arXiv subjects

R. Kailasham

Publications and source records attributed to R. Kailasham.

10 recordsLinked to original sources

arXiv2025

Dissipative response of driven bead-spring-dashpot chains

The work dissipated in pulling a polymer chain with internal friction is numerically calculated by considering a sequence of $N$ spring-dashpots tethered at one end and being pulled at the other using a harmonic trap via linear and symmetric protocols. The variation of the dissipation with the chain length, pulling trap stiffness, and the internal friction parameter are examined in detail for both the protocols. {While the dissipation increases with $N$ for chains without internal friction, the relationship between the dissipation and $N$ for chains with internal friction depends on the pulling trap stiffness. For chains with internal friction, the dissipation \textit{decreases} (increases) with $N$ as the the pulling trap stiffness is \textit{increased} (decreased), keeping all other parameters constant. Therefore, unlike in the case of a single-mode spring-dashpot ($N=1$) for which a simple relationship exists between the damping coefficient of the dashpot and the dissipated work [as shown in Phys. Rev. Res. \textbf{2}, 013331 (2020)], the same is not true for the general case of $N>1$ due to the stiffness-dependent dissipative response of bead-spring-dashpot chains.

cond-mat.soft↗

arXiv2024

The influence of active agent motility on SIRS epidemiological dynamics

Active Brownian disks moving in two dimensions that exchange information about their internal state stochastically are chosen to model epidemic spread in a self-propelled population of agents under the susceptible-infected-recovered-susceptible (SIRS) framework. The state of infection of an agent, or disk, governs its self-propulsion speed; consequently, the activity of the agents in the system varies in time. Two different protocols (one-to-one and one-to-many) are considered for the transmission of disease from the infected to susceptible populations. The effectiveness of the two protocols are practically identical at high values of the infection transmission rate. The one-to-many protocol, however, outperforms the one-to-one protocol at lower values of the infection transmission rate. Salient features of the macroscopic SIRS model are revisited, and compared to predictions from the agent-based model. Lastly, the motility induced phase separation in a population of such agents with a fluctuating fraction of active disks is found to be well-described by theories governing phase separation in a mixture of active and passive particles with a constant fraction of passive disks.

cond-mat.soft↗

arXiv2023

Effect of speed fluctuations on the collective dynamics of active disks

Numerical simulations are performed on the collective dynamics of active disks, whose self-propulsion speed ($U$) varies in time, and whose orientation evolves according to rotational Brownian motion. Two protocols for the evolution of speed are considered: (i) a deterministic one involving a periodic change in $U$ at a frequency $\omega$; and (ii) a stochastic one in which the speeds are drawn from a power-law distribution at time-intervals governed by a Poissonian process of rate $\beta$. In the first case, an increase in $\omega$ causes the disks to go from a clustered state to a homogeneous one through an apparent phase-transition, provided that the direction of self-propulsion is allowed to reverse. Similarly, in the second case, for a fixed value of $\beta$, the extent of cluster-breakup is larger when reversals in the self-propulsion direction are permitted. Motility-induced phase separation of the disks may therefore be avoided in active matter suspensions in which the constituents are allowed to reverse their self-propulsion direction, immaterial of the precise temporal nature of the reversal (deterministic or stochastic). Equally, our results demonstrate that phase separation could occur even in the absence of a time-averaged motility of an individual active agent, provided that the rate of direction reversals is smaller than the orientational diffusion rate.

cond-mat.soft↗

arXiv2022

Non-Brownian diffusion and chaotic rheology of autophoretic disks

The dynamics of a two dimensional autophoretic disk is quantified as a minimal model for the chaotic trajectories undertaken by active droplets. Via direct numerical simulations, we show that the mean-square displacement of the disk in a quiescent fluid is linear at long times. Surprisingly, however, this apparently diffusive behavior is non-Brownian, owing to strong cross-correlations in the displacement tensor. The effect of a shear flow field on the chaotic motion of a 2D autophoretic disk is examined. Here, the stresslet on the disk is chaotic for weak shear flows; a dilute suspension of such disks would exhibit a chaotic shear rheology. This chaotic rheology is quenched first into a periodic state and ultimately a steady state as the flow strength is increased.

physics.flu-dyn↗

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.

cond-mat.soft↗

arXiv2022

Dynamics of forced and unforced autophoretic particles

Chemically active, or autophoretic, particles that isotropically emit or absorb solute molecules undergo spontaneous self-propulsion when their activity is increased beyond a critical P\'{e}clet number ($Pe$). Here, we conduct numerical computations, using a spectral-element based method, of a rigid, spherical autophoretic particle in unsteady rectilinear translation. The particle can be freely suspended (or `unforced') or subject to an external force field (or `forced'). The motion of an unforced particle progresses through four regimes as $Pe$ is increased: quiescent, steady, stirring, and chaos. The particle is stationary in the quiescent regime, and the solute profile is isotropic about the particle. At $Pe=4$ the fore-aft symmetry in the solute profile is broken, resulting in its steady self-propulsion. Our computations indicate that the self-propulsion speed scales linearly with $Pe-4$ near the onset of self-propulsion, as has been predicted in previous studies. A further increase in $Pe$ gives rise to the stirring regime at $Pe\approx27$, where the fluid undergoes recirculation, while the particle remains essentially stationary. As $Pe$ is increased even further, the particle dynamics are marked by chaotic oscillations at $Pe\approx55$ and higher, which we characterize in terms of the mean square displacement and velocity autocorrelation of the particle. Our results for an autophoretic particle under a weak external force are in good agreement with recent asymptotic predictions (Saha, Yariv, and Schnitzer, J. Fluid Mech., vol. 916, A47, 2021). Additionally, we demonstrate that the strength and temporal scheduling of the external force may be tuned to modulate the chaotic dynamics at large $Pe$.

physics.flu-dyn↗

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.

cond-mat.soft↗

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.

cond-mat.soft↗

arXiv2020

Wet and dry internal friction can be measured with the Jarzynski equality

The existence of two types of internal friction wet and dry is revisited, and a simple protocol is proposed for distinguishing between the two types and extracting the appropriate internal friction coefficient. The scheme requires repeatedly stretching a polymer molecule, and measuring the average work dissipated in the process by applying the Jarzynski equality. The internal friction coefficient is then estimated from the average dissipated work in the extrapolated limit of zero solvent viscosity. The validity of the protocol is established through analytical calculations on a one-dimensional free-draining Hookean spring-dashpot model for a polymer, and Brownian dynamics simulations of: (a) a single-mode nonlinear spring-dashpot model for a polymer, and (b) a finitely extensible bead-spring chain with cohesive intra-chain interactions, both of which incorporate fluctuating hydrodynamic interactions. Well-established single-molecule manipulation techniques, such as optical tweezer-based pulling, can be used to implement the suggested protocol experimentally.

cond-mat.soft↗

arXiv2018

Rheological consequences of wet and dry friction in a dumbbell model with hydrodynamic interactions and internal viscosity

The effect of fluctuating internal viscosity and hydrodynamic interactions on a range of rheological properties of dilute polymer solutions is examined using a finitely extensible dumbbell model for a polymer. Brownian dynamics simulations are used to compute both transient and steady state viscometric functions in shear flow. The results enable a careful differentiation of the influence, on rheological properties, of solvent-mediated friction from that of a dissipative mechanism that is independent of solvent viscosity. In particular, hydrodynamic interactions have a significant influence on the magnitude of the stress jump at the inception of shear flow, and on the transient viscometric functions, but a negligible effect on the steady state viscometric functions at high shear rates. Zero-shear rate viscometric functions of free-draining dumbbells remain essentially independent of the internal viscosity parameter, as predicted by the Gaussian approximation, but the inclusion of hydrodynamic interactions induces a dependence on both the hydrodynamic interaction and the internal viscosity parameter. Large values of the internal viscosity parameter lead to linear viscoelastic predictions that mimic the behavior of rigid dumbbell solutions. On the other hand, steady-shear viscometric functions at high shear rates differ in general from those for rigid dumbbells, depending crucially on the finite extensibility of the dumbbell spring.

cond-mat.soft↗