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Apratim Chatterji

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cond-mat.soft Biological Physics cond-mat.mes-hall cond-mat.mtrl-sci cond-mat.stat-mech

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preprint2026arXiv

Kinetics of segregation of topologically-modified ring polymers in cylindrical confinement

In Escherichia coli (E. coli), entropic repulsion between the two daughter DNA ring polymers under cylindrical confinement is believed to be an important factor governing chromosomal segregation. The repulsion can be enhanced by topological modifications, i.e., by the introduction of internal loops at certain locations along the contour of the circular DNA. However, the effect of topological modifications on the rate of segregation of ring polymers remains unclear. Therefore, we systematically varied the number and the contour length of loops introduced at selected locations by crosslinking monomers. The appropriate crosslinking was motivated by observations that extruded loops are located mainly near the origin of replication (ori-proximal) region of the E. coli chromosome. This resulted in the chains becoming intrinsically anisotropic. Using Langevin dynamics simulations of these topologically modified bead-spring polymers, we calculated the time required for segregation under cylinder confinement. With certain caveats, we found that increasing the number of loops resulted in a decrease in the time of segregation. In line with past work, we propose that this is due to the increase in the entropic repulsion between the polymers upon increasing the number of loops. In addition to the number of loops, the contour length of the loops and the mutual orientation of the (anisotropic) chains in the initial configurations played a role in determining the time of segregation.

preprint2014arXiv

Heirarchical Self Assembly: Self Organized nano-structures in a nematically ordered matrix of self assembled polymeric chains

We report many different nano-structures which are formed when model nano-particles of different sizes (diameter σ n ) are allowed to aggregate in a background matrix of semi-flexible self assembled polymeric worm like micellar chains. The different nano-structures are formed by the dynamical arrest of phase-separating mixtures of micellar monomers and nano-particles. The different mor- phologies obtained are the result of an interplay of the available free volume, the elastic energy of deformation of polymers, the density (chemical potential) of the nano-particles in the polymer ma- trix and, of course, the ratio of the size of self assembling nano-particles and self avoidance diameter of polymeric chains. We have used a hybrid semi-grand canonical Monte Carlo simulation scheme to obtain the (non-equilibrium) phase diagram of the self-assembled nano-structures. We observe rod-like structures of nano-particles which get self assembled in the gaps between the nematically ordered chains as well as percolating gel-like network of conjoined nanotubes. We also find a totally unexpected interlocked crystalline phase of nano-particles and monomers, in which each crytal plane of nanoparticles is separated by planes of perfectly organized polymer chains. We identified the con- dition which leads to such interlocked crystal structure. We suggest experimental possibilities of how the results presented in this paper could be used to obtain different nano-structures in the lab.

preprint2013arXiv

Self assembly of monodisperse CdS nano-cylinders with a pore

We present investigate the self assembly and growth of an array of $CdS$ nanotubes: a consequence of a fine balance of directed motion, diffusion and aggregation of reacting ${\rm Cd^{+2}}$ and ${\rm S^{-2}}$ ions. In a previous communication [J. Kiruthiga, A. Chatterji, J. Chem. Phys., {\bf 138} 024905 (2013)], we identified the mechanism of a unexpected growth of a very uniform $CdS$ nano-cylinder from the end of a nano-channel. Furthermore, the cylinder had a pore along the axis but were closed at one end. This unique phenomenon of self assembly of {\em monodisperse} CdS nano-cylinders had been observed in a rather simple experiment where two chambers containing 0.1 M ${\rm Cd Cl_2}$ and 0.1 M ${\rm Na_2 S}$ solutions were joined by an array of anodized aluminium oxide (AAO) nano-channels [A. Varghese, S. Datta, Phys. Rev. E., {\bf 85}, 056104 (2012)]. Our previous study identified the principles governing the growth of a single nano-tube at the exit point of a single AAO-nano-channel. In this communication, we identify factors affecting the self-assembly process for nano-tubes growing out an array of closely spaced AAO nano-channel exits. Our model is not $Cd^{+2}$ or $S^{2-}$ specific, the experimental scheme can be extended to self assemble a general class of reacting-diffusing A and B ions with A ( ${\rm Cd^{+2}}$ ) selectively migrating out from a nano-channel. In particular, we note that after the initial prolonged growth of nanotubes, there can arise a severe deficiency of B-ions ( ${\rm S^{-2}}$ ) ions near the AAO-nano-channel exits, the points where the reaction and aggregation occurs to form the $CdS$ nanotube, thus impeding further growth of uniform CdS nano-tubes. Thereby we predict the necessary characteristics of reacting systems which can be self assembled using suitable adaptations of previous experiments.

preprint2006arXiv

Electrophoretic Properties of Highly Charged Colloids: A Hybrid MD/LB Simulation Study

Using computer simulations, the electrophoretic motion of a positively charged colloid (macroion) in an electrolyte solution is studied in the framework of the primitive model. Hydrodynamic interactions are fully taken into account by applying a hybrid simulation scheme, where the charged ions (i.e. macroion and electrolyte), propagated via molecular dynamics (MD), are coupled to a Lattice Boltzmann (LB) fluid. In a recent experiment it was shown that, for multivalent salt ions, the mobility $μ$ initially increases with charge density $σ$ , reaches a maximum and then decreases with further increase of $σ$ . The aim of the present work is to elucidate the behaviour of $μ$ at high values of $σ$ . Even for the case of monovalent microions, we find a decrease of $μ$ with $σ$ . A dynamic Stern layer is defined that includes all the counterions that move with the macroion while subject to an external electrical field. The number of counterions in the Stern layer, $q_0$ , is a crucial parameter for the behavior of $μ$ at high values of $σ$ . In this case, the mobility $μ$ depends primarily on the ratio $q_0/Q$ (with $Q$ the valency of the macroion). The previous contention that the increase in the distortion of the electric double layer (EDL) with increasing $σ$ leads to the lowering of $μ$ does not hold for high $σ$ . In fact, we show that the deformation of the EDL decreases with increase of $σ$ . The role of hydrodynamic interactions is inferred from direct comparisons to Langevin simulations where the coupling to the LB fluid is switched off. Moreover, systems with divalent counterions are considered. In this case, at high values of $σ$ the phenomenon of charge inversion is found.

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