arXiv subjects

M. R. Ejtehadi

Publications and source records attributed to M. R. Ejtehadi.

At least 19 recordsLinked to original sources

arXiv2016

Stiffer double-stranded DNA in two-dimensional confinement due to bending anisotropy

Using analytical approach and Monte-Carlo (MC) simulations, we study the elastic behaviour of the intrinsically twisted elastic ribbons with bending anisotropy, such as double-stranded DNA (dsDNA), in two-dimensional (2D) confinement. We show that, due to the bending anisotropy, the persistence length of dsDNA in 2D conformations is always greater than 3D conformations. This result is in consistence with the measured values for DNA persistence length in 2D and 3D in equal biological conditions. We also show that in 2D, an anisotropic, intrinsically twisted polymer exhibits an implicit twist-bend coupling, which leads to the kink formations with a half helical turn periodicity along the bent polymer.

cond-mat.soft↗

arXiv2015

Extreme bendability of DNA double helix due to bending asymmetry

Experimental data of the DNA cyclization (J-factor) at short length scales, as a way to study the elastic behavior of tightly bent DNA, exceed the theoretical expectation based on the wormlike chain (WLC) model by several orders of magnitude. Here, we propose that asymmetric bending rigidity of the double helix in the groove direction can be responsible for extreme bendability of DNA at short length scales and it also facilitates DNA loop formation at these lengths. To account for the bending asymmetry, we consider the asymmetric elastic rod (AER) model which has been introduced and parametrized in an earlier study (B. Eslami-Mossallam and M. Ejtehadi, Phys. Rev. E 80, 011919 (2009)). Exploiting a coarse grained representation of DNA molecule at base pair (bp) level, and using the Monte Carlo simulation method in combination with the umbrella sampling technique, we calculate the loop formation probability of DNA in the AER model. We show that, for DNA molecule has a larger J-factor compared to the WLC model which is in excellent agreement with recent experimental data.

cond-mat.soft↗

arXiv2014

Particle selection through topographic surface patterns in nematic colloids

We propose the use of topographic modulation of surfaces to select and localize particles in nematic colloids. By considering convex and concave deformations of one of the confining surfaces we show that the colloid-flat surface repulsion may be enhanced or switched into an attraction. In particular, we find that when the colloidal particles have the same anchoring conditions as the patterned surfaces, they are strongly attracted to concave dimples, while if they exhibit different anchoring conditions they are pinned at the top of convex protrusions. Although dominated by elastic interactions the first mechanism is reminiscent of the depletion induced attraction or of the key-lock mechanism, while the second is specific to liquid crystal colloids. These long-ranged, highly tunable, surface-colloid interactions contribute for the development of template-assisted assembly of large colloidal crystals, with well defined symmetries, required for applications.

cond-mat.soft↗

arXiv2012

A self-organized graph evolution model with preferential network random walk

We introduce a self-organized model of graph evolution associated with preferential network random walkers. The idea is developed by using two different types of walkers, the interactions of which lead to a dynamic graph. The walkers of the first type cause an enhancement in link attachments, while the second types have a destructive behavior. The statistical properties of the resulting network, including weight distributions, clustering, spectral densities and average path length are evaluated. As the ratio of the population of two types is balanced, the network faces a phase transition. We show that in the transition point, the graph behaves as a scale-free network, with a scaling exponent of \sim -1.7.

cond-mat.stat-mech↗

arXiv2011

Directed motion of C60 on a graphene sheet subjected to a temperature gradient

Nonequilibrium molecular dynamics simulations is used to study the motion of a C60 molecule on a graphene sheet subjected to a temperature gradient. The C60 molecule is actuated and moves along the system while it just randomly dances along the perpendicular direction. Increasing the temperature gradient increases the directed velocity of C60. It is found that the free energy decreases as the C60 molecule moves toward the cold end. The driving mechanism based on the temperature gradient suggests the construction of nanoscale graphene-based motors.

cond-mat.mes-hall↗

arXiv2009

Diffusive motion of C60 on a graphene sheet

The motion of a C60 molecule over a graphene sheet at finite temperature is investigated both theoretically and computationally. We show that a graphene sheet generates a van der Waals laterally periodic potential, which directly influences the motion of external objects in its proximity. The translational motion of a C60 molecule near a graphene sheet is found to be diffusive in the lateral directions. While, in the perpendicular direction, the motion may be described as diffusion in an effective harmonic potential which is determined from the distribution function of the position of the C60 molecule. We also examine the rotational diffusion of C60 and show that its motion over the graphene sheet is not a rolling motion.

cond-mat.mes-hall↗

arXiv2009

An Asymmetric Elastic Rod Model for DNA

In this paper we consider the anharmonic corrections to the anisotropic elastic rod model for DNA. Our model accounts for the difference between the bending energies of positive and negative rolls, which comes from the asymmetric structure of the DNA molecule. We will show that the model can explain the high flexibility of DNA at small length scales, as well as kink formation at high deformation limit.

cond-mat.soft↗

arXiv2008

Anisotropic Elastic Model for Short DNA Loops

Effect of bending anisotropy on a planar DNA loop, using energy minimization and neglecting entropic effects, is studied. We show that the anisotropy results in polygonal shape of the loop and increasing the anisotropy makes the edges sharper. Calculating the energy of such a loop lets us to find effective persistence length as the geometrical mean of hard and soft rigidities, which is quite different from harmonic mean for an unconstrained long DNA.

cond-mat.soft↗

arXiv2008

A Liquid Film Motor

It is well known that electro-hydrodynamical effects in freely suspended liquid films can flow the liquid. Here we report a purely electrically driven rotation in water and some other liquid suspended films with full control on the velocity and the chirality of the rotating vortices. The device, which is called ``film motor'', consists of a quasi two-dimensional electrolysis cell in an external in-plane electric field, crossing the mean electrolysis current density. If either the external field or the electrolysis voltage exceeds some threshold (while the other one is not zero), the liquid film begins to rotate. The device works perfectly with both DC and AC fields.

cond-mat.soft↗

arXiv2008

Stretching An Anisotropic DNA

We present a perturbation theory to find the response of an anisotropic DNA to the external tension. It is shown that the anisotropy has a nonzero but small contribution to the force-extension curve of the DNA. Thus an anisotropic DNA behaves like an isotropic one with an effective bending constant equal to the harmonic average of its soft and hard bending constants.

cond-mat.soft↗

arXiv2006

Analytical First Derivatives of the RE-squared Interaction Potential

We derive exact expressions for the forces and torques between biaxial molecules interacting via the RE-squared potential, a recent variant of the Gay-Berne potential. Moreover, efficient routines have been provided for rigid body MD simulations, resulting in 1.6 times speedup compared to the two-point finite difference approach. It has also been shown that the time cost of a MD simulation will be almost equal to a similar MC simulation, making use of the provided routines.

cond-mat.soft↗

arXiv2006

A water film motor

We report on electrically-induced rotations in water films, which can function at many length scales. The device consists of a two-dimensional cell used for electrolysis of water films, as simple as an insulator frame with two electrodes on the sides, to which an external in-plane electric field perpendicular to the mean electrolysis current density is applied. If either the external field or the electrolysis current exceeds some threshold (while the other one is not zero), the liquid film begins to rotate.

cond-mat.soft↗

arXiv2006

Coarse-grained Interaction Potentials for Anisotropic Molecules

We have proposed an efficient parameterization method for a recent variant of the Gay-Berne potential for dissimilar and biaxial particles and demonstrated it for a set of small organic molecules. Compared to the previously proposed coarse-grained models, the new potential exhibits a superior performance in close contact and large distant interactions. The repercussions of thermal vibrations and elasticity has been studied through a statistical method. The study justifies that the potential of mean force is representable with the same functional form, extending the application of this coarse-grained description to a broader range of molecules. Moreover, the advantage of employing coarse-grained models over truncated atomistic summations with large distance cutoffs has been briefly studied.

cond-mat.soft↗

arXiv2005

Conservation of statistical results under the reduction of pair-contact interactions to solvation interactions

We show that the hydrophobicity of sequences is the leading term in Miyazawa-Jernigan interactions. Being the source of additive (solvation) terms in pair-contact interactions, they were used to reduce the energy parameters while resulting in a clear vector manipulation of energy. The reduced (additive) potential performs considerably successful in predicting the statistical properties of arbitrary structures. The evaluated designabilities of the structures by both models are highly correlated. Suggesting geometrically non-degenerate vectors (structures) as protein-like structures, the additive model is a powerful tool for protein design. Moreover, a crossing point in the log-linear diagram of designability-ranking shows that about 1/e of the structures have designabilities above the average, independent on the used model.

q-bio.BM↗

arXiv2004

Three-body Interactions Improve the Prediction of Rate and Mechanism in Protein Folding Models

Here we study the effects of many-body interactions on rate and mechanism in protein folding, using the results of molecular dynamics simulations on numerous coarse-grained C-alpha-model single-domain proteins. After adding three-body interactions explicitly as a perturbation to a Go-like Hamiltonian with native pair-wise interactions only, we have found 1) a significantly increased correlation with experimental phi-values and folding rates, 2) a stronger correlation of folding rate with contact order, matching the experimental range in rates when the fraction of three-body energy in the native state is ~ 20%, and 3) a considerably larger amount of 3-body energy present in Chymotripsin inhibitor than other proteins studied.

q-bio.QM↗

arXiv2004

Protein folding rates correlate with heterogeneity of folding mechanism

By observing trends in the folding kinetics of experimental 2-state proteins at their transition midpoints, and by observing trends in the barrier heights of numerous simulations of coarse grained, C-alpha model, Go proteins, we show that folding rates correlate with the degree of heterogeneity in the formation of native contacts. Statistically significant correlations are observed between folding rates and measures of heterogeneity inherent in the native topology, as well as between rates and the variance in the distribution of either experimentally measured or simulated phi-values.

q-bio.QM↗

arXiv2003

Interaction potentials for soft and hard ellipsoids

Using results from colloid science we derive interaction potentials for computer simulations of mixtures of soft or hard ellipsoids of arbitrary shape and size. Our results are in many respects reminicent of potentials of the Gay-Berne type but have a well-defined microscopic interpretation and no adjustable parameters. Since our potentials require the calculation of similar variables, the modification of existing simulation codes for Gay-Berne potentials is straightforward. The computational performance should remain unaffected.

cond-mat.soft↗

arXiv2000

An asymmetric exclusion model with overtaking a numerical and simulation study

An asymmetric exclusion model on an open chain with random rates for hopping particles, where overtaking is also possible, is studied numerically and by computer simulation. The phase structure of the model and the density profiles near the high and low density coexistence line are obtained. The effect of a site impurity is also studied.

cond-mat.stat-mech↗