arXiv subjects

Dwaipayan Chakrabarti

Publications and source records attributed to Dwaipayan Chakrabarti.

14 recordsLinked to original sources

arXiv2024

Effect of coat-protein concentration on the self-assembly of bacteriophage MS2 capsids around RNA

Self-assembly is a vital part of the life cycle of certain icosahedral RNA viruses. Furthermore, the assembly process can be harnessed to make icosahedral virus-like particles (VLPs) from coat protein and RNA in vitro. Although much previous work has explored the effects of RNA-protein interactions on the assembly products, relatively little research has explored the effects of coat-protein concentration. We mix coat protein and RNA from bacteriophage MS2, and we use a combination of gel electrophoresis, dynamic light scattering, and transmission electron microscopy to investigate the assembly products. We show that with increasing coat-protein concentration, the products transition from well-formed MS2 VLPs to ``monster'' particles consisting of multiple partial capsids to RNA-protein condensates consisting of large networks of RNA and partially assembled capsids. We argue that the transition from well-formed to monster particles arises because the assembly follows a nucleation-and-growth pathway in which the nucleation rate depends sensitively on the coat-protein concentration, such that at high protein concentrations, multiple nuclei can form on each RNA strand. To understand the formation of the condensates, which occurs at even higher coat-protein concentrations, we use Monte Carlo simulations with coarse-grained models of capsomers and RNA. These simulations suggest that the the formation of condensates occurs by the adsorption of protein to the RNA followed by the assembly of capsids. Multiple RNA molecules can become trapped when a capsid grows from capsomers attached to two different RNA molecules or when excess protein bridges together growing capsids on different RNA molecules. Our results provide insight into an important biophysical process and could inform design rules for making VLPs for various applications.

physics.bio-ph↗

arXiv2014

Design principles for Bernal spirals and helices with tunable pitch

Using the framework of potential energy landscape theory, we describe two in silico designs for self-assembling helical colloidal superstructures based upon dipolar dumbbells and Janus-type building blocks, respectively. Helical superstructures with controllable pitch length are obtained using external magnetic field driven assembly of asymmetric dumbbells involving screened electrostatic as well as magnetic dipolar interactions. The pitch of the helix is tuned by modulating the Debye screening length over an experimentally accessible range. The second design is based on building blocks composed of rigidly linked spheres with short-range anisotropic interactions, which are predicted to self-assemble into Bernal spirals. These spirals are quite flexible, and longer helices undergo rearrangements via cooperative, hinge-like moves, in agreement with experiment.

cond-mat.soft↗

arXiv2013

Energy landscapes, structural topologies and rearrangement mechanisms in clusters of dipolar particles

Clusters of spherical particles with isotropic attraction favour compact structures that maximise the number of energetically optimal nearest-neighbour interactions. In contrast, dipolar interactions lead to the formation of chains with a low coordination number. When both isotropic and dipolar interactions are present, the competition between them can lead to intricate knot, link and coil structures. Here, we investigate how these structures may self-organise and interconvert in clusters bound by the Stockmayer potential (Lennard-Jones plus point dipole). We map out the low-lying region of the energy landscape using disconnectivity graphs to follow how it evolves as the strength of the dipolar interactions increases. From comprehensive surveys of isomerisation pathways, we identify a number of rearrangement mechanisms that allow the topology of chain-like structures to interconvert.

cond-mat.soft↗

arXiv2007

Orientational relaxation in a discotic liquid crystal

We investigate orientational relaxation of a model discotic liquid crystal, consists of disc-like molecules, by molecular dynamics simulations along two isobars starting from the high temperature isotropic phase. The two isobars have been so chosen that (A) the phase sequence isotropic (I)-nematic (N)-columnar (C) appears upon cooling along one of them and (B) the sequence isotropic (I)-columnar (C) along the other. While the orientational relaxation in the isotropic phase near the I-N phase transition in system (A) shows a power law decay at short to intermediate times, such power law relaxation is not observed in the isotropic phase near the I-C phase boundary in system (B). In order to understand this difference (the existence or the absence of the power law decay), we calculated the the growth of the orientational pair distribution functions (OPDF) near the I-N phase boundary and also near the I-C phase boundary. We find that OPDF shows a marked growth in long range correlation as the I-N phase boundary is approached in the I-N-C system (A), but such a growth is absent in the I-C system, which appears to be consistent with the result that I-N phase transition in the former is weakly first order while the the I-C phase transition in the later is not weak. As the system settles into the nematic phase, the decay of the single-particle second-rank orientational OTCF follows a pattern that is similar to what is observed with calamitic liquid crystals and supercooled molecular liquids.

cond-mat.soft↗

arXiv2007

How glassy are orientational dynamics of rodlike molecules near the isotropic-nematic transition?

In an attempt to quantitatively characterize the recently observed slow dynamics in the isotropic and nematic phase of liquid crystals, we investigate the single-particle orientational dynamics of rodlike molecules across the isotropic-nematic transition in computer simulations of a family of model systems of thermotropic liquid crystals. Several remarkable features of glassy dynamics are on display including non-exponential relaxation, dynamical heterogeneity, and non-Arrhenius temperature dependence of the orientational relaxation time. In order to obtain a quantitative measure of glassy dynamics in line with the estbalished methods in supercooled liquids, we construct a relaxation time versus scaled inverse temperature plot, and demonstrate that one can indeed define a 'fragility index' for thermotropic liquid crystals, that depends on density and aspect ratio. The values of the fragility parameter are surprisingly in the range one observed for glass forming liquids. A plausible correlation between the energy landscape features and the observed fragility is discussed.

cond-mat.soft↗

arXiv2006

Anisotropic translational diffusion in the nematic phase: Dynamical signature of the coupling between orientational and translational order in the energy landscape

We find in a model system of thermotropic liquid crystals that the translational diffusion coefficient parallel to the director $D_{\parallel}$ first increases and then decreases as temperature drops through the nematic phase, and this reversal occurs where the smectic order parameter of the underlying inherent structures becomes significant for the first time. We argue, based on an energy landscape analysis, that the coupling between orientational and translational order can play a role in inducing the non-monotonic temperature behavior of $D_{\parallel}$. Such a view is likely to form the foundation of a theoretical framework to explain the anisotropic translation diffusion.

cond-mat.soft↗

arXiv2006

Power law relaxation and glassy dynamics in Lebwohl-Lasher model near isotropic-nematic phase transition

Orientational dynamics in a liquid crystalline system near the isotropic-nematic (I-N) phase transition is studied using Molecular Dynamics simulations of the well-known Lebwohl-Lasher (LL) model. As the I-N transition temperature is approached from the isotropic side, we find that the decay of the orientational time correlation functions (OTCF) slows down noticeably, giving rise to a power law decay at intermediate timescales. The angular velocity time correlation function also exhibits a rather pronounced power law decay near the I-N boundary. In the mean squared angular displacement at comparable timescales, we observe the emergence of a \emph{subdiffusive regime} which is followed by a \emph{superdiffusive regime} before the onset of the long-time diffusive behavior. We observe signature of dynamical heterogeneity through \emph{pronounced non-Gaussian behavior in orientational motion} particularly at lower temperatures. This behavior closely resembles what is usually observed in supercooled liquids. We obtain the free energy as a function of orientational order parameter by the use of transition matrix Monte Carlo method. The free energy surface is flat for the system considered here and the barrier between isotropic and nematic phases is vanishingly small for this weakly first-order phase transition, hence allowing large scale, collective and correlated orientational density fluctuations. This might be responsible for the observed power law decay of the OTCFs.

cond-mat.soft↗

arXiv2005

Complete breakdown of the Debye model of rotational relaxation near the isotropic-nematic phase boundary: Effects of intermolecular correlations in orientational dynamics

The Debye-Stokes-Einstein (DSE) model of rotational diffusion predicts that the rotational correlation times $τ_{l}$ vary as $[l(l+1)]^{-1}$, where $l$ is the rank of the orientational correlation function (given in terms of the Legendre polynomial of rank $l$). One often finds significant deviation from this prediction, in either direction. In supercooled molecular liquids where the ratio $τ_{1}/τ_{2}$ falls considerably below three (the Debye limit), one usually invokes a jump diffusion model to explain the approach of the ratio $τ_{1}/τ_{2}$ to unity. Here we show in a computer simulation study of a standard model system for thermotropic liquid crystals that this ratio becomes much less than unity as the isotropic-nematic phase boundary is approached from the isotropic side. Simultaneously, the ratio $τ_2/η$ (where $η$ is the shear viscosity of the liquid) becomes {\it much larger} than hydrodynamic value near the I-N transition. We have also analyzed the break down of the Debye model of rotational diffusion in ratios of higher order rotational correlation times. We show that the break down of the DSE model is due to the growth of orientational pair correlation and provide a mode coupling theory analysis to explain the results.

cond-mat.soft↗

arXiv2005

Decoupling phenomena in supercooled liquids: Signatures in the energy landscape

A significant deviation from the Debye model of rotational diffusion in the dynamics of orientational degrees of freedom in an equimolar mixture of ellipsoids of revolution and spheres is found to begin precisely at a temperature at which the average inherent structure energy of the system starts falling with drop in temperature. We argue that this onset temperature corresponds to the emergence of the alpha-process as a distinct mode of orientational relaxation. Equally important, we find that the coupling between the rotational and translational diffusion breaks down at a still lower temperature where a sharp change occurs in the temperature dependence of the average inherent structure energy.

cond-mat.soft↗

arXiv2005

Universal power law in the orientational relaxation in thermotropic liquid crystals

We observe a surprisingly general power law decay at short to intermediate times in orientational relaxation in a variety of model systems (both calamitic and discotic, and also discrete) for thermotropic liquid crystals. As all these systems transit across the isotropic-nematic phase boundary, two power law relaxation regimes, separated by a plateau, emerge giving rise to a step-like feature (well-known in glassy liquids) in the single-particle second-rank orientational time correlation function. In contrast to its probable dynamical origin in supercooled liquids, we show that the power law here can originate from the thermodynamic fluctuations of the orientational order parameter, driven by the rapid growth in the second-rank orientational correlation length.

cond-mat.soft↗

arXiv2005

Anomalous glassy relaxation near the isotropic-nematic phase transition

Dynamical heterogeneity in a system of Gay-Berne ellipsoids near its isotropic-nematic (I-N) transition and also in an equimolar mixture of Lennard-Jones spheres and Gay-Berne ellipsoids in deeply supercooled regime is probed by the time evolution of non-Gaussian parameter (NGP). The appearance of a dominant second peak in the rotational NGP near the I-N transition signals the growth of pseudonematic domains. Surprisingly such a second peak is instead observed in the translational NGP for glassy binary mixture. Localization of orientational motion near the I-N transition is found to be responsible for the observed anomalous orientational relaxation.

cond-mat.soft↗

arXiv2004

Frequency dependent heat capacity within a kinetic model of glassy dynamics

There has been renewed interest in the frequency dependent specific heat of supercooled liquids in recent years with computer simulation studies exploring the whole frequency range of relaxation. The simulation studies can thus supplement the existing experimental results to provide an insight into the energy landscape dynamics. We here investigate a kinetic model of cooperative dynamics within the landscape paradigm for the dynamic heat capacity behavior. In this picture, the beta-process is modeled as a thermally activated event in a two-level system and the alpha-process is described as a beta-relaxation mediated cooperative transition in a double well. The model provides a description of the activated hopping in the energy landscape in close relation with the cooperative nature of the hopping event. For suitable choice of parameters, the model predicts a frequency dependent heat capacity that reflects the two-step relaxation behavior. Although experimentally obtained specific heat spectra of supercooled liquids till date could not capture the two-step relaxation behavior, this has been observed in a computer simulation study by Scheidler et. al. [Phys. Rev. B 63, 104204 (2001)]. The temperature dependence of the position of the low-frequency peak, due to the alpha-relaxation, shows a non-Arrhenius behavior as observed experimentally by Birge and Nagel [Phys. Rev. Lett. 54, 2674 (1985)]. The shape of the alpha-peak is, however, found to be temperature independent, in agreement with the simulation result. The high-frequency peak appears with considerably larger amplitude than the alpha-peak. We attempt a plausible reason for this observation that is in contrast with the general feature revealed by the dielectric spectroscopy.

cond-mat.soft↗

arXiv2003

Anomalous Temperature Dependence of Heat Capacity During a Cooling-Heating Cycle in Glassy Systems

Anomalous temperature dependence of heat capacity of glassy systems during a cooling-heating cycle has remained an ill-understood problem for a long time. Most of the features observed in the experimental measurement of the heat capacity of a supercooled liquid are shown here to be adequately explained by a general model. The model that we propose is motivated by the success of landscape paradigm, and describes βrelaxation in terms of a collection of two-level systems and conceives αrelaxation as a βrelaxation mediated cooperative transition in a double-well. The anomalous sharp rise in the heat capacity observed during heating is shown to have a kinetic origin, being caused by delayed energy relaxation due to nonequilibrium effects.

cond-mat.soft↗

arXiv2003

Relationship between Entropic Bottleneck in Free Energy Landscape, Nonexponential Relaxation and Fragility of Glass-Forming Liquids

A mesoscopic model is proposed to explain the anomalous dynamics in a supercooled liquid as its glass transition temperature is approached from above. The model is based on the assumption of $β$ organized $α$ process, with the requirement of coherent excitation of a minimum critical number $N_{c}$ of $β$ processes in the surroundings of a total $N_β$. Numerical evaluation of the model shows that the growth in this critical number in the background of a modest $N_β$ can lead to a severe entropic bottleneck and slow down the dynamics to an extent observed near real glass transition. The fragility of the glass-forming liquid is shown to be correlated with the growth of the ratio $γ(= N_{c}/N_β)$.

cond-mat.soft↗