled using different geometrical shapes. We find that multivalent ions induce a significant attraction between the DNA molecules whose strength can be tuned by the averaged valency of the ions. The physical origin of the attraction is traced back either to electrostatics or to entropic contributions. For multivalent counterions and monovalent salt ions, we find a salt-enhanced repulsion effect: the force is first attractive but gets repulsive with increasing salt concentration. Furthermore, we show that the multivalent-ion-induced attraction does not necessarily correlate with DNA overcharging.

Binding Sites↗

PubMed2003

Adsorption of monovalent and multivalent cations and anions on DNA molecules.

Adsorption of monovalent and multivalent cations and anions on a deoxyribose nucleic acid (DNA) molecule from a salt solution is investigated by computer simulation. The ions are modeled as charged hard spheres, the DNA molecule as a point charge pattern following the double-helical phosphate strands. The geometrical shape of the DNA molecules is modeled on different levels ranging from a simple cylindrical shape to structured models which include the major and minor grooves between the phosphate strands. The densities of the ions adsorbed on the phosphate strands in the major and in the minor grooves are calculated. First, we find that the adsorption pattern on the DNA surface depends strongly on its geometrical shape: counterions adsorb preferentially along the phosphate strands for a cylindrical model shape, but in the minor groove for a geometrically structured model. Second, we find that an addition of monovalent salt ions results in an increase of the charge density in the minor groove while the total charge density of ions adsorbed in the major groove stays unchanged. The adsorbed ion densities are highly structured along the minor groove while they are almost smeared along the major groove. Furthermore, for a fixed amount of added salt, the major-groove cationic charge is independent of the counterion valency. For increasing salt concentration the major groove is neutralized while the total charge adsorbed in the minor groove is constant. DNA overcharging is detected for multivalent salts. Simulations for larger ion radii, which mimic the effect of ion hydration, indicate an increased adsorbtion of cations in the major groove.

Anions↗

PubMed2003

Nonmonotonic variation with salt concentration of the second virial coefficient in protein solutions.

The osmotic virial coefficient B2 of globular protein solutions is calculated as a function of added salt concentration at fixed pH by computer simulations of the "primitive model." The salt and counterions as well as a discrete charge pattern on the protein surface are explicitly incorporated. For parameters roughly corresponding to lysozyme, we find that B2 first decreases with added salt concentration up to a threshold concentration, then increases to a maximum, and then decreases again upon further raising the ionic strength. Our studies demonstrate that the existence of a discrete charge pattern on the protein surface profoundly influences the effective interactions and that linear and nonlinear Poisson Boltzmann theories fail for large ionic strength. The observed nonmonotonicity of B2 is compared with experiments. Implications for protein crystallization are discussed.

Journal Article↗

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.

Journal Article↗

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.

Journal Article↗

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.

Journal Article↗

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.

Journal Article↗