arXiv subjects

Roya Zandi

Publications and source records attributed to Roya Zandi.

59 records · Page 4Linked to original sources

arXiv2003

Anomalous bending of a polyelectrolyte

We report on a study of the shape of a stiff, charged rod that is subjected to equal and opposite force couples at its two ends. Unlike a neutral elastic rod, which forms a constant curvature configuration under such influences, the charged rod tends to flatten in the interior and accumulate the curvature in the end points, to maximally reduce the electrostatic self-repulsion. The effect of this nonuniform bending on the effective elasticity and on the statistical conformations of a fluctuating charged rod is discussed. An alternative definition for the electrostatic persistence length is suggested. This new definition is found to be consistent with a corresponding length that can be deduced from the end-to-end distribution function of a fluctuating polyelectrolyte.

cond-mat.soft↗

arXiv2003

What drives the translocation of stiff chains?

We study the dynamics of the passage of a stiff chain through a pore into a cell containing particles that bind reversibly to it. Using Brownian Molecular Dynamics simulations we investigate the mean-first-passage time as a function of the length of the chain inside, for different concentrations of binding particles. As a consequence of the interactions with these particles, the chain experiences a net force along its length whose calculated value from the simulations accounts for the velocity at which it enters the cell. This force can in turn be obtained from the solution of a generalized diffusion equation incorporating an effective Langmuir adsorption free energy for the chain plus binding particles. These results suggest a role of binding particles in the translocation process which is in general quite different from that of a Brownian ratchet. Furthermore, non-equilibrium effects contribute significantly to the dynamics, \emph{e.g.}, the chain often enters the cell faster than particle binding can be saturated, resulting in a force several times smaller than the equilibrium value.

cond-mat.soft↗

arXiv2003

Probing Polyelectrolyte Elasticity Using Radial Distribution Function

We study the effect of electrostatic interactions on the distribution function of the end-to-end distance of a single polyelectrolyte chain in the rodlike limit. The extent to which the radial distribution function of a polyelectrolyte is reproduced by that of a wormlike chain with an adjusted persistence length is investigated. Strong evidence is found for a universal scaling formula connecting the effective persistence length of a polyelectrolyte with its linear charge density and the Debye screening of its self-interaction. An alternative definition of the electrostatic persistence length is proposed based on matching of the maximum of the distribution with that of an effective wormlike chain, as opposed to the traditional matching of the first or the second moments of the distributions. It is shown that this definition provides a more accurate probe of the affinity of the distribution to that of the wormlike chains, as compared to the traditional definition. It is also found that the length of a polyelectrolyte segment can act as a crucial parameter in determining its elastic properties.

cond-mat.soft↗

arXiv2002

Radial Distribution Function of Rodlike Polyelectrolytes

We study the effect of electrostatic interactions on the distribution function of the end-to-end distance of a single polyelectrolyte chain in a rodlike configuration. We investigate the validity of the concept of electrostatic persistence length for uniformly charged wormlike chains for both screened and unscreened Coulomb interactions. We find that the distribution function of a polyelectrolyte often differs significantly from the distribution function of a wormlike chain.

cond-mat.soft↗

arXiv2001

Constraints, Histones, and the 30 Nanometer Spiral

We investigate the mechanical stability of a segment of DNA wrapped around a histone in the nucleosome configuration. The assumption underlying this investigation is that the proper model for this packaging arrangement is that of an elastic rod that is free to twist and that writhes subject to mechanical constraints. We find that the number of constraints required to stabilize the nuclesome configuration is determined by the length of the segment, the number of times the DNA wraps around the histone spool, and the specific constraints utilized. While it can be shown that four constraints suffice, in principle, to insure stability of the nucleosome, a proper choice must be made to guarantee the effectiveness of this minimal number. The optimal choice of constraints appears to bear a relation to the existence of a spiral ridge on the surface of the histone octamer. The particular configuration that we investigate is related to the 30 nanometer spiral, a higher-order organization of DNA in chromatin.

cond-mat.soft↗