arXiv subjects

Rajarshi Chakrabarti

Publications and source records attributed to Rajarshi Chakrabarti.

At least 19 recordsLinked to original sources

arXiv2025

Behavior of passive polymeric tracers of different topologies in a dilute bath of active Brownian particles

Using computer simulations in two dimensions we investigate the dynamics and structure of passive polymeric tracer with different topologies immersed in a low-density active particle bath. One of the key observations is that polymer exhibit faster dynamics compared to passive colloidal particles at high activity, for the same particle density, in both linear and star polymer topologies. This enhanced motion is attributed to the accumulation of active particles, which induces prolonged and persistent movement of the polymer. Further analysis reveals that star polymers exhibit more complex and intriguing behavior than their linear counterparts. Notably, the accumulation of active particles promotes the pairing of arms in star polymers. For instance, a three-armed star polymer adopts a conformation similar to a linear polymer with two-arms due to this pairing as a result, at high activity, the dynamics of both the polymers converge. Finally, we explore the dynamics of a linear polymer with the same total number of beads as the star polymer. Interestingly, at high activity -- where arm pairing in the star polymer is significant -- the star polymer demonstrates faster dynamics than the linear polymer, despite having the identical number of beads. These findings contribute to a broader understanding of the interactions between active and passive components of varying topologies in dilute systems and highlight their potential for innovative applications ranging from materials science to biomedicine.

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arXiv2025

A theoretical framework for investigating the role of stiffness heterogeneity in structure and dynamics of flexible polymer

Heteropolymers are ubiquitous in both synthetic systems, such as block copolymers, and biological macromolecules, including proteins and nucleic acids. Beyond their chemical composition, these polymers often exhibit spatial variations in physical properties. For instance, in biopolymers such as chromatin, stiffness heterogeneity arises from inherent molecular features as well as extensile or contractile active forces. In this letter, we develop a theoretical framework that extends the physics of flexible polymers, a widely used tool to describe biopolymer dynamics, to incorporate spatially varying stiffness. Using this approach, we specifically analyze the structure and dynamics of flexible heteropolymers with periodic stepwise stiffness profiles. We find that stiffness heterogeneity leads to qualitative deviations in dynamical observables such as mean squared displacement while also increasing structural anisotropy. Altogether, this framework provides a platform to interpret stiffness heterogeneity from experimental data especially for biopolymers as well as to design heteropolymers with tailored structural and dynamic properties.

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arXiv2024

Dynamic Clustering of Active Rings

A collection of rings made of active Brownian particles (ABPs) for different packing fractions and activities is investigated using computer simulations. We show that active rings display an emergent dynamic clustering instead of the conventional motility-induced phase separation (MIPS) as in the case of collection of ABPs. Surprisingly, increasing packing fraction of rings exhibits a non-monotonicity in the dynamics due to the formation of a large number of small clusters. The conformational fluctuations of the polymers suppress the usual MIPS exhibited by ABPs. Our findings demonstrate how the motion of a collection of rings is influenced by the interplay of activity, topology, and connectivity.

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arXiv2023

Escape dynamics of a self-propelled nanorod from circular confinements with narrow openings

We perform computer simulations to explore the escape dynamics of a self-propelled (active) nanorod from circular confinements with narrow opening(s). Our results clearly demonstrate how the persistent and directed motion of the nanorod helps it to escape. Such escape events are absent if the nanorod is passive. To quantify the escape dynamics, we compute the radial probability density function (RPDF) and mean first escape time (MFET) and show how the activity is responsible for the bimodality of RPDF, which is clearly absent if the nanorod is passive. The broadening of displacement distributions with activity has also been observed. The computed mean first escape time decreases with activity. In contrast, the fluctuations of the first escape times vary in a non-monotonic way. This results high values of the coefficient of variation and indicates the presence of multiple timescales in first escape time distributions and multimodality in uniformity index distributions. We hope our study will help in differentiating activity-driven escape dynamics from purely thermal passive diffusion in confinement.

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arXiv2023

Active Dynamics of Linear Chains and Rings in Porous Media

To understand the dynamical and conformational properties of deformable active agents in porous media, we computationally investigate the dynamics of linear chains and rings made of active Brownian monomers. In porous media, flexible linear chains and rings always migrate smoothly and undergo activity-induced swelling. However, semiflexible linear chains though navigate smoothly, shrink at lower activities, followed by swelling at higher activities, while semiflexible rings exhibit a contrasting behavior. Semiflexible rings shrink, get trapped at lower activities, and escape at higher activities. This demonstrates how activity and topology interplay and control the structure and dynamics of linear chains and rings in porous media. We envision that our study will shed light on understanding the mode of transport of shape-changing active agents in porous media.

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arXiv2023

A Polymer Chain with Dipolar Active Forces in Connection to Spatial Organization of Chromatin

A living cell is an active environment where the organization and dynamics of chromatin are affected by different forms of activity. Optical experiments report that loci show subdiffusive dynamics and the chromatin fiber is seen to be coherent over micrometer-scale regions. Using a bead-spring polymer chain with dipolar active forces, we study how the subdiffusive motion of the loci generate large-scale coherent motion of the chromatin. We show that in the presence of extensile (contractile) activity, the dynamics of loci grows faster (slower) and the spatial correlation length increases (decreases) compared to the case with no dipolar forces. Hence, both the dipolar active forces modify the elasticity of the chain. Interestingly in our model, the dynamics and organization of such dipolar active chains largely differ from the passive chain with renormalized elasticity.

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arXiv2022

Dynamics of a spherical self-propelled tracer in a polymeric medium: interplay of self-propulsion, stickiness, and crowding

We employ computer simulations to study the dynamics of a self-propelled spherical tracer particle in a viscoelastic medium, made of a long polymer chain. Here, the interplay between viscoelasticity, stickiness, and activity (self-propulsion) brings additional complexity to the tracer dynamics. Our simulation shows that on increasing the stickiness of the tracer particle to the polymer beads, the dynamics of the tracer particle slows down as it gets stuck to the polymer chain, and moves along with it. But with increasing the self-propulsion velocity, the dynamics gets enhanced. In case of increasing stickiness as well as activity, the non-Gaussian parameter (NGP) exhibits non-monotonic behavior, which also shows up in the re-scaled self part of the van-Hove function. Non-Gaussianity results owing to the enhanced binding events, and the sticky motion of the tracer along with the chain with increasing stickiness. On the other hand, with increasing activity, initially non-Gaussianity increases as the tracer moves through the heterogenous polymeric environment but for higher activity, escapes resulting negative NGP. For higher values of stickiness, the trapping time distributions of the passive tracer particle broadens and have long tails. On the other hand, for a given stickiness with increasing self-propulsion force, the same becomes narrower and have short tails. We believe that our current simulation study will be helpful in elucidating the complex motion of activity-driven probes in viscoelastic media.

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arXiv2022

Dynamics of self-propelled tracer particles inside a polymer network

Transport of tracer particles through mesh-like environments such as biological hydrogels and polymer matrices is ubiquitous in nature. These tracers could be passive, such as colloids or active (self-propelled), such as synthetic nanomotors or bacteria. Computer simulations in principle should be extremely useful in exploring the mechanism of active (self-propelled) transport of tracer particles through the mesh-like environments. Therefore, we construct a polymer network on a diamond lattice and use computer simulations to investigate the dynamics of spherical self-propelled particles inside the network. Our main objective is to elucidate the effect of the self-propulsion on the dynamics of the tracer particle as a function of tracer size and stiffness of the polymer network. We compute the time-averaged mean-squared displacement (MSD) and the van-Hove correlations of the tracer. On one hand, in the case of the bigger sticky particle, caging caused by the network particles wins over the escape assisted by the self-propulsion. This results intermediate-time subdiffusion. On the other hand, smaller tracers or tracers with high self-propulsion velocities can easily escape from the cages and show intermediate-time superdiffusion. Stiffer the network, slower the dynamics of the tracer, and the bigger tracers exhibit longer lived intermediate time superdiffusion, as the persistence time scales as $\sim σ^3$, where $σ$ is the diameter of the tracer. In intermediate time, non-Gaussianity is more pronounced for active tracers. In the long time, the dynamics of the tracer, if passive or weakly active, becomes Gaussian and diffusive, but remains flat for tracers with high self-propulsion, accounting for their seemingly unrestricted motion inside the network.

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arXiv2022

Reconfiguration, swelling and tagged monomer dynamics of a single polymer chain in Gaussian and non-Gaussian active baths

In this topical review, we give an overview of the structure and dynamics of a single polymer chain in active baths, Gaussian or non-Gaussian. The review begins with the discussion of single flexible or semiflexible linear polymer chains subjected to two noises, thermal and active. The active noise has either Gaussian or non-Gaussian distribution but has a memory, accounting for the persistent motion of the active bath particles. This finite persistence makes the reconfiguration dynamics of the chain slow as compared to the purely thermal case and the chain swells. The active noise also results superdiffusive or ballistic motion of the tagged monomer. We present all the calculations in details but mainly focus on the analytically exact or almost exact results on the topic, as obtained from our group in recent years. In addition, we briefly mention important works of other groups and include some of our new results. The review concludes with pointing out the implications of polymer chains in active bath in biologically relevant context and its future directions.

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arXiv2022

Shear viscosity for finitely extensible chains with fluctuating internal friction and hydrodynamic interactions

An exact solution of coarse-grained polymer models with fluctuating internal friction and hydrodynamic interactions has not been proposed so far due to a one-to-all coupling between the connector vector velocities that precludes the formulation of the governing stochastic differential equations. A methodology for the removal of this coupling is presented, and the governing stochastic differential equations, obtained by attaching a kinetic interpretation to the Fokker-Planck equation for the system, are integrated numerically using Brownian dynamics simulations. The proposed computational route eliminates the calculation of the divergence of the diffusion tensor which appears in models with internal friction, and is about an order of magnitude faster than the recursion-based algorithm for the decoupling of connector-vector velocities previously developed [J. Rheol., 65, 903 (2021)] for the solution of freely draining models with internal friction. The effects of the interplay of various combinations of finite extensibility, internal friction and hydrodynamic interactions on the steady-shear-viscosity is examined. While finite extensibility leads solely to shear-thinning, both internal friction and hydrodynamic interactions result in shear-thinning followed by shear-thickening. The shear-thickening induced by internal friction effects are more pronounced than that due to hydrodynamic interactions.

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arXiv2022

Migration of Active Rings in Porous Media

Inspired by how the shape deformations in active organisms help them to migrate through disordered porous environments, we simulate active ring polymers in two-dimensional random porous media. Flexible and inextensible active ring polymers navigate smoothly through the disordered media. In contrast, semiflexible rings undergo transient trapping inside the pore space; the degree of trapping is inversely correlated with the increase in activity. We discover that flexible rings swell while inextensible and semiflexible rings monotonically shrink upon increasing the activity. Together, our findings identify the optimal migration of active ring polymers through porous media.

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arXiv2022

Chemically symmetric and asymmetric self-driven rigid dumbbells in 2D polymer gel

We employ computer simulations to unveil the translational and rotational dynamics of the self-driven chemically symmetric and asymmetric rigid dumbbells in two-dimensional polymer gel. Our results show that activity or the self-propulsion always enhances the dynamics of the dumbbells. Making the self-propelled dumbbell chemically asymmetric leads to further enhancement in dynamics. Additionally, the direction of self-propulsion is a key factor for the chemically asymmetric dumbbells, where self-propulsion towards the non-sticky half of the dumbbell results in faster translational and rotational dynamics compare to the case with the self-propulsion towards the sticky half of the dumbbell. Our analyses show that both the symmetric and asymmetric passive rigid dumbbells get trapped inside the mesh of the polymer gel, but the chemical asymmetry always facilitates mesh to mesh motion of the dumbbell and it is even more pronounced when the dumbbell is self-propelled. This results multiple peaks in the van Hove function with increasing self-propulsion. In a nutshell, we believe that our in silico study can guide the researchers design efficient artificial microswimmers possessing potential applications in site-specific delivery.

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arXiv2022

Motion of an active particle with dynamical disorder

We propose a model for the motion of a single active particle in a heterogeneous environment where the heterogeneity may arise due to the crowding, conformational fluctuations and/or slow rearrangement of the surroundings. Describing the active particle in terms of the Ornstein-Uhlenbeck process (OUP) and incorporating the heterogeneity in the thermal bath using the two separate models, namely "diffusing diffusivity" and "switching diffusion", we explore the essential dynamical properties of the particle for its one-dimensional motion. In addition, we show how the dynamical behavior is controlled by two timescales, namely diffusive time and persistence time. Our model is relevant in the context of single particle dynamics in crowded environment, driven by activity.

cond-mat.stat-mech↗

arXiv2022

Transport of a self-propelled tracer through a hairy cylindrical channel: interplay of stickiness and activity

Active transport of biomolecules assisted by motor proteins is imperative for the proper functioning of cellular activities. Inspired by the diffusion of active agents in crowded cellular channels, we computationally investigate the transport of an active tracer through a polymer grafted cylindrical channel by varying the activity of the tracer and stickiness of the tracer to the polymers. Our results reveal that the passive tracer exhibits profound subdiffusion with increasing stickiness by exploring deep into the grafted polymeric zone, while purely repulsive one prefers to diffuse through the pore-like space created along the cylindrical axis of the channel. In contrast, the active tracer shows faster dynamics and intermediate superdiffusion even though the tracer preferentially stays close to the dense polymeric region. This observation is further supported by the sharp peaks in the density profile of the probability of radial displacement of the tracer. We discover that the activity plays an important role in deciding the pathway that the tracer takes through the narrow channel. Interestingly, increasing the activity washes out the effect of stickiness. Adding to this, van-Hove functions manifest that the active tracer dynamics deviates from Gaussianity, and the degree of deviation grows with the activity. Our work has direct implications on how effective transportation and delivery of cargo can be achieved through a confined medium where activity, interactions, and crowding are interplaying. Looking ahead, these factors will be crucial for understanding the mechanism of artificial self-powered machines navigating through the cellular channels and performing in vivo challenging tasks.

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arXiv2021

Stochastic resetting and first arrival subjected to Gaussian noise and Poisson white noise

We study the dynamics of an overdamped Brownian particle subjected to Poissonian stochastic resetting in a nonthermal bath, characterized by a Poisson white noise and a Gaussian noise. Applying the renewal theory we find an exact analytical expression for the spatial distribution at the steady state. Unlike the single exponential distribution as observed in the case of a purely thermal bath, the distribution is double exponential. Relaxation of the transient spatial distributions to the stationary one, for the limiting cases of Poissonian rate, is investigated carefully. In addition, we study the first-arrival properties of the system in the presence of a delta-function sink with strength $κ$, where $κ=0$ and $κ=\infty$ correspond to fully nonreactive and fully reactive sinks, respectively. We explore the effect of two competitive mechanisms: the diffusive spread in the presence of two noises and the increase in probability density around the initial position due to stochastic resetting. We show that there exists an optimal resetting rate, which minimizes the mean first-arrival time (MFAT) to the sink for a given value of the sink strength. We also explore the effect of the strength of the Poissonian noise on MFAT, in addition to sink strength. Our formalism generalizes the diffusion-limited reaction under resetting in a nonequilibrium bath and provides an efficient search strategy for a reactant to find a target site, relevant in a range of biophysical processes.

cond-mat.stat-mech↗

arXiv2021

How important are fluctuations in the treatment of internal friction in polymers?

The Rouse model with internal friction (RIF), a widely used theoretical framework to interpret the effects of internal friction on conformational transitions in biomolecules, is shown to be an approximate treatment that is based on preaveraging internal friction. By comparison with Brownian dynamics simulations of an exact coarse-grained model that incorporates fluctuations in internal friction, the accuracy of the preaveraged model predictions is examined both at and away from equilibrium. While the two models predict intrachain autocorrelations that approach each other for long enough chain segments, they differ in their predictions for shorter segments. Furthermore, the two models differ qualitatively in their predictions for the chain extension and viscosity in shear flow, which is taken to represent a prototypical out-of-equilibrium condition.

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arXiv2021

Rouse model with fluctuating internal friction

A coarse-grained bead-spring-dashpot chain model with the dashpots representing the presence of internal friction, is solved exactly numerically, for the case of chains with more than two beads. Using a decoupling procedure to remove the explicit coupling of a bead's velocity with that of its nearest neighbors, the governing set of stochastic differential equations are solved with Brownian dynamics simulations to obtain material functions in oscillatory and steady simple shear flow. Simulation results for the real and imaginary components of the complex viscosity have been compared with the results of previously derived semi-analytical approximations, and the difference in the predictions are seen to diminish with an increase in the number of beads in the chain. The inclusion of internal friction results in a non-monotonous variation of the viscosity with shear rate, with the occurrence of continuous shear-thickening following an initial shear-thinning regime. The onset of shear-thickening in the first normal stress coefficient is pushed to lower shear rates with an increase in the internal friction parameter.

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arXiv2020

Translational and rotational dynamics of a self-propelled Janus probe in crowded environments

We computationally investigate the dynamics of a self-propelled Janus probe in crowded environments. The crowding is caused by the presence of viscoelastic polymers or non-viscoelastic disconnected monomers. Our simulations show that the translational, as well as rotational mean square displacements, have a distinctive three-step growth for fixed values of self-propulsion force, and steadily increase with self-propulsion, irrespective of the nature of the crowder. On the other hand, in the absence of crowders, the rotational dynamics of the Janus probe is independent of self-propulsion force. On replacing the repulsive polymers with sticky ones, translational and rotational mean square displacements of the Janus probe show a sharp drop. Since different faces of a Janus particle interact differently with the environment, we show that the direction of self-propulsion also affects its dynamics. The ratio of long-time translational and rotational diffusivities of the self-propelled probe with a fixed self-propulsion, when plotted against the area fraction of the crowders, passes through a minima and at higher area fraction merges to its value in the absence of the crowder. This points towards the decoupling of translational and rotational dynamics of the self-propelled probe at intermediate area fraction of the crowders. However, such translational-rotational decoupling is absent for passive probes.

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