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Pashan, India

Kiruthiga J.,Pondicherry University | Chatterji A.,IISER Pune
Journal of Chemical Physics | Year: 2013

We present a theoretical model, which elucidates the physical principles involved in the formation of very uniform CdS nanocylinders of different radii by combining the physics of flow, diffusion, self assembly, and aggregation of constituent particles. Very recent experiments report that when 0.1M solutions of CdCl2 and Na2S were allowed to mix through some anodised aluminium oxide (AAO) nanochannels, one observes the growth of an array of CdS nano-cylinders on only one end of the AAO template [A. Varghese and S. Datta, Phys. Rev. E 85, 056104 (2012)]. These cylinders have a pore along the center of the cylinder but closed at one end. The reaction happens only in the Na2S chamber, and growth of cylinders of uniform size and shape continues as long as the supply of the reactant molecules (CdCl2 and Na2S) is maintained. To try to understand the physics of the observed phenomenon, we propose a model where the Cd+2 ions exit the AAO-nanochannel to enter Na2S chamber with a finite velocity; these ions then react with the diffusing S-2 ions to form CdS, which then self assemble to form cylinders of uniform width and cross-section. The flow of Cd+2 out of the AAO nano-channel is the key symmetry breaking feature, which facilitates the formation of uniform cylindrical structures of CdS instead of a CdS precipitate. Since our model does not crucially depend on the chemical details of the reaction, this mechanism can be extended to self-assemble other structures of relevance. © 2013 American Institute of Physics. Source

Ghatage D.,College of Engineering, Pune | Chatterji A.,IISER Pune
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics | Year: 2013

We introduce a method to obtain steady-state uniaxial exponential- stretching flow of a fluid (akin to extensional flow) in the incompressible limit, which enables us to study the response of suspended macromolecules to the flow by computer simulations. The flow field in this flow is defined by v x=εx, where vx is the velocity of the fluid and ε is the stretch flow gradient. To eliminate the effect of confining boundaries, we produce the flow in a channel of uniform square cross section with periodic boundary conditions in directions perpendicular to the flow, but simultaneously maintain uniform density of fluid along the length of the tube. In experiments a perfect elongational flow is obtained only along the axis of symmetry in a four-roll geometry or a filament-stretching rheometer. We can reproduce flow conditions very similar to extensional flow near the axis of symmetry by exponential-stretching flow; we do this by adding the right amounts of fluid along the length of the flow in our simulations. The fluid particles added along the length of the tube are the same fluid particles which exit the channel due to the flow; thus mass conservation is maintained in our model by default. We also suggest a scheme for possible realization of exponential-stretching flow in experiments. To establish our method as a useful tool to study various soft matter systems in extensional flow, we embed (i) spherical colloids with excluded volume interactions (modeled by the Weeks-Chandler potential) as well as (ii) a bead-spring model of star polymers in the fluid to study their responses to the exponential-stretched flow and show that the responses of macromolecules in the two flows are very similar. We demonstrate that the variation of number density of the suspended colloids along the direction of flow is in tune with our expectations. We also conclude from our study of the deformation of star polymers with different numbers of arms f that the critical flow gradient εc at which the star undergoes the coil-to-stretch transition is independent of f for f=2,5,10, and 20. © 2013 American Physical Society. Source

Kiruthiga J.,Pondicherry University | Chatterji A.,IISER Pune
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics | Year: 2014

We present our conclusions of the investigation of 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 Cd+2 and S-2 ions. In a previous communication [Kiruthiga and Chatterji, J. Chem. Phys. 138, 024905 (2013)JCPSA60021-960610.1063/1.4773279], we identified the mechanism of an unexpected growth of a CdS nanocylinder of uniform radial cross section from the end of a nanochannel. Furthermore, the cylinder had a pore along the axis but was closed at one end. This unique phenomenon of self-assembly of very monodisperse CdS nanocylinders had been observed in a rather simple experiment where two chambers containing 0.1M CdCl2 and 0.1M Na2S solutions were joined by an array of anodized aluminium oxide (AAO) nanochannels [Varghese and Datta, Phys. Rev. E 85, 056104 (2012)PLEEE81539-375510.1103/PhysRevE.85.056104]. Interestingly, the growth of CdS nanotubes was observed only in the Na2S chamber. The primary focus of our previous study was on identifying the principles governing the growth of a single nanotube at the exit point of a single AAO nanochannel. In this communication, we identify factors affecting the self-assembly of a nanotube in the presence of other similar neighboring nanotubes growing out from an array of closely spaced AAO nanochannel exit points, a scenario closer to the experimental situation. Our model is not Cd+2 or S-2 specific, thus our conclusions suggest that the experimental scheme can be extended to the self-assembly of a general class of reacting-diffusing A and B ions with A (in this case Cd+2 ions) selectively migrating out from a nanochannel. In particular, we note that after the initial growth of nanotubes for a period of time, there can arise a severe deficiency of B ions (S-2) near the AAO-nanochannel exits. The low concentration of B near the nanochannel exits impedes further growth of uniform CdS nanotubes. We further identify the parameters which can be tuned to obtain an improved crop of monodisperse nanotubes. Thereby we predict the necessary characteristics of reacting systems which can be self-assembled using suitable adaptations of experiments used to grow CdS cylinders. © 2014 American Physical Society. Source

Saha R.,Jadavpur University | Joarder B.,IISER Pune | Roy A.S.,Kalyani University | Manirul Islam S.,Kalyani University | Kumar S.,Jadavpur University
Chemistry - A European Journal | Year: 2013

Assimilation of open metal sites (OMSs) and free functional organic sites (FOSs) with a framework strut has opened up a new route for the fabrication of novel metal-organic materials, thereby providing a unique opportunity to explore their multiple functionalities. A new metal-organic framework (MOF), {[Cu(ina)2(H2O)][Cu(ina)2(bipy)]·2 H2O}n (1) (ina=isonicotinate, bipy=4,4′-bipyridine), has been synthesized and characterized. Complex 1 is crystallized in the orthorhombic noncentrosymmetric space group Aba2 and consists of two different 2D coordination polymers, [Cu(ina)2(H2O)]n and [Cu(ina)2(bipy)]n, with entrapped solvent water molecules. Hydrogen-bonding interactions assemble these two different 2D coordination layers in a single-crystal structure with interdigitation of pendant 4,4′-bipy from one layer into the groove of another. Upon removal of guest molecules, 1 undergoes a structural transformation in single-crystal-to-single- crystal fashion with expansion of the effective void space. Each metal center is five-coordinated and thus can potentially behave as an OMS, and the free pyridyl groups of pendant 4,4′-bipy moieties and free -C=O groups can act as free FOSs. Thus, owing to presence of both OMSs and free FOSs, the framework exhibits multifunctional properties. Owing to the presence of OMSs, the framework can act as a Lewis acid catalyst as well as a small-molecule sensor material, and in a similar way, owing to the presence of free FOSs, it performs as a Lewis base catalyst and a cation sensor material. Furthermore, owing to noncentrosymmetry with large polarity along a particular direction, it shows strong second-harmonic generation/nonlinear optical (SHG-NLO) activity. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Source

Athale C.A.,IISER Pune | Dinarina A.,EMBL | Dinarina A.,Thermo Fisher Scientific | Nedelec F.,EMBL | Karsenti E.,EMBL
Physical Biology | Year: 2014

Microtubules (MTs) nucleated by centrosomes form star-shaped structures referred to as asters. Aster motility and dynamics is vital for genome stability, cell division, polarization and differentiation. Asters move either toward the cell center or away from it. Here, we focus on the centering mechanism in a membrane independent system of Xenopus cytoplasmic egg extracts. Using live microscopy and single particle tracking, we find that asters move toward chromatinized DNA structures. The velocity and directionality profiles suggest a random-walk with drift directed toward DNA. We have developed a theoretical model that can explain this movement as a result of a gradient of MT length dynamics and MT gliding on immobilized dynein motors. In simulations, the antagonistic action of the motor species on the radial array of MTs leads to a tug-of-war purely due to geometric considerations and aster motility resembles a directed random-walk. Additionally, our model predicts that aster velocities do not change greatly with varying initial distance from DNA. The movement of asymmetric asters becomes increasingly super-diffusive with increasing motor density, but for symmetric asters it becomes less super-diffusive. The transition of symmetric asters from superdiffusive to diffusive mobility is the result of number fluctuations in bound motors in the tug-of-war. Overall, our model is in good agreement with experimental data in Xenopus cytoplasmic extracts and predicts novel features of the collective effects of motor-MT interactions. © 2014 IOP Publishing Ltd. Source

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