Biology subjects

Gopinath, A.

Publications and source records attributed to Gopinath, A..

41 records · Page 3Linked to original sources

bioRxiv2020

Elastohydrodynamical instabilities of active filaments, arrays and carpets analyzed using slender body theory

The rhythmic motions and wave-like planar oscillations in filamentous soft structures are ubiquitous in biology. Inspired by these, recent work has focused on the creation of synthetic colloid-based active mimics that can be used to move, transport cargo, and generate fluid flows. Underlying the functionality of these mimics is the coupling between elasticity, geometry, dissipation due to the fluid, and active force or moment generated by the system. Here, we use slender body theory to analyze the linear stability of a subset of these - active elastic filaments, filament arrays and filament carpets - animated by follower forces. Follower forces can be external or internal forces that always act along the filament contour. The application of slender body theory enables the accurate inclusion of hydrodynamic effects, screening due to boundaries, and interactions between filaments. We first study the stability of fixed and freely suspended sphere-filament assemblies, calculate neutral stability curves separating stable oscillatory states from stable straight states, and quantify the frequency of emergent oscillations. When shadowing effects due to the physical presence of the spherical boundary are taken into account, the results from the slender body theory differ from that obtained using local resistivity theory. Next, we examine the onset of instabilities in a small cluster of filaments attached to a wall and examine how the critical force for onset of instability and the frequency of sustained oscillations depend on the number of filaments and the spacing between the filaments. Our results emphasize the role of hydrodynamic interactions in driving the system towards perfectly in-phase or perfectly out of phase responses depending on the nature of the instability. Specifically, the first bifurcation corresponds to filaments oscillating in-phase with each other. We then extend our analysis to filamentous (line) array and (square) carpets of filaments and investigate the variation of the critical parameters for the onset of oscillations and the frequency of oscillations on the inter-filament spacing. The square carpet also produces a uniform flow at infinity and we determine the ratio of the mean-squared flow at infinity to the energy input by active forces. We conclude by analyzing the bending and buckling instabilities of a straight passive filament attached to a wall and placed in a viscous stagnant flow - a problem related to the growth of biofilms, and also to mechanosensing in passive cilia and microvilli. Taken together, our results provide the foundation for more detailed non-linear analyses of spatiotemporal patterns in active filament systems.

bioengineering↗

bioRxiv2019

Instabilities and Spatiotemporal Dynamics of Active Elastic Filaments

Biological filaments driven by molecular motors tend to experience tangential propulsive forces also known as active follower forces. When such a filament encounters an obstacle, it deforms, which reorients its follower forces and alters its entire motion. If the filament pushes a cargo, the friction on the cargo can be enough to deform the filament, thus affecting the transport properties of the cargo. Motivated by cytoskeletal filament motility assays, we study the dynamic buckling instabilities of a two-dimensional slender elastic filament driven through a dissipative medium by tangential propulsive forces in the presence of obstacles or cargo. We observe two distinct instabilities. When the filaments head is pinned or experiences significant translational but little rotational drag from its cargo, it buckles into a steadily rotating coiled state. When it is clamped or experiences both significant translational and rotational drag from its cargo, it buckles into a periodically beating, overall translating state. Using minimal analytically tractable models, linear stability theory, and fully non-linear computations, we study the onset of each buckling instability, characterize each buckled state, and map out the phase diagram of the system. Finally, we use particle-based Brownian dynamics simulations to show our main results are robust to moderate noise and steric repulsion. Overall, our results provide a unified framework to understand the dynamics of tangentially propelled filaments and filament-cargo assemblies.

biophysics↗

bioRxiv2018

Filament extensibility and shear stiffening control persistence of strain and loss of coherence in cross-linked motor-filament assemblies

Cross-linked flexible filaments deformed by active molecular motors occur in many natural and synthetic settings including eukaryotic flagella, the cytoskeleton and in vitro motor assays. In these systems, an important quantity that controls spatial coordination and emergent collective behavior is the length scale over which elastic strains persist. We estimate this quantity in the context of ordered composites comprised of cross-linked elastic filaments sheared by active motors. Combining a mean-field theory valid for negligibly noisy systems with discrete simulations for noisy systems, we show that the effect of localized strains - be they steady or oscillatory - persist over distances determined by motor kinetics, motor elasticity and filament extensibility. The cut-off length that emerges from these effects controls the transmission of mechanical information and determines the criterion for spatially separated motor groups to stay synchronized. Our results generalize the notion of persistence in passive, Brownian filaments to active, cross-linked filaments.

biophysics↗

bioRxiv2018

Quenching a swarm: Effect of light exposure on suppression of collective motility in swarming Serratia marcescens

Swarming colonies of the light responsive bacteria Serratia marcescens grown on agar exhibit robust fluctuating large-scale collective flows that include arrayed vortices, jets, and sinuous streamers. We study the immobilization and quenching of these large-scale flows when the moving swarm is exposed to light with a substantial ultra-violet component. We map the response to light in terms of two independent parameters - the light intensity and duration of exposure and identify the conditions under which mobility is affected significantly. For small exposure times and/or low intensities, we find collective mobility to be negligibly affected. Increasing exposure times and/or intensity to higher values temporarily suppresses collective mobility. Terminating exposure allows bacteria regain motility and eventually reestablish large scale flows. For long exposure times or at high intensities, exposed bacteria become paralyzed, with macroscopic speeds eventually reducing to zero. In this process, they form highly aligned, jammed domains. Individual domains eventually coalesce into a large macroscopic domain with mean radial extent growing as the square root of exposure time. Post exposure, active bacteria dislodge exposed bacteria from these jammed configurations; initial dissolution rates are found to be strongly dependent on duration of exposure suggesting that caging effects are substantial at higher exposure times. Based on our experimental observations, we propose a minimal Brownian dynamics model to examine the escape of exposed bacteria from the region of exposure. Our results complement studies on planktonic bacteria and inform models for pattern formation in gradated illumination.

biophysics↗

bioRxiv2018

The propagation of active-passive interfaces in bacterial swarms

Propagating interfaces are ubiquitous in nature, underlying instabilities and pattern formation in biology and material science. Physical principles governing interface growth are well understood in passive settings; however, our understanding of interfaces in active systems is still in its infancy. Here, we study the evolution of an active-passive interface using a model active matter system, bacterial swarms. We use ultra-violet light exposure to create compact domains of passive bacteria within Serratia marcescens swarms, thereby creating interfaces separating motile and immotile cells. Post-exposure, the boundary re-shapes and erodes due to self-emergent collective flows. We demonstrate that the active-passive boundary acts as a diffuse interface with mechanical properties set by the flow. Intriguingly, interfacial velocity couples to local swarm speed and interface curvature, suggesting that an active analogue to classic Gibbs-Thomson-Stefan conditions controls boundary propagation. Our results generalize interface theories to mixing and segregation in active systems with collective flows.

biophysics↗